{"action":"created","issue":{"url":"https://api.github.com/repos/ndaniel/fusioncatcher/issues/8","labels_url":"https://api.github.com/repos/ndaniel/fusioncatcher/issues/8/labels{/name}","comments_url":"https://api.github.com/repos/ndaniel/fusioncatcher/issues/8/comments","events_url":"https://api.github.com/repos/ndaniel/fusioncatcher/issues/8/events","html_url":"https://github.com/ndaniel/fusioncatcher/issues/8","id":100690002,"number":8,"title":"Could not locate a Bowtie index rtrna_mt_index","user":{"login":"2015kiran","id":13776038,"avatar_url":"https://avatars.githubusercontent.com/u/13776038?v=3","gravatar_id":"","url":"https://api.github.com/users/2015kiran","html_url":"https://github.com/2015kiran","followers_url":"https://api.github.com/users/2015kiran/followers","following_url":"https://api.github.com/users/2015kiran/following{/other_user}","gists_url":"https://api.github.com/users/2015kiran/gists{/gist_id}","starred_url":"https://api.github.com/users/2015kiran/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/2015kiran/subscriptions","organizations_url":"https://api.github.com/users/2015kiran/orgs","repos_url":"https://api.github.com/users/2015kiran/repos","events_url":"https://api.github.com/users/2015kiran/events{/privacy}","received_events_url":"https://api.github.com/users/2015kiran/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":2,"created_at":"2015-08-13T04:51:45Z","updated_at":"2015-08-18T09:07:41Z","closed_at":null,"body":"Hi Daniel,\r\n\r\ni am using Fusioncatcher, 0.99.4b version i could run fine on the test samples with the same build Ensembl 79 vesion. but when i ran with my RNA-seqdata, half way it threw Error saying could;t locate rna_index which was't there even when i ran with test samples,\r\n\r\nHow to Manipulate to skip some steps in fusioncatcher so it will be user friendly...?\r\nlike to skip Bowtie of rtrna.\r\n\r\nHow and where to reduce the Threads used by Fusion catcher.. as it is now -p 64..?\r\n\r\nhere is my Info.txt cant attach file..\r\n\r\nhttps://code.google.com/p/fusioncatcher/wiki/Manual_v0_93#FUSIONCATCHER # \r\nIssues cannot be reported in the above link anymore..\r\n```\r\n----------------\r\n\r\n   bowtie \\\r\n   -t  \\\r\n   -v 2 \\\r\n   -p 64 \\\r\n   -k 1 \\\r\n   --solexa1.3-quals  \\\r\n   --tryhard  \\\r\n   --chunkmbs 128 \\\r\n   --un /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB_RI_T19/reads-filtered_temp.fq \\\r\n   --max /dev/null \\\r\n    /data/current/rtrna_mt_index/ \\\r\n    /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB_RI_T19/reads_acgt.fq \\\r\n    /dev/null \\\r\n   2> /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB_RI_T19/log_bowtie_reads-filtered-out.stdout.txt\r\n----------------\r\n  * Size '/MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB_RI_T19/reads-filtered_temp.fq' = 0 bytes\r\n  * Size '/data/current/rtrna_mt_index/' = 0 bytes\r\n  * Size '/MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB_RI_T19/reads_acgt.fq' = 27456195340 bytes\r\n  * Size '/MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB_RI_T19/log_bowtie_reads-filtered-out.stdout.txt' = 400 bytes\r\nCould not locate a Bowtie index corresponding to basename \"/data/current/rtrna_mt_index/\"\r\nOverall time: 00:00:00\r\nCommand: bowtie -t -v 2 -p 64 -k 1 --solexa1.3-quals --tryhard --chunkmbs 128 --un /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB_RI_T19/reads-filtered_temp.fq --max /dev/null /data/current/rtrna_mt_index/ /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB_RI_T19/reads_acgt.fq /dev/null \r\n\r\n----------\r\n\r\nFound 40405 reads with poly-A/C/G/T/N tails (equal or more 20 repeat nucleotides)\r\nTotal number of input reads = 117508227\r\nTotal number of reads written in the output = 117495305\r\nCount of all short reads after removing reads due to missing their mate read:\r\n-----------------------------------------------------------------------------\r\n104396180\r\nAdjusted automatically mismatches_psl and trim_psl_3end_keep (105,3) because reads of maximum length of 125 bp were found!.\r\n```\r\n\r\nWhat  need to be done continue the further steps..\r\n\r\nThank you\r\n\r\n\r\n "},"comment":{"url":"https://api.github.com/repos/ndaniel/fusioncatcher/issues/comments/132127260","html_url":"https://github.com/ndaniel/fusioncatcher/issues/8#issuecomment-132127260","issue_url":"https://api.github.com/repos/ndaniel/fusioncatcher/issues/8","id":132127260,"user":{"login":"2015kiran","id":13776038,"avatar_url":"https://avatars.githubusercontent.com/u/13776038?v=3","gravatar_id":"","url":"https://api.github.com/users/2015kiran","html_url":"https://github.com/2015kiran","followers_url":"https://api.github.com/users/2015kiran/followers","following_url":"https://api.github.com/users/2015kiran/following{/other_user}","gists_url":"https://api.github.com/users/2015kiran/gists{/gist_id}","starred_url":"https://api.github.com/users/2015kiran/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/2015kiran/subscriptions","organizations_url":"https://api.github.com/users/2015kiran/orgs","repos_url":"https://api.github.com/users/2015kiran/repos","events_url":"https://api.github.com/users/2015kiran/events{/privacy}","received_events_url":"https://api.github.com/users/2015kiran/received_events","type":"User","site_admin":false},"created_at":"2015-08-18T09:07:40Z","updated_at":"2015-08-18T09:07:40Z","body":"Hi Daniel,\r\nUnfortunately only files with extension PNG, GIF and JPG are supported here to attach,\r\n\r\nWe dont get any alerts on reply to this query as google code..\r\nhere is my Info.txt \r\n\r\n----\r\n\r\n================================================\r\nSotware version: fusioncatcher.py 0.99.4b beta\r\n================================================\r\n===================================\r\nGENOME INFORMATION:\r\n===================================\r\n\r\n================================================================================\r\nWARNING: This is an OLD version of FusionCatcher! There is a newer\r\n         version available! Please, update to the newest version!\r\n - Current version:   0.99.4b beta\r\n - New version:       0.99.4c beta\r\n================================================================================\r\n\r\n===================================\r\nGenome FASTA files:\r\n===================================\r\n\r\n================================================================================\r\nWARNING: This is an OLD version of FusionCatcher! There is a newer\r\n         version available! Please, update to the newest version!\r\n - Current version:   0.99.4b beta\r\n - New version:       0.99.4c beta\r\n================================================================================\r\n\r\n\r\nLinux:\r\n------\r\nRed Hat Enterprise Linux Server release 6.5 (Santiago)\r\nKernel \\r on an \\m\r\n\r\n\r\nPython:\r\n------\r\nPython version: 2.6.6 (r266:84292, Sep  4 2013, 07:46:00) \r\n[GCC 4.4.7 20120313 (Red Hat 4.4.7-3)]\r\nPython executable: /usr/bin/python\r\n\r\nBioPython:\r\n------\r\n1.65\r\n\r\n===========\r\nTOOLS:\r\n===========\r\n\r\nSORT:\r\n------\r\nsort (GNU coreutils) 8.4\r\n\r\nBOWTIE:\r\n------\r\nbowtie version 1.1.1\r\n64-bit\r\n\r\nPIGZ:\r\n------\r\npigz 2.3.1\r\n\r\nfastq-dump (from SRA Toolkit):\r\n--------------\r\nfastq-dump : 2.4.2\r\n\r\nSAMTools:\r\n---------\r\nVersion: 0.1.19-44428cd\r\n\r\nliftOver:\r\n---------\r\nliftOver - Move annotations from one assembly to another\r\n\r\nSeqTK:\r\n---------\r\nVersion: 1.0-r68e-dirty\r\n\r\nsed:\r\n---------\r\nGNU sed version 4.2.1\r\n\r\nawk:\r\n---------\r\nGNU Awk 3.1.7\r\n\r\nBLAT:\r\n------\r\nblat - Standalone BLAT v. 35x1 fast sequence search command line tool\r\n\r\nfaToTwoBit (from BLAT toolbox):\r\n----------------\r\nfaToTwoBit - Convert DNA from fasta to 2bit format\r\n\r\nSTAR:\r\n------\r\nSTAR_2.4.1c\r\n\r\n\r\n\r\nPipeline parameters:\r\n====================\r\naligners = blat,star\r\nall_reads_junction = False\r\nambiguous_mismatches = 2\r\nassembly = False\r\nbatch_mode = False\r\nbiotypes = 7skrna,ambiguous,banned,bodymap2,conjoing,cta_gene,ctb_gene,ctc_gene,ctd_gene,distance1000bp,ensembl_fully_overlapping,ensembl_same_strand_overlapping,healthy,metazoa,mirna,mt,pair_pseudo_genes,paralogs,refseq_fully_overlapping,refseq_same_strand_overlapping,removed,rp11_gene,rp_gene,rrna,similar_reads,similar_symbols,snorna,snrna,trna,yrna\r\nchecksums_filename = checksums.txt\r\nchunkmbs = 128\r\nconfiguration_filename = /MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher/etc/configuration.cfg,/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher/bin/configuration.cfg\r\ndata_directory = /data/current/\r\nextract_buffer_size = 2000000000\r\nfilter_mismatches = 2\r\nhash = no\r\nhighly_sensitive = False\r\nhomolog = 1.25e-05\r\ninput_filename = /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Tobe_shipped/Transcriptome_PairedEnd/RAW_FASTQ/MDB.RI.T40_R1.fastq.gz,/MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Tobe_shipped/Transcriptome_PairedEnd/RAW_FASTQ/MDB.RI.T40_R2.fastq.gz\r\nkeep_temporary_files = False\r\nkeep_unmapped_reads = False\r\nkeep_viruses = False\r\nlength_anchor = 17,17,17,17,17\r\nlength_anchor2 = 47\r\nlimit_blat = 3221225472\r\nlimit_bowtie = 4294867296\r\nlimit_bowtie2 = 30000000\r\nlimit_bwa = 1\r\nlimit_star = 30000000\r\nmildly_sensitive = False\r\nmin_dist = 200000\r\nmismatches = 2\r\nmismatches_psl = 2\r\nno_seqtk_subseq = False\r\noutput_directory = /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40\r\nparanoid_sensitive = False\r\nprocesses = 64\r\npsl_visualization = False\r\nsam_visualization = True\r\nsensitive = False\r\nskip_adapter_filtering = False\r\nskip_ambiguous_filtering = False\r\nskip_automatic_scaling = False\r\nskip_b_filtering = False\r\nskip_banned_fusions = False\r\nskip_blat = False\r\nskip_bowtie2 = True\r\nskip_bwa = True\r\nskip_compress_ids = False\r\nskip_conversion_grch37 = False\r\nskip_hla_filtering = False\r\nskip_interleave_processing = False\r\nskip_known_fusions = False\r\nskip_mitochondrion_filtering = False\r\nskip_phix174_filtering = False\r\nskip_prefiltering_psl = False\r\nskip_readthroughs = False\r\nskip_star = False\r\nskip_star_bowtie = False\r\nskip_str_filtering = False\r\nskip_update_check = False\r\nskip_viruses_filtering = False\r\nspanning_pairs = 3,3,3,3,3\r\nspanning_pairs_count = 10000\r\nspanning_reads = 2,2,2,2,2\r\nstart_step = 0\r\ntmp_directory = /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/tmp\r\ntrim_3end = 0\r\ntrim_3end_keep = 0\r\ntrim_5end = 0\r\ntrim_psl = False\r\ntrim_psl_3end_keep = 82\r\ntrim_psl_5end = False\r\ntrim_quality = 5\r\ntrim_wiggle = 0\r\nmain_script = /MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher/bin/fusioncatcher.py\r\nmain_script_version = fusioncatcher.py 0.99.4b beta\r\n\r\nCurrent working directory:\r\n---------------------------\r\n/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher\r\n\r\nCommand line used for launching FusionCatcher:\r\n----------------------------------------------\r\nbin/fusioncatcher.py \\ \r\n--visualization-sam \\ \r\n--5keep \\ \r\n0 \\ \r\n-d \\ \r\n/data/current/ \\ \r\n-i \\ \r\n/MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Tobe_shipped/Transcriptome_PairedEnd/RAW_FASTQ/MDB.RI.T40_R1.fastq.gz,/MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Tobe_shipped/Transcriptome_PairedEnd/RAW_FASTQ/MDB.RI.T40_R2.fastq.gz \\ \r\n-o \\ \r\n/MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40\r\n----------------------------------------------\r\n\r\n===================\r\nCONFIGURATION.CFG:\r\n===================\r\n[paths]\r\npython = /usr/bin\r\ndata = /MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher/data/ensembl_v79b\r\nscripts = /MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher/bin\r\nbowtie = /MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher/tools/bowtie\r\nbowtie2 = /MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher/tools/bowtie2\r\nbwa = /MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher/tools/bwa\r\nblat = /MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher/tools/blat\r\nliftover = /opt/kent/liftOver\r\nstar = /MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher/tools/star/source\r\nvelvet = /MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher/tools/velvet\r\nfatotwobit = /MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher/tools/fatotwobit\r\nsamtools = /MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher/tools/samtools\r\nseqtk = /MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher/tools/seqtk\r\nsra = /MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher/tools/sratoolkit/bin\r\nnumpy = /usr/lib64/python2.6/site-packages/numpy\r\nbiopython = /MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher/tools/biopython\r\nxlrd = /MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher/tools/xlrd\r\nopenpyxl = /MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher/tools/openpyxl\r\nlzo = /MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher/tools/lzo\r\nlzop = /MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher/tools/lzop/src\r\ncoreutils = /MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher/tools/coreutils/src\r\npigz = /MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher/tools/pigz\r\npicard = /MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher/tools/picard\r\njava = /usr/bin\r\n\r\n[paths]\r\nfusioncatcher = 0.99.4b beta\r\n\r\n\r\n\r\n\r\n============\r\nDATA DIRECTORY:\r\n============\r\n/data/current/\r\nIt is not a link!\r\n\r\n\r\n\r\n================================================================================\r\nWARNING: This is an OLD version of FusionCatcher! There is a newer\r\n         version available! Please, update to the newest version!\r\n - Current version:   0.99.4b beta\r\n - New version:       0.99.4c beta\r\n================================================================================\r\n\r\n\r\n============\r\nMEMORY:\r\n============\r\n             total       used       free     shared    buffers     cached\r\nMem:        258276      60783     197493          0         11      26997\r\n-/+ buffers/cache:      33774     224502\r\nSwap:        31999          2      31997\r\n\r\nTotal installed RAM memory = 258276 MB\r\n\r\n\r\n\r\nInput files (which contain the short reads):\r\n--------------------------------------------\r\n/MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Tobe_shipped/Transcriptome_PairedEnd/RAW_FASTQ/MDB.RI.T40_R1.fastq.gz\r\n/MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Tobe_shipped/Transcriptome_PairedEnd/RAW_FASTQ/MDB.RI.T40_R2.fastq.gz\r\n\r\n\r\n\r\n\r\n\r\nFirst 8 lines of input FASTQ file: /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/init-1_MDB.RI.T40_R2.fastq\r\n-------------------------\r\n@HWI-D00464:61:C66DDACXX:7:1101:1337:2042 2:N:0:GTCCGCA\r\nNTTCTTCTTTCAAAGTCATACTTCAACAAAGTTGCTATTGAATATGTCTGACTAAACATGTTAGCTATATGATAAGATGGCTGGATAAGAGATAAATATA\r\n+\r\n#0<0BFFFFFFFFBFFFIIIIIIFFFFIIIIBFFIFFFIFBBFBFFFFIIFIFFFIFIIFFFIIIIFFBFFFIIBFFFFIIIIFBFFFFBFBBFBBFBBF\r\n@HWI-D00464:61:C66DDACXX:7:1101:1356:2065 2:N:0:GTCCGCA\r\nGGCTGACCGGATGGTTGAAAAAGGCCATTTTGCTGAGCTCTCACAGCTGCTAGGGATGCTCAATGACTCCCAATACAACCCAAAGAGACAAACGCTTGTT\r\n+\r\n<<7<7'0'<77<0<<7'0'<<7'''<0<BBB000<7<<B7<7'7707<7'770''0<BBB########################################\r\n\r\n\r\nFirst 8 lines of input FASTQ file: /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/init-0_MDB.RI.T40_R1.fastq\r\n-------------------------\r\n@HWI-D00464:61:C66DDACXX:7:1101:1337:2042 1:N:0:GTCCGCA\r\nNTTATAAATTTCTTAGTAGATTTATGTCTAAATATTTTACGGTTTGCTACTATTATGAATCAAATAGTTATTAGTTTTCCATTTTAATTCCTAAAGGGTT\r\n+\r\n#0<BFFFFFFFFFIIIFIB<BFFFFIIIIFFBFFIFFFBFFFFFFIFFFFIBFFFIFBFFBFFFFIIFFFFIIIFFFFBBFFFFF<BFFFFFFB<BBB<B\r\n@HWI-D00464:61:C66DDACXX:7:1101:1356:2065 1:N:0:GTCCGCA\r\nNTTCTTATGAAGGATTCGAGCAGGAGCCTGATGCACCAGGGTGAGTGTGGCAGAAAAAACAAGCGTTTGTCTCTTTGGGTTGTATTGGGAGTCATTGAGC\r\n+\r\n#0<BBF<BBFBBFB<F<FF<BF<F0B7<BBFFBBF<B7B70007B0077B<BBBFFB<B0<7B<B7<B77<<<'<<<<77<770<BB<<777<BB<<<<B\r\n\r\n\r\nLast 8 lines of input FASTQ file: /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/init-1_MDB.RI.T40_R2.fastq\r\n-------------------------\r\n@HWI-D00464:61:C66DDACXX:7:2316:21241:100858 2:N:0:GTCCGCA\r\nCAGCCACTGGAGCACTTGGGAGTACCAGTACACGTCACTACACCTGGCTAATTTTTTGTATTTTTAGTAGAGAGGGGGTTTTGCCGAGTTGTACAGGCTG\r\n+\r\n<7<<<B'<<B7B0<<<'<<B<'<77<<B7<<BBB0070'<<<<BBBB0<<<777<<<B<<B<<0<7<<<B<B############################\r\n@HWI-D00464:61:C66DDACXX:7:2316:21275:100842 2:N:0:GTCCGAA\r\nTGTACCAAGATTGAGAAACCTGTCTCAAGACAACGTGCATTGTTTTTATCTGGTTGCTCTCAAGATTATCTCTTTACAACTATAGTTTTCAGAGATCGGA\r\n+\r\n<B<BBFBFFFBFBBBBFFBBBB<BBFFFFF<BFFFBFBFFBFFFFFIFBFBFFFFFFF<FFB<FFBFBFFFIF<<07B<BF<0<B<<BBBBB<B0<BBBB\r\n\r\n\r\nLast 8 lines of input FASTQ file: /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/init-0_MDB.RI.T40_R1.fastq\r\n-------------------------\r\n@HWI-D00464:61:C66DDACXX:7:2316:21241:100858 1:N:0:GTCCGCA\r\nCTCGACAAATCAACTTTTTTAGGCCAGGTGTGGTGGCTCACGCCCGTAATCCCAACACTTTGGGAGGCTGAGGCAGGCAGATCACCTGAGTCCAGGAGTN\r\n+\r\n0<0000<BBBB<BBBBBBBFBFIFFFFI7B<BF0BF<BBFBFBBBFBBFBBFFFFB<BBBFBBBBBBBBBBBBBBBBB<BBB<BB7<BBB<BBBBBBB##\r\n@HWI-D00464:61:C66DDACXX:7:2316:21275:100842 1:N:0:GTCCGAA\r\nCTGAAAACTATAGTTGTAAAGAGATAATCTTGAGAGCAACCAGATAAAAACAATGCACGTTGTCTTGAGACAGGTTTCTCAATCTTGGTACAAGATCGGN\r\n+\r\n<<BBB<BFBBB<FBBF<<BFIFFBB<<BFF<FFFFFFBBFBFFI<FFFBBBFFBBFBFFBFFFBBFFFFFFFFF7<BB<BBBFFBBBBBBBBBBBB<BB#\r\n\r\n\r\n\r\nPair-reads overlappings:\r\n------------------------\r\nInput FASTQ file 1: /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/init-0_MDB.RI.T40_R1.fastq\r\nInput FASTQ file 2: /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/init-1_MDB.RI.T40_R2.fastq\r\nLength read 1: 100\r\nLength read 2: 100\r\nMinimum overlapping size considered by the program: 15\r\nTotal count pair-reads: 67248746 [100.000%]\r\nTotal count reads: 134497492 [200.000%]\r\nCount pair-reads overlapping: 51038121 [75.895%]\r\nCount total wasted nucleotides (due to overlappings): 3229164183 [24.009%]\r\nMost common fragment size amont overlapping pair-reads: 126\r\nCount of the most common fragment size among overlapping pair-reads: 804551\r\n\r\nFragment_length\tpair-reads_counts\tpair-reads_percentage\tCumulative_pair-reads_percentage\r\n18\t2260\t0.003%\t0.003%\r\n19\t2193\t0.003%\t0.007%\r\n20\t2063\t0.003%\t0.010%\r\n21\t2485\t0.004%\t0.013%\r\n22\t2302\t0.003%\t0.017%\r\n23\t2190\t0.003%\t0.020%\r\n24\t2247\t0.003%\t0.023%\r\n25\t3395\t0.005%\t0.028%\r\n26\t2341\t0.003%\t0.032%\r\n27\t2554\t0.004%\t0.036%\r\n28\t2663\t0.004%\t0.040%\r\n29\t2685\t0.004%\t0.044%\r\n30\t2710\t0.004%\t0.048%\r\n31\t2756\t0.004%\t0.052%\r\n32\t2672\t0.004%\t0.056%\r\n33\t2586\t0.004%\t0.060%\r\n34\t2726\t0.004%\t0.064%\r\n35\t2733\t0.004%\t0.068%\r\n36\t2767\t0.004%\t0.072%\r\n37\t3139\t0.005%\t0.077%\r\n38\t3105\t0.005%\t0.081%\r\n39\t3061\t0.005%\t0.086%\r\n40\t3128\t0.005%\t0.090%\r\n41\t2977\t0.004%\t0.095%\r\n42\t2981\t0.004%\t0.099%\r\n43\t2927\t0.004%\t0.104%\r\n44\t2952\t0.004%\t0.108%\r\n45\t3098\t0.005%\t0.113%\r\n46\t3041\t0.005%\t0.117%\r\n47\t3232\t0.005%\t0.122%\r\n48\t3292\t0.005%\t0.127%\r\n49\t3295\t0.005%\t0.132%\r\n50\t3489\t0.005%\t0.137%\r\n51\t3492\t0.005%\t0.142%\r\n52\t3518\t0.005%\t0.147%\r\n53\t3607\t0.005%\t0.153%\r\n54\t3516\t0.005%\t0.158%\r\n55\t3607\t0.005%\t0.163%\r\n56\t3585\t0.005%\t0.169%\r\n57\t3768\t0.006%\t0.174%\r\n58\t3842\t0.006%\t0.180%\r\n59\t4032\t0.006%\t0.186%\r\n60\t4506\t0.007%\t0.193%\r\n61\t5123\t0.008%\t0.200%\r\n62\t5108\t0.008%\t0.208%\r\n63\t5408\t0.008%\t0.216%\r\n64\t5751\t0.009%\t0.224%\r\n65\t6113\t0.009%\t0.233%\r\n66\t6441\t0.010%\t0.243%\r\n67\t6854\t0.010%\t0.253%\r\n68\t7260\t0.011%\t0.264%\r\n69\t7875\t0.012%\t0.276%\r\n70\t8700\t0.013%\t0.289%\r\n71\t9550\t0.014%\t0.303%\r\n72\t11066\t0.016%\t0.319%\r\n73\t12347\t0.018%\t0.338%\r\n74\t13878\t0.021%\t0.358%\r\n75\t15793\t0.023%\t0.382%\r\n76\t15810\t0.024%\t0.405%\r\n77\t18339\t0.027%\t0.433%\r\n78\t19936\t0.030%\t0.462%\r\n79\t23106\t0.034%\t0.497%\r\n80\t26206\t0.039%\t0.536%\r\n81\t29999\t0.045%\t0.580%\r\n82\t33967\t0.051%\t0.631%\r\n83\t39868\t0.059%\t0.690%\r\n84\t44334\t0.066%\t0.756%\r\n85\t51243\t0.076%\t0.832%\r\n86\t57159\t0.085%\t0.917%\r\n87\t63511\t0.094%\t1.012%\r\n88\t68315\t0.102%\t1.113%\r\n89\t74196\t0.110%\t1.223%\r\n90\t83346\t0.124%\t1.347%\r\n91\t99122\t0.147%\t1.495%\r\n92\t109138\t0.162%\t1.657%\r\n93\t132354\t0.197%\t1.854%\r\n94\t142493\t0.212%\t2.066%\r\n95\t161024\t0.239%\t2.305%\r\n96\t182111\t0.271%\t2.576%\r\n97\t192809\t0.287%\t2.863%\r\n98\t219411\t0.326%\t3.189%\r\n99\t230816\t0.343%\t3.532%\r\n100\t257211\t0.382%\t3.915%\r\n101\t287137\t0.427%\t4.342%\r\n102\t329062\t0.489%\t4.831%\r\n103\t341602\t0.508%\t5.339%\r\n104\t372476\t0.554%\t5.893%\r\n105\t391284\t0.582%\t6.475%\r\n106\t434759\t0.646%\t7.121%\r\n107\t441100\t0.656%\t7.777%\r\n108\t463774\t0.690%\t8.467%\r\n109\t500414\t0.744%\t9.211%\r\n110\t542413\t0.807%\t10.017%\r\n111\t547553\t0.814%\t10.832%\r\n112\t576472\t0.857%\t11.689%\r\n113\t612038\t0.910%\t12.599%\r\n114\t645374\t0.960%\t13.559%\r\n115\t667309\t0.992%\t14.551%\r\n116\t695723\t1.035%\t15.586%\r\n117\t724514\t1.077%\t16.663%\r\n118\t713465\t1.061%\t17.724%\r\n119\t701869\t1.044%\t18.768%\r\n120\t710874\t1.057%\t19.825%\r\n121\t725885\t1.079%\t20.904%\r\n122\t741321\t1.102%\t22.006%\r\n123\t747960\t1.112%\t23.119%\r\n124\t781371\t1.162%\t24.281%\r\n125\t801325\t1.192%\t25.472%\r\n126\t804551\t1.196%\t26.669%\r\n127\t801198\t1.191%\t27.860%\r\n128\t801935\t1.192%\t29.052%\r\n129\t779036\t1.158%\t30.211%\r\n130\t787899\t1.172%\t31.382%\r\n131\t773474\t1.150%\t32.533%\r\n132\t774100\t1.151%\t33.684%\r\n133\t761366\t1.132%\t34.816%\r\n134\t783848\t1.166%\t35.981%\r\n135\t776254\t1.154%\t37.136%\r\n136\t778937\t1.158%\t38.294%\r\n137\t768682\t1.143%\t39.437%\r\n138\t757944\t1.127%\t40.564%\r\n139\t750922\t1.117%\t41.681%\r\n140\t727927\t1.082%\t42.763%\r\n141\t723065\t1.075%\t43.838%\r\n142\t728694\t1.084%\t44.922%\r\n143\t712443\t1.059%\t45.981%\r\n144\t745475\t1.109%\t47.090%\r\n145\t762486\t1.134%\t48.224%\r\n146\t721872\t1.073%\t49.297%\r\n147\t703064\t1.045%\t50.343%\r\n148\t682273\t1.015%\t51.357%\r\n149\t679153\t1.010%\t52.367%\r\n150\t637389\t0.948%\t53.315%\r\n151\t635048\t0.944%\t54.259%\r\n152\t610624\t0.908%\t55.167%\r\n153\t615929\t0.916%\t56.083%\r\n154\t598097\t0.889%\t56.973%\r\n155\t611455\t0.909%\t57.882%\r\n156\t580156\t0.863%\t58.745%\r\n157\t566577\t0.843%\t59.587%\r\n158\t562129\t0.836%\t60.423%\r\n159\t553132\t0.823%\t61.245%\r\n160\t565009\t0.840%\t62.086%\r\n161\t548311\t0.815%\t62.901%\r\n162\t522347\t0.777%\t63.678%\r\n163\t517433\t0.769%\t64.447%\r\n164\t491598\t0.731%\t65.178%\r\n165\t491652\t0.731%\t65.909%\r\n166\t486718\t0.724%\t66.633%\r\n167\t483837\t0.719%\t67.353%\r\n168\t455958\t0.678%\t68.031%\r\n169\t445667\t0.663%\t68.693%\r\n170\t433840\t0.645%\t69.338%\r\n171\t415577\t0.618%\t69.956%\r\n172\t400158\t0.595%\t70.551%\r\n173\t399617\t0.594%\t71.146%\r\n174\t380927\t0.566%\t71.712%\r\n175\t373052\t0.555%\t72.267%\r\n176\t376231\t0.559%\t72.826%\r\n177\t361912\t0.538%\t73.364%\r\n178\t358852\t0.534%\t73.898%\r\n179\t346233\t0.515%\t74.413%\r\n180\t331185\t0.492%\t74.905%\r\n181\t324288\t0.482%\t75.388%\r\n182\t340902\t0.507%\t75.895%\r\n>182\t16210625\t24.105%\t100.000%\r\n\r\n\r\n\r\n\r\n\r\nAdapters information:\r\n--------------------\r\nReading the files for automated finding of adapters...\r\n -  /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/init-0_MDB.RI.T40_R1.fastq\r\n -  /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/init-1_MDB.RI.T40_R2.fastq\r\nAdapter 3' end found!\r\n   [AGATCGGAAGAGC...]\r\n   [reverse-complement:...GCTCTTCCGATCT]\r\n   [count=22482/3000000] (0.74940%)\r\nAdapter 5' end found!\r\n   [AGATCGGAAGAGC...]\r\n   [reverse-complement:...GCTCTTCCGATCT]\r\n   [count=22386/3000000 (0.74620%)]\r\nNOTE: Too few adapters found in order to use several processes! Only one CPU will be used!\r\nUsing 1 process(es)...\r\nScanning for adapters...\r\n   10000000 pair-reads [ 722659 (3.613295%) reads trimmed ]\r\n   20000000 pair-reads [ 1437460 (3.593650%) reads trimmed ]\r\n   30000000 pair-reads [ 2147615 (3.579358%) reads trimmed ]\r\n   40000000 pair-reads [ 2863730 (3.579662%) reads trimmed ]\r\n   50000000 pair-reads [ 3572218 (3.572218%) reads trimmed ]\r\n   60000000 pair-reads [ 4282831 (3.569026%) reads trimmed ]\r\nTotal count reads = 134495738\r\nCount trimmed reads = 4796244 [3.566094%]\r\nCount joined pair-reads = 2504472 [3.724240%]\r\nCount of fixed Ns = 17039\r\n\r\n\r\n\r\nReads (mate 1 from pair) removed because being marked as bad by Illumina:\r\n-------------------------------------------------------------------------\r\n0 (0.000%) reads out of 67247869 total reads were removed due to being labeled as bad quality by Illumina!\r\n\r\n\r\n\r\nReads (mate 2 from pair) removed because being marked as bad by Illumina:\r\n-------------------------------------------------------------------------\r\n0 (0.000%) reads out of 67247869 total reads were removed due to being labeled as bad quality by Illumina!\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\nTotal Count of reads (from all FASTQ files given as input and before any read removal is done, i.e. quality filtering, pre-processing):\r\n--------------\r\n/MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/init-shuffle-sra-clear-noadapt-0_MDB.RI.T40_R1.fastq = 134495738\r\n\r\n\r\n\r\nLength of all original reads:\r\n-----------------------------\r\n100\r\n99\r\n98\r\n97\r\n96\r\n95\r\n94\r\n93\r\n92\r\n91\r\n90\r\n89\r\n88\r\n87\r\n86\r\n85\r\n84\r\n83\r\n82\r\n81\r\n80\r\n79\r\n78\r\n77\r\n76\r\n75\r\n74\r\n73\r\n72\r\n71\r\n70\r\n69\r\n68\r\n67\r\n66\r\n65\r\n64\r\n63\r\n62\r\n61\r\n60\r\n59\r\n58\r\n57\r\n56\r\n55\r\n54\r\n53\r\n52\r\n51\r\n50\r\n49\r\n48\r\n47\r\n46\r\n45\r\n44\r\n43\r\n42\r\n41\r\n40\r\n39\r\n38\r\n37\r\n36\r\n35\r\n34\r\n33\r\n32\r\n31\r\n30\r\n29\r\n28\r\n27\r\n26\r\n25\r\n24\r\n23\r\n22\r\n21\r\n20\r\n1\r\n\r\n\r\n\r\nTotal counts of all original reads (after the reads marked by Illumina as bad have been removed):\r\n-------------------------------------------------------------------------------------------------\r\n134495738\r\n\r\n\r\n\r\nLengths of all reads after trimming:\r\n------------------------------------\r\n100\r\n99\r\n98\r\n97\r\n96\r\n95\r\n94\r\n93\r\n92\r\n91\r\n90\r\n89\r\n88\r\n87\r\n86\r\n85\r\n84\r\n83\r\n82\r\n81\r\n80\r\n79\r\n78\r\n77\r\n76\r\n75\r\n74\r\n73\r\n72\r\n71\r\n70\r\n69\r\n68\r\n67\r\n66\r\n65\r\n64\r\n63\r\n62\r\n61\r\n60\r\n59\r\n58\r\n57\r\n56\r\n55\r\n54\r\n53\r\n52\r\n51\r\n50\r\n49\r\n48\r\n47\r\n46\r\n45\r\n44\r\n43\r\n42\r\n41\r\n40\r\n39\r\n38\r\n37\r\n36\r\n35\r\n34\r\n33\r\n32\r\n31\r\n30\r\n29\r\n28\r\n27\r\n26\r\n25\r\n24\r\n23\r\n22\r\n21\r\n20\r\n1\r\n\r\n\r\n\r\n\r\n================================================================================\r\nWARNING: This is an OLD version of FusionCatcher! There is a newer\r\n         version available! Please, update to the newest version!\r\n - Current version:   0.99.4b beta\r\n - New version:       0.99.4c beta\r\n================================================================================\r\n\r\nFound 89490 reads with poly-A/C/G/T/N tails (equal or more 20 repeat nucleotides)\r\nTotal number of input reads = 119283138\r\nTotal number of reads written in the output = 119222860\r\nCount of all short reads after removing reads due to missing their mate read:\r\n-----------------------------------------------------------------------------\r\n112660512\r\n\r\n\r\n\r\n\r\n============\r\nMEMORY (before using BOWTIE):\r\n============\r\n             total       used       free     shared    buffers     cached\r\nMem:        193654      67585     126068          0          7      46241\r\n-/+ buffers/cache:      21336     172317\r\nSwap:        31999      10432      21567\r\n\r\n------------\r\nfusion.log\r\n--------\r\nLog of the pipeline:\r\n--------------------------------------------------------------------------------\r\nStarting execution with step 96.\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 1   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:0m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\nprintf \\\r\n\"\r\n================================================\r\nSotware version: fusioncatcher.py 0.99.4b beta\r\n================================================\r\n\"  \\\r\n> /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/info.txt\r\n--------------------------------------------------------------------------------\r\n|==> SKIPPED because of the step count.\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 2   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:0m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\nprintf \\\r\n\"\r\nSotware version: fusioncatcher.py 0.99.4b beta\r\n\"  \\\r\n>> /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/fusioncatcher.log\r\n--------------------------------------------------------------------------------\r\n|==> SKIPPED because of the step count.\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 3   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:0m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\n\r\n--------------------------------------------------------------------------------\r\n|==> SKIPPED because of the step count.\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 4   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\n\r\n--------------------------------------------------------------------------------\r\n|==> SKIPPED because of the step count.\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 5   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\nSkipping from erasing '/data/current/version.txt' (size: 0 bytes)\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 6   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\n\r\n--------------------------------------------------------------------------------\r\n|==> SKIPPED because of the step count.\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 7   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\nSkipping from erasing '/data/current/genome_information.txt' (size: 0 bytes)\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 8   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\nprintf \\\r\n\"\r\nLinux:\r\n------\r\n\"  \\\r\n>> /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/info.txt\r\n--------------------------------------------------------------------------------\r\n|==> SKIPPED because of the step count.\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 9   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\ncat \\\r\n/etc/issue  \\\r\n2>&1  \\\r\n>> /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/info.txt\r\n--------------------------------------------------------------------------------\r\n|==> SKIPPED because of the step count.\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 10   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\nprintf \\\r\n\"\r\nPython:\r\n------\r\n\"  \\\r\n>> /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/info.txt\r\n--------------------------------------------------------------------------------\r\n|==> SKIPPED because of the step count.\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 11   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\npython_version.py \\\r\n>> /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/info.txt\r\n--------------------------------------------------------------------------------\r\n|==> SKIPPED because of the step count.\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 12   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\nprintf \\\r\n\"\r\nBioPython:\r\n------\r\n\"  \\\r\n>> /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/info.txt\r\n--------------------------------------------------------------------------------\r\n|==> SKIPPED because of the step count.\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 13   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\nbiopython_version.py \\\r\n>> /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/info.txt\r\n--------------------------------------------------------------------------------\r\n|==> SKIPPED because of the step count.\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 14   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\nprintf \\\r\n\"\r\n===========\r\nTOOLS:\r\n===========\r\n\"  \\\r\n>> /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/info.txt\r\n--------------------------------------------------------------------------------\r\n|==> SKIPPED because of the step count.\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 15   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\nprintf \\\r\n\"\r\nSORT:\r\n------\r\n\"  \\\r\n>> /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/info.txt\r\n--------------------------------------------------------------------------------\r\n|==> SKIPPED because of the step count.\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 16   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\nsort \\\r\n--version  \\\r\n|  \\\r\nhead -1 \\\r\n>> /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/info.txt\r\n--------------------------------------------------------------------------------\r\n|==> SKIPPED because of the step count.\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 17   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\nprintf \\\r\n\"\r\nBOWTIE:\r\n------\r\n\"  \\\r\n>> /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/info.txt\r\n--------------------------------------------------------------------------------\r\n|==> SKIPPED because of the step count.\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 18   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\nbowtie \\\r\n--version  \\\r\n|  \\\r\nhead -2 \\\r\n>> /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/info.txt\r\n--------------------------------------------------------------------------------\r\n|==> SKIPPED because of the step count.\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 19   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\nprintf \\\r\n\"\r\nPIGZ:\r\n------\r\n\"  \\\r\n>> /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/info.txt\r\n--------------------------------------------------------------------------------\r\n|==> SKIPPED because of the step count.\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 20   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\npigz \\\r\n-V  \\\r\n2>> /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/info.txt\r\n--------------------------------------------------------------------------------\r\n|==> SKIPPED because of the step count.\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 21   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\nprintf \\\r\n\"\r\nfastq-dump (from SRA Toolkit):\r\n--------------\r\n\"  \\\r\n>> /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/info.txt\r\n--------------------------------------------------------------------------------\r\n|==> SKIPPED because of the step count.\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 22   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\nfastq-dump \\\r\n2>&1  \\\r\n|  \\\r\ntail -2 \\\r\n|  \\\r\nhead -1 \\\r\n>> /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/info.txt\r\n--------------------------------------------------------------------------------\r\n|==> SKIPPED because of the step count.\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 23   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\nprintf \\\r\n\"\r\nSAMTools:\r\n---------\r\n\"  \\\r\n>> /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/info.txt\r\n--------------------------------------------------------------------------------\r\n|==> SKIPPED because of the step count.\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 24   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\nsamtools \\\r\n2>&1  \\\r\n|  \\\r\nhead -3 \\\r\n|  \\\r\ntail -1 \\\r\n>> /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/info.txt\r\n--------------------------------------------------------------------------------\r\n|==> SKIPPED because of the step count.\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 25   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\nprintf \\\r\n\"\r\nliftOver:\r\n---------\r\n\"  \\\r\n>> /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/info.txt\r\n--------------------------------------------------------------------------------\r\n|==> SKIPPED because of the step count.\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 26   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\nliftOver \\\r\n2>&1  \\\r\n|  \\\r\nhead -1 \\\r\n>> /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/info.txt\r\n--------------------------------------------------------------------------------\r\n|==> SKIPPED because of the step count.\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 27   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\nprintf \\\r\n\"\r\nSeqTK:\r\n---------\r\n\"  \\\r\n>> /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/info.txt\r\n--------------------------------------------------------------------------------\r\n|==> SKIPPED because of the step count.\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 28   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\nseqtk \\\r\n2>&1  \\\r\n|  \\\r\nhead -3 \\\r\n|  \\\r\ntail -1 \\\r\n>> /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/info.txt\r\n--------------------------------------------------------------------------------\r\n|==> SKIPPED because of the step count.\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 29   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\nprintf \\\r\n\"\r\nsed:\r\n---------\r\n\"  \\\r\n>> /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/info.txt\r\n--------------------------------------------------------------------------------\r\n|==> SKIPPED because of the step count.\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 30   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\nsed \\\r\n--version  \\\r\n2>&1  \\\r\n|  \\\r\nhead -1 \\\r\n>> /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/info.txt\r\n--------------------------------------------------------------------------------\r\n|==> SKIPPED because of the step count.\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 31   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\nprintf \\\r\n\"\r\nawk:\r\n---------\r\n\"  \\\r\n>> /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/info.txt\r\n--------------------------------------------------------------------------------\r\n|==> SKIPPED because of the step count.\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 32   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\nawk \\\r\n--version  \\\r\n2>&1  \\\r\n|  \\\r\nhead -1 \\\r\n>> /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/info.txt\r\n--------------------------------------------------------------------------------\r\n|==> SKIPPED because of the step count.\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 33   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\nprintf \\\r\n\"\r\nBLAT:\r\n------\r\n\"  \\\r\n>> /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/info.txt\r\n--------------------------------------------------------------------------------\r\n|==> SKIPPED because of the step count.\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 34   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\nblat \\\r\n|  \\\r\nhead -1 \\\r\n>> /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/info.txt\r\n--------------------------------------------------------------------------------\r\n|==> SKIPPED because of the step count.\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 35   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\nprintf \\\r\n\"\r\nfaToTwoBit (from BLAT toolbox):\r\n----------------\r\n\"  \\\r\n>> /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/info.txt\r\n--------------------------------------------------------------------------------\r\n|==> SKIPPED because of the step count.\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 36   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\nfaToTwoBit \\\r\n2>&1  \\\r\n> /dev/null \\\r\n|  \\\r\nhead -1 \\\r\n>> /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/info.txt\r\n--------------------------------------------------------------------------------\r\n|==> SKIPPED because of the step count.\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 37   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\nprintf \\\r\n\"\r\nSTAR:\r\n------\r\n\"  \\\r\n>> /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/info.txt\r\n--------------------------------------------------------------------------------\r\n|==> SKIPPED because of the step count.\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 38   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\nSTAR \\\r\n--version  \\\r\n>> /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/info.txt\r\n--------------------------------------------------------------------------------\r\n|==> SKIPPED because of the step count.\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 39   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\nprintf \\\r\n\"\r\n\r\n\r\n\"  \\\r\n>> /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/info.txt\r\n--------------------------------------------------------------------------------\r\n|==> SKIPPED because of the step count.\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 40   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\n\r\n--------------------------------------------------------------------------------\r\n|==> SKIPPED because of the step count.\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 41   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\n\r\n--------------------------------------------------------------------------------\r\n|==> SKIPPED because of the step count.\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 42   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\nSkipping from erasing '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher/etc/configuration.cfg' (size: 1510 bytes)\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 43   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\nprintf \\\r\n\"\r\n============\r\nDATA DIRECTORY:\r\n============\r\n/data/current/\r\nIt is not a link!\r\n\r\n\r\n\"  \\\r\n>> /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/info.txt\r\n--------------------------------------------------------------------------------\r\n|==> SKIPPED because of the step count.\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 44   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\n\r\n--------------------------------------------------------------------------------\r\n|==> SKIPPED because of the step count.\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 45   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\nprintf \\\r\n\"\r\n============\r\nMEMORY:\r\n============\r\n\"  \\\r\n>> /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/info.txt\r\n--------------------------------------------------------------------------------\r\n|==> SKIPPED because of the step count.\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 46   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\nfree \\\r\n-m  \\\r\n>> /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/info.txt\r\n--------------------------------------------------------------------------------\r\n|==> SKIPPED because of the step count.\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 47   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\nprintf \\\r\n\"\r\nTotal installed RAM memory = 193654 MB\"  \\\r\n>> /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/info.txt\r\n--------------------------------------------------------------------------------\r\n|==> SKIPPED because of the step count.\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 48   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\nprintf \\\r\n\"\r\n\r\n\r\n\"  \\\r\n>> /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/info.txt\r\n--------------------------------------------------------------------------------\r\n|==> SKIPPED because of the step count.\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\nInput files (which contain the short reads):\r\n/MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Tobe_shipped/Transcriptome_PairedEnd/RAW_FASTQ/MDB.RI.T40_R1.fastq.gz\r\n/MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Tobe_shipped/Transcriptome_PairedEnd/RAW_FASTQ/MDB.RI.T40_R2.fastq.gz\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 49   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\n\r\n--------------------------------------------------------------------------------\r\n|==> SKIPPED because of the step count.\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 50   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\npigz \\\r\n-p 64 \\\r\n-d  \\\r\n-f  \\\r\n-c  \\\r\n /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Tobe_shipped/Transcriptome_PairedEnd/RAW_FASTQ/MDB.RI.T40_R1.fastq.gz \\\r\n> /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/init-0_MDB.RI.T40_R1.fastq\r\n--------------------------------------------------------------------------------\r\n|==> SKIPPED because of the step count.\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 51   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\npigz \\\r\n-p 64 \\\r\n-d  \\\r\n-f  \\\r\n-c  \\\r\n /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Tobe_shipped/Transcriptome_PairedEnd/RAW_FASTQ/MDB.RI.T40_R2.fastq.gz \\\r\n> /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/init-1_MDB.RI.T40_R2.fastq\r\n--------------------------------------------------------------------------------\r\n|==> SKIPPED because of the step count.\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 52   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\nprintf \\\r\n\"\r\n\r\nFirst 8 lines of input FASTQ file: /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/init-1_MDB.RI.T40_R2.fastq\r\n-------------------------\r\n\"  \\\r\n>> /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/info.txt\r\n--------------------------------------------------------------------------------\r\n|==> SKIPPED because of the step count.\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 53   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\nhead \\\r\n-8 /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/init-1_MDB.RI.T40_R2.fastq \\\r\n>> /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/info.txt\r\n--------------------------------------------------------------------------------\r\n|==> SKIPPED because of the step count.\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 54   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\nprintf \\\r\n\"\r\n\r\nFirst 8 lines of input FASTQ file: /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/init-0_MDB.RI.T40_R1.fastq\r\n-------------------------\r\n\"  \\\r\n>> /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/info.txt\r\n--------------------------------------------------------------------------------\r\n|==> SKIPPED because of the step count.\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 55   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\nhead \\\r\n-8 /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/init-0_MDB.RI.T40_R1.fastq \\\r\n>> /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/info.txt\r\n--------------------------------------------------------------------------------\r\n|==> SKIPPED because of the step count.\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 56   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\nprintf \\\r\n\"\r\n\r\nLast 8 lines of input FASTQ file: /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/init-1_MDB.RI.T40_R2.fastq\r\n-------------------------\r\n\"  \\\r\n>> /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/info.txt\r\n--------------------------------------------------------------------------------\r\n|==> SKIPPED because of the step count.\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 57   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\ntail \\\r\n-8 /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/init-1_MDB.RI.T40_R2.fastq \\\r\n>> /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/info.txt\r\n--------------------------------------------------------------------------------\r\n|==> SKIPPED because of the step count.\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 58   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\nprintf \\\r\n\"\r\n\r\nLast 8 lines of input FASTQ file: /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/init-0_MDB.RI.T40_R1.fastq\r\n-------------------------\r\n\"  \\\r\n>> /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/info.txt\r\n--------------------------------------------------------------------------------\r\n|==> SKIPPED because of the step count.\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 59   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\ntail \\\r\n-8 /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/init-0_MDB.RI.T40_R1.fastq \\\r\n>> /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/info.txt\r\n--------------------------------------------------------------------------------\r\n|==> SKIPPED because of the step count.\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 60   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\noverlap.py \\\r\n--input_1 /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/init-0_MDB.RI.T40_R1.fastq \\\r\n--input_2 /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/init-1_MDB.RI.T40_R2.fastq \\\r\n--processes 64 \\\r\n--fail-gracefully  \\\r\n--output /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/log_overlaps__0.txt \\\r\n2> /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/log_overlaps_error__0.txt\r\n--------------------------------------------------------------------------------\r\n|==> SKIPPED because of the step count.\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 61   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\n|==> SKIPPED workflow's IF because of the step count (value returned in the previous run is used).\r\nResult of IF = FALSE [Unique Id = #DIFFERENT_SIZES_OF_READS_OVERLAP_0#]\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 62   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\n\r\n--------------------------------------------------------------------------------\r\n|==> SKIPPED because of the step count.\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 63   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\nErasing '/MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/log_overlaps__0.txt' (size: 0 bytes)\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 64   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\nErasing '/MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/log_overlaps_error__0.txt' (size: 0 bytes)\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 65   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\nremove_adapter.py \\\r\n--processes 64 \\\r\n--input_1 /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/init-0_MDB.RI.T40_R1.fastq \\\r\n--input_2 /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/init-1_MDB.RI.T40_R2.fastq \\\r\n--output_1 /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/init-noadapt-0_MDB.RI.T40_R1.fastq \\\r\n--output_2 /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/init-noadapt-1_MDB.RI.T40_R2.fastq \\\r\n--link hard \\\r\n> /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/log_adapters_0.txt \\\r\n2>&1 \r\n--------------------------------------------------------------------------------\r\n|==> SKIPPED because of the step count.\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 66   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\n\r\n--------------------------------------------------------------------------------\r\n|==> SKIPPED because of the step count.\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 67   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\nErasing '/MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/log_adapters_0.txt' (size: 0 bytes)\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 68   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\nremove-bad-illumina.py \\\r\n--input /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/init-noadapt-0_MDB.RI.T40_R1.fastq \\\r\n--output /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/init-clear-noadapt-0_MDB.RI.T40_R1.fastq \\\r\n--link hard \\\r\n2> /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/log_bad_illumina_1_0.txt\r\n--------------------------------------------------------------------------------\r\n|==> SKIPPED because of the step count.\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 69   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\n\r\n--------------------------------------------------------------------------------\r\n|==> SKIPPED because of the step count.\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 70   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\nErasing '/MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/log_bad_illumina_1_0.txt' (size: 0 bytes)\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 71   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\nremove-bad-illumina.py \\\r\n--input /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/init-noadapt-1_MDB.RI.T40_R2.fastq \\\r\n--output /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/init-clear-noadapt-1_MDB.RI.T40_R2.fastq \\\r\n--link hard \\\r\n2> /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/log_bad_illumina_2_0.txt\r\n--------------------------------------------------------------------------------\r\n|==> SKIPPED because of the step count.\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 72   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\n\r\n--------------------------------------------------------------------------------\r\n|==> SKIPPED because of the step count.\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 73   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\nErasing '/MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/log_bad_illumina_2_0.txt' (size: 0 bytes)\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 74   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\nsra2illumina.py \\\r\n--input_1 /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/init-clear-noadapt-0_MDB.RI.T40_R1.fastq \\\r\n--input_2 /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/init-clear-noadapt-1_MDB.RI.T40_R2.fastq \\\r\n--output_1 /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/init-sra-clear-noadapt-0_MDB.RI.T40_R1.fastq \\\r\n--output_2 /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/init-sra-clear-noadapt-1_MDB.RI.T40_R2.fastq \\\r\n--link hard \\\r\n--tmp_dir /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/tmp/\r\n--------------------------------------------------------------------------------\r\n|==> SKIPPED because of the step count.\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 75   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\nseqtk \\\r\nmergepe  \\\r\n /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/init-sra-clear-noadapt-0_MDB.RI.T40_R1.fastq \\\r\n /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/init-sra-clear-noadapt-1_MDB.RI.T40_R2.fastq \\\r\n> /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/init-shuffle-sra-clear-noadapt-0_MDB.RI.T40_R1.fastq\r\n--------------------------------------------------------------------------------\r\n|==> SKIPPED because of the step count.\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 76   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\nprintf \\\r\n\"\r\n\r\n\r\n\"  \\\r\n>> /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/info.txt\r\n--------------------------------------------------------------------------------\r\n|==> SKIPPED because of the step count.\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 77   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\nprintf \\\r\n\"\r\nTotal Count of reads (from all FASTQ files given as input and before any read removal is done, i.e. quality filtering, pre-processing):\r\n--------------\r\n\"  \\\r\n>> /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/info.txt\r\n--------------------------------------------------------------------------------\r\n|==> SKIPPED because of the step count.\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 78   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\nprintf \\\r\n\"/MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/init-shuffle-sra-clear-noadapt-0_MDB.RI.T40_R1.fastq = \"  \\\r\n>> /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/info.txt\r\n--------------------------------------------------------------------------------\r\n|==> SKIPPED because of the step count.\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 79   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\ncat \\\r\n /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/init-shuffle-sra-clear-noadapt-0_MDB.RI.T40_R1.fastq \\\r\n|  \\\r\necho $((`wc -l`/4))  \\\r\n>> /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/info.txt\r\n--------------------------------------------------------------------------------\r\n|==> SKIPPED because of the step count.\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 80   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\nsolexa18to15.py \\\r\n--fail  \\\r\n--input /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/init-shuffle-sra-clear-noadapt-0_MDB.RI.T40_R1.fastq \\\r\n--output /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/init-head-shuffle-sra-clear-noadapt-0_MDB.RI.T40_R1.fastq \\\r\n--link hard\r\n--------------------------------------------------------------------------------\r\n|==> SKIPPED because of the step count.\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 81   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\nphred.py \\\r\n--link hard \\\r\n--input /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/init-head-shuffle-sra-clear-noadapt-0_MDB.RI.T40_R1.fastq \\\r\n--output /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/init-phred-head-shuffle-sra-clear-noadapt-0_MDB.RI.T40_R1.fastq \\\r\n--input_type auto-detect \\\r\n--output_type illumina-1.5 \\\r\n--tmp_dir /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/tmp/\r\n--------------------------------------------------------------------------------\r\n|==> SKIPPED because of the step count.\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 82   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\nprintf \\\r\n\"\r\n\r\n\r\n\"  \\\r\n>> /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/info.txt\r\n--------------------------------------------------------------------------------\r\n|==> SKIPPED because of the step count.\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 83   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\nSkipping the moving from:\r\n'/MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/init-phred-head-shuffle-sra-clear-noadapt-0_MDB.RI.T40_R1.fastq'\r\nto:\r\n'/MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/origin.fq'\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 84   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\nlengths_reads.py \\\r\n--input /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/origin.fq \\\r\n--output /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/log_lengths_original_reads.txt \\\r\n--counts /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/log_counts_original_reads.txt\r\n--------------------------------------------------------------------------------\r\n|==> SKIPPED because of the step count.\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 85   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\ncompress-reads-ids.py \\\r\n--input /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/origin.fq \\\r\n--output /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/original.fq \\\r\n--count-reads /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/log_counts_original_reads.txt \\\r\n--lowercase \r\n--------------------------------------------------------------------------------\r\n|==> SKIPPED because of the step count.\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 86   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\n\r\n--------------------------------------------------------------------------------\r\n|==> SKIPPED because of the step count.\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 87   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\nSkipping from erasing '/MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/log_lengths_original_reads.txt' (size: 246 bytes)\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 88   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\n\r\n--------------------------------------------------------------------------------\r\n|==> SKIPPED because of the step count.\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 89   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\nErasing '/MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/log_counts_original_reads.txt' (size: 0 bytes)\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 90   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\nSkipping the soft linking from:\r\n'/MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/original.fq'\r\nto:\r\n'/MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/original-t5-t3.fq'\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 91   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\nSkipping the moving from:\r\n'/MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/original-t5-t3.fq'\r\nto:\r\n'/MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/reads.fq'\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 92   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\nlengths_reads.py \\\r\n--input /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/reads.fq \\\r\n--output /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/log_lengths_reads.txt\r\n--------------------------------------------------------------------------------\r\n|==> SKIPPED because of the step count.\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 93   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\n\r\n--------------------------------------------------------------------------------\r\n|==> SKIPPED because of the step count.\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 94   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\n\r\n--------------------------------------------------------------------------------\r\n|==> SKIPPED because of the step count.\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 95   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\nSkipping from erasing '/MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/log_lengths_reads.txt' (size: 246 bytes)\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 96   Time: 21:15   Date: 2015-08-12 (elapsed time: 0d:0h:1m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\nfastq_b2n.py \\\r\n--input /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/reads.fq \\\r\n--replacement A \\\r\n--ambiguous  \\\r\n--threshold 100 \\\r\n--output - \\\r\n|  \\\r\ntrim_poly_tails.py  \\\r\n--input - \\\r\n--repeats 20 \\\r\n--output - \\\r\n2>> /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/info.txt \\\r\n|  \\\r\nseqtk  \\\r\nseq  \\\r\n-L 100 \\\r\n-  \\\r\n> /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/reads_no-shorts.fq\r\n--------------------------------------------------------------------------------\r\n+-->EXECUTING...\r\n==> Erasing file: '/MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/reads.fq' (size: 28551728260 bytes)\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 44 minute(s), and 34 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 97   Time: 22:00   Date: 2015-08-12 (elapsed time: 0d:0h:45m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\npigz \\\r\n-p 64 \\\r\n-c /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/original.fq \\\r\n> /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/original.fq.gz\r\n--------------------------------------------------------------------------------\r\n+-->EXECUTING...\r\n==> Erasing file: '/MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/original.fq' (size: 28551728260 bytes)\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 3 minute(s), and 4 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 98   Time: 22:03   Date: 2015-08-12 (elapsed time: 0d:0h:48m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\nseqtk \\\r\ndropse  \\\r\n /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/reads_no-shorts.fq \\\r\n> /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/reads_acgt.fq\r\n--------------------------------------------------------------------------------\r\n+-->EXECUTING...\r\n==> Erasing file: '/MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/reads_no-shorts.fq' (size: 25379345328 bytes)\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 5 minute(s), and 9 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 99   Time: 22:08   Date: 2015-08-12 (elapsed time: 0d:0h:53m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\ncat \\\r\n /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/reads_acgt.fq \\\r\n|  \\\r\necho $((`wc -l`/4))  \\\r\n>> /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/log_removed_single_reads1.txt\r\n--------------------------------------------------------------------------------\r\n+-->EXECUTING...\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 2 minute(s), and 14 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 100   Time: 22:10   Date: 2015-08-12 (elapsed time: 0d:0h:56m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\n\r\n--------------------------------------------------------------------------------\r\n+-->MOCK EXECUTION (i.e. code executed outside of workflow)...\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\nAPPENDING to file: '/MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/info.txt'.\r\n>Count of all short reads after removing reads due to missing their mate read:\r\n>-----------------------------------------------------------------------------\r\n>from file: '/MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/log_removed_single_reads1.txt'\r\n>\r\n>\r\n>\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 101   Time: 22:10   Date: 2015-08-12 (elapsed time: 0d:0h:56m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\nSkipping from erasing '/MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/log_removed_single_reads1.txt' (size: 10 bytes)\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 102   Time: 22:10   Date: 2015-08-12 (elapsed time: 0d:0h:56m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\n+-->EXECUTING workflow's IF...\r\nResult of IF = FALSE [Unique Id = #READS_ACGT.FQ#]\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 103   Time: 22:10   Date: 2015-08-12 (elapsed time: 0d:0h:56m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\n\r\n--------------------------------------------------------------------------------\r\n+-->MOCK EXECUTION (i.e. code executed outside of workflow)...\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 104   Time: 22:10   Date: 2015-08-12 (elapsed time: 0d:0h:56m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\nprintf \\\r\n\"\r\n============\r\nMEMORY (before using BOWTIE):\r\n============\r\n\"  \\\r\n>> /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/info.txt\r\n--------------------------------------------------------------------------------\r\n+-->EXECUTING...\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 105   Time: 22:10   Date: 2015-08-12 (elapsed time: 0d:0h:56m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\nfree \\\r\n-m  \\\r\n>> /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/info.txt\r\n--------------------------------------------------------------------------------\r\n+-->EXECUTING...\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 106   Time: 22:10   Date: 2015-08-12 (elapsed time: 0d:0h:56m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\nprintf \\\r\n\"\r\n\r\n\r\n\"  \\\r\n>> /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/info.txt\r\n--------------------------------------------------------------------------------\r\n+-->EXECUTING...\r\n--------------------------------------------------------------------------------\r\n==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)\r\n////////////////////////////////////////////////////////////////////////////////\r\n  Running: step = 107   Time: 22:10   Date: 2015-08-12 (elapsed time: 0d:0h:56m)\r\n\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\r\n==> Current working directory: '/MGMSTAR1/SHARED/STAFF/KIRAN.P/fusioncatcher'\r\nbowtie \\\r\n-t  \\\r\n-v 2 \\\r\n-p 64 \\\r\n-k 1 \\\r\n--solexa1.3-quals  \\\r\n--tryhard  \\\r\n--chunkmbs 128 \\\r\n--un /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/reads-filtered_temp.fq \\\r\n--max /dev/null \\\r\n /data/current/rtrna_mt_index/ \\\r\n /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/reads_acgt.fq \\\r\n /dev/null \\\r\n2> /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/log_bowtie_reads-filtered-out.stdout.txt\r\n--------------------------------------------------------------------------------\r\n+-->EXECUTING...\r\n\r\n\r\nERROR: Workflow execution failed at step 107 while executing:\r\n----------------\r\n   bowtie \\\r\n   -t  \\\r\n   -v 2 \\\r\n   -p 64 \\\r\n   -k 1 \\\r\n   --solexa1.3-quals  \\\r\n   --tryhard  \\\r\n   --chunkmbs 128 \\\r\n   --un /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/reads-filtered_temp.fq \\\r\n   --max /dev/null \\\r\n    /data/current/rtrna_mt_index/ \\\r\n    /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/reads_acgt.fq \\\r\n    /dev/null \\\r\n   2> /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/log_bowtie_reads-filtered-out.stdout.txt\r\n----------------\r\n  * Size '/MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/reads-filtered_temp.fq' = 0 bytes\r\n  * Size '/data/current/rtrna_mt_index/' = 0 bytes\r\n  * Size '/MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/reads_acgt.fq' = 23996689056 bytes\r\n  * Size '/MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/log_bowtie_reads-filtered-out.stdout.txt' = 418 bytes\r\nCould not locate a Bowtie index corresponding to basename \"/data/current/rtrna_mt_index/\"\r\nOverall time: 00:00:00\r\nCommand: bowtie --wrapper basic-0 -t -v 2 -p 64 -k 1 --solexa1.3-quals --tryhard --chunkmbs 128 --un /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/reads-filtered_temp.fq --max /dev/null /data/current/rtrna_mt_index/ /MGMSTAR1/SHARED/ANALYSIS/NGS_P1216/Fusions/MDB.RI.T40/reads_acgt.fq /dev/null \r\n################################################################################\r\n################################################################################\r\nTOTAL RUNNING TIME: 0 day(s), 0 hour(s), 55 minute(s), and 5 second(s) \r\n################################################################################\r\n################################################################################\r\n\r\n\r\nI could run the fusion with the same data build with empty rtrna_mt_index\r\n\r\nThank you looking forward for solution, i have 20 Cancer samples to Run.\r\n\r\nThank you\r\n\r\n\r\n\r\n\r\n\r\n"}}