{"action":"created","issue":{"url":"https://api.github.com/repos/upendrak/lincRNA_pipeline/issues/2","labels_url":"https://api.github.com/repos/upendrak/lincRNA_pipeline/issues/2/labels{/name}","comments_url":"https://api.github.com/repos/upendrak/lincRNA_pipeline/issues/2/comments","events_url":"https://api.github.com/repos/upendrak/lincRNA_pipeline/issues/2/events","html_url":"https://github.com/upendrak/lincRNA_pipeline/issues/2","id":62301101,"number":2,"title":"Error messages, etc.","user":{"login":"mfcovington","id":1494842,"avatar_url":"https://avatars.githubusercontent.com/u/1494842?v=3","gravatar_id":"","url":"https://api.github.com/users/mfcovington","html_url":"https://github.com/mfcovington","followers_url":"https://api.github.com/users/mfcovington/followers","following_url":"https://api.github.com/users/mfcovington/following{/other_user}","gists_url":"https://api.github.com/users/mfcovington/gists{/gist_id}","starred_url":"https://api.github.com/users/mfcovington/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mfcovington/subscriptions","organizations_url":"https://api.github.com/users/mfcovington/orgs","repos_url":"https://api.github.com/users/mfcovington/repos","events_url":"https://api.github.com/users/mfcovington/events{/privacy}","received_events_url":"https://api.github.com/users/mfcovington/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":6,"created_at":"2015-03-17T06:21:35Z","updated_at":"2015-03-20T22:23:17Z","closed_at":null,"body":"I ran the pipeline on my laptop like this:\r\n\r\n```sh\r\ntime sh lincRNA_pipeline.sh -c sample.data/cuffcompare_out_annot_no_annot.combined.gtf -g sample.data/Brapa_sequence_v1.2.fa -r sample.data/Brassica_rapa_v1.2.cds -b sample.data/TE_RNA_transcripts.fa\r\n```\r\n\r\nHere's the output:\r\n\r\n```\r\n--2015-03-16 16:34:26--  https://github.com/TransDecoder/TransDecoder/archive/2.0.1.tar.gz\r\nResolving github.com... 192.30.252.130\r\nConnecting to github.com|192.30.252.130|:443... connected.\r\nHTTP request sent, awaiting response... 302 Found\r\nLocation: https://codeload.github.com/TransDecoder/TransDecoder/tar.gz/2.0.1 [following]\r\n--2015-03-16 16:34:26--  https://codeload.github.com/TransDecoder/TransDecoder/tar.gz/2.0.1\r\nResolving codeload.github.com... 192.30.252.145\r\nConnecting to codeload.github.com|192.30.252.145|:443... connected.\r\nHTTP request sent, awaiting response... 200 OK\r\nLength: 9925281 (9.5M) [application/x-gzip]\r\nSaving to: 'STDOUT'\r\n\r\n 0% [                                                                                                                                            ] 0           --.-K/s              x TransDecoder-2.0.1/\r\nx TransDecoder-2.0.1/LICENSE.txt\r\nx TransDecoder-2.0.1/Makefile\r\nx TransDecoder-2.0.1/PerlLib/\r\nx TransDecoder-2.0.1/PerlLib/Fasta_reader.pm\r\nx TransDecoder-2.0.1/PerlLib/GFF3_utils.pm\r\nx TransDecoder-2.0.1/PerlLib/Gene_obj.pm\r\nx TransDecoder-2.0.1/PerlLib/Gene_obj_indexer.pm\r\nx TransDecoder-2.0.1/PerlLib/Longest_orf.pm\r\nx TransDecoder-2.0.1/PerlLib/Nuc_translator.pm\r\nx TransDecoder-2.0.1/PerlLib/TiedHash.pm\r\nx TransDecoder-2.0.1/README\r\nx TransDecoder-2.0.1/README.md\r\nx TransDecoder-2.0.1/Release.Notes\r\n 0% [                                                                                                                                            ] 47,513       223KB/s             \r\nx TransDecoder-2.0.1/TransDecoder.Predict\r\nx TransDecoder-2.0.1/notes\r\nx TransDecoder-2.0.1/sample_data/\r\nx TransDecoder-2.0.1/sample_data/blastp.results.outfmt6.gz\r\nx TransDecoder-2.0.1/sample_data/cleanme.pl\r\nx TransDecoder-2.0.1/sample_data/pfam.domtblout.gz\r\nx TransDecoder-2.0.1/sample_data/runMe.sh\r\n 1% [>                                                                                                                                           ] 139,079      324KB/s             \r\n92% [=================================================================================================================================>          ] 9,219,351    212KB/s  eta 4s     \r\nx TransDecoder-2.0.1/sample_data/transcripts.gtf.gz\r\nx TransDecoder-2.0.1/transdecoder_plugins/\r\nx TransDecoder-2.0.1/transdecoder_plugins/Makefile\r\n99% [==========================================================================================================================================> ] 9,909,633    176KB/s  eta 1s     \r\nx TransDecoder-2.0.1/util/\r\nx TransDecoder-2.0.1/util/bin/\r\nx TransDecoder-2.0.1/util/bin/.hidden\r\n100%[===========================================================================================================================================>] 9,925,281    179KB/s   in 52s    \r\n\r\n2015-03-16 16:35:18 (188 KB/s) - written to stdout [9925281/9925281]\r\n\r\n\r\nx TransDecoder-2.0.1/util/compute_base_probs.pl\r\nx TransDecoder-2.0.1/util/cufflinks_gtf_genome_to_cdna_fasta.pl\r\nx TransDecoder-2.0.1/util/cufflinks_gtf_to_alignment_gff3.pl\r\nx TransDecoder-2.0.1/util/cufflinks_gtf_to_bed.pl\r\nx TransDecoder-2.0.1/util/ffindex_resume.pl\r\nx TransDecoder-2.0.1/util/gene_list_to_gff.pl\r\nx TransDecoder-2.0.1/util/get_top_longest_fasta_entries.pl\r\nx TransDecoder-2.0.1/util/gff3_file_to_bed.pl\r\nx TransDecoder-2.0.1/util/gff3_file_to_proteins.pl\r\nx TransDecoder-2.0.1/util/index_gff3_files_by_isoform.pl\r\nx TransDecoder-2.0.1/util/nr_ORFs_gff3.pl\r\nx TransDecoder-2.0.1/util/pfam_mpi.pbs\r\nx TransDecoder-2.0.1/util/pfam_runner.pl\r\nx TransDecoder-2.0.1/util/remove_eclipsed_ORFs.pl\r\nx TransDecoder-2.0.1/util/score_CDS_liklihood_all_6_frames.pl\r\nx TransDecoder-2.0.1/util/seq_n_baseprobs_to_logliklihood_vals.pl\r\ndyld: Library not loaded: /usr/local/lib/gcc/x86_64-apple-darwin13.3.0/4.8.3/libgomp.1.dylib\r\n  Referenced from: /usr/local/bin/makeblastdb\r\n  Reason: image not found\r\nlincRNA_pipeline.sh: line 41: 74333 Trace/BPT trap: 5       makeblastdb -in $blastfile -dbtype nucl -out $blastfile.blast.out\r\ndyld: Library not loaded: /usr/local/lib/gcc/x86_64-apple-darwin13.3.0/4.8.3/libgomp.1.dylib\r\n  Referenced from: /usr/local/bin/makeblastdb\r\n  Reason: image not found\r\nlincRNA_pipeline.sh: line 43: 74335 Trace/BPT trap: 5       makeblastdb -in $referenceCDS -dbtype nucl -out $referenceCDS.blast.out\r\nlincRNA_pipeline.sh: line 46: gffread: command not found\r\nsed: transcripts_u_filter.fa: No such file or directory\r\nlincRNA_pipeline.sh: line 53: cd: transcripts_u_filter.fa.transdecoder_dir: No such file or directory\r\nsed: longest_orfs.cds: No such file or directory\r\n/usr/local/Cellar/python/2.7.8_2/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python: can't open file '../extract_sequences.py': [Errno 2] No such file or directory\r\nsed: longest_orfs.cds.genes.not.genes.fa: No such file or directory\r\ndyld: Library not loaded: /usr/local/lib/gcc/x86_64-apple-darwin13.3.0/4.8.3/libgomp.1.dylib\r\n  Referenced from: /usr/local/bin/blastn\r\n  Reason: image not found\r\nlincRNA_pipeline.sh: line 70: 74348 Trace/BPT trap: 5       blastn -query longest_orfs.cds.genes.not.genes.fa -db ../$blastfile.blast.out -out longest_orfs.cds.genes.not.genes.fa.blast.out -outfmt 6\r\n/usr/local/Cellar/python/2.7.8_2/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python: can't open file '../filter_sequences.py': [Errno 2] No such file or directory\r\ngrep: longest_orfs.cds.genes.not.genes.fa: No such file or directory\r\n/usr/local/Cellar/python/2.7.8_2/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python: can't open file '../fasta_remove.py': [Errno 2] No such file or directory\r\nsed: lincRNA.genes: No such file or directory\r\n/usr/local/Cellar/python/2.7.8_2/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python: can't open file '../extract_sequences-1.py': [Errno 2] No such file or directory\r\nlincRNA_pipeline.sh: line 83: cap3: command not found\r\ncat: lincRNA.genes.fa.cap.singlets: No such file or directory\r\ncat: lincRNA.genes.fa.cap.contigs: No such file or directory\r\ndyld: Library not loaded: /usr/local/lib/gcc/x86_64-apple-darwin13.3.0/4.8.3/libgomp.1.dylib\r\n  Referenced from: /usr/local/bin/blastn\r\n  Reason: image not found\r\nlincRNA_pipeline.sh: line 92: 74358 Trace/BPT trap: 5       blastn -query lincRNA_genes_non_redundant.fa -db ../$referenceCDS.blast.out -out lincRNA_non_redundant.fa_cds_blast.out -evalue 1e-30 -outfmt 6\r\n/usr/local/Cellar/python/2.7.8_2/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python: can't open file '../linc_RNA_filter.py': [Errno 2] No such file or directory\r\ngrep: lincRNA_non_redundant.fa_cds_blast.out.filtered: No such file or directory\r\n/usr/local/Cellar/python/2.7.8_2/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python: can't open file '../extract_sequences-1.py': [Errno 2] No such file or directory\r\ngrep: lincRNA_non_redundant_filtered.genes.fa: No such file or directory\r\ndyld: Library not loaded: /usr/local/lib/gcc/x86_64-apple-darwin13.3.0/4.8.3/libgomp.1.dylib\r\n  Referenced from: /usr/local/bin/makeblastdb\r\n  Reason: image not found\r\nlincRNA_pipeline.sh: line 104: 74363 Trace/BPT trap: 5       makeblastdb -in lincRNA_non_redundant_filtered.genes.fa -dbtype nucl -out lincRNA_non_redundant_filtered_blast.out\r\ndyld: Library not loaded: /usr/local/lib/gcc/x86_64-apple-darwin13.3.0/4.8.3/libgomp.1.dylib\r\n  Referenced from: /usr/local/bin/blastn\r\n  Reason: image not found\r\nlincRNA_pipeline.sh: line 106: 74364 Trace/BPT trap: 5       blastn -query lincRNA_non_redundant_filtered.genes.fa -db lincRNA_non_redundant_filtered_blast.out -out lincRNA_non_redundant_filtered_blast.out.blast.out -evalue 1e-30 -outfmt 6\r\n/usr/local/Cellar/python/2.7.8_2/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python: can't open file '../linc_RNA_filter-1.py': [Errno 2] No such file or directory\r\ngrep: lincRNA_non_redundant_filtered_blast.out.blast.out.uniq: No such file or directory\r\n/usr/local/Cellar/python/2.7.8_2/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python: can't open file '../extract_sequences-1.py': [Errno 2] No such file or directory\r\n/usr/local/Cellar/python/2.7.8_2/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python: can't open file '../fasta_header_rename.py': [Errno 2] No such file or directory\r\n\r\nreal    0m54.186s\r\nuser    0m0.319s\r\nsys 0m0.534s\r\n```\r\n\r\nA few things that should probably be done:\r\n\r\n- [ ] Only download/install TransDecoder if it isn't installed. Alternatively, just specify it as a prerequisite and verify that the correct version is installed in `PATH`\r\n- [ ] Verify that binaries are properly installed:\r\n    - [ ] `makeblastdb`\r\n    - [ ] `blastn`\r\n    - [ ] `gffread` \r\n    - [ ] `cap3`\r\n- [ ] Call `mkdir transcripts_u_filter.fa.transdecoder_dir` before `cd transcripts_u_filter.fa.transdecoder_dir`\r\n- [ ] Avoid errors like `can't open file '../fasta_header_rename.py': [Errno 2] No such file or directory` by working out problems related to relative file paths or adding a directory containing the scripts to `PATH`."},"comment":{"url":"https://api.github.com/repos/upendrak/lincRNA_pipeline/issues/comments/84169325","html_url":"https://github.com/upendrak/lincRNA_pipeline/issues/2#issuecomment-84169325","issue_url":"https://api.github.com/repos/upendrak/lincRNA_pipeline/issues/2","id":84169325,"user":{"login":"jkhta13","id":8594183,"avatar_url":"https://avatars.githubusercontent.com/u/8594183?v=3","gravatar_id":"","url":"https://api.github.com/users/jkhta13","html_url":"https://github.com/jkhta13","followers_url":"https://api.github.com/users/jkhta13/followers","following_url":"https://api.github.com/users/jkhta13/following{/other_user}","gists_url":"https://api.github.com/users/jkhta13/gists{/gist_id}","starred_url":"https://api.github.com/users/jkhta13/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jkhta13/subscriptions","organizations_url":"https://api.github.com/users/jkhta13/orgs","repos_url":"https://api.github.com/users/jkhta13/repos","events_url":"https://api.github.com/users/jkhta13/events{/privacy}","received_events_url":"https://api.github.com/users/jkhta13/received_events","type":"User","site_admin":false},"created_at":"2015-03-20T22:23:17Z","updated_at":"2015-03-20T22:23:17Z","body":"No I meant a million bucks.\n\n\nOn Fri, Mar 20, 2015 at 3:22 PM, Upendra Kumar Devisetty <\nnotifications@github.com> wrote:\n\n> @jkhta13 <https://github.com/jkhta13> how about i offer you authorship?\n>\n> —\n> Reply to this email directly or view it on GitHub\n> <https://github.com/upendrak/lincRNA_pipeline/issues/2#issuecomment-84169227>\n> .\n>\n"}}