{"action":"created","issue":{"url":"https://api.github.com/repos/loeblab/Duplex-Sequencing/issues/18","labels_url":"https://api.github.com/repos/loeblab/Duplex-Sequencing/issues/18/labels{/name}","comments_url":"https://api.github.com/repos/loeblab/Duplex-Sequencing/issues/18/comments","events_url":"https://api.github.com/repos/loeblab/Duplex-Sequencing/issues/18/events","html_url":"https://github.com/loeblab/Duplex-Sequencing/issues/18","id":118489111,"number":18,"title":"Error with PE_BASH_MAKER.py","user":{"login":"KonstantinosC","id":15989335,"avatar_url":"https://avatars.githubusercontent.com/u/15989335?v=3","gravatar_id":"","url":"https://api.github.com/users/KonstantinosC","html_url":"https://github.com/KonstantinosC","followers_url":"https://api.github.com/users/KonstantinosC/followers","following_url":"https://api.github.com/users/KonstantinosC/following{/other_user}","gists_url":"https://api.github.com/users/KonstantinosC/gists{/gist_id}","starred_url":"https://api.github.com/users/KonstantinosC/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/KonstantinosC/subscriptions","organizations_url":"https://api.github.com/users/KonstantinosC/orgs","repos_url":"https://api.github.com/users/KonstantinosC/repos","events_url":"https://api.github.com/users/KonstantinosC/events{/privacy}","received_events_url":"https://api.github.com/users/KonstantinosC/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":8,"created_at":"2015-11-23T22:36:24Z","updated_at":"2015-12-03T03:47:49Z","closed_at":null,"body":"I was getting this error when running the PE_BASH_MAKER.py\r\n\r\nTraceback (most recent call last):\r\n  File \"PE_BASH_MAKER.py\", line 183, in <module>\r\n    main()\r\n  File \"PE_BASH_MAKER.py\", line 131, in main\r\n    inBash = open(spath + \"/bash_template.sh\", \"r\")\r\nIOError: [Errno 20] Not a directory: 'PE_BASH_MAKER.py/bash_template.sh'\r\n\r\nI changed the line 131 by erasing the \"spath +\" and it run fine. Let me know if by doing that I messed anything up.\r\n\r\nThank you "},"comment":{"url":"https://api.github.com/repos/loeblab/Duplex-Sequencing/issues/comments/161507281","html_url":"https://github.com/loeblab/Duplex-Sequencing/issues/18#issuecomment-161507281","issue_url":"https://api.github.com/repos/loeblab/Duplex-Sequencing/issues/18","id":161507281,"user":{"login":"loeblab","id":2035536,"avatar_url":"https://avatars.githubusercontent.com/u/2035536?v=3","gravatar_id":"","url":"https://api.github.com/users/loeblab","html_url":"https://github.com/loeblab","followers_url":"https://api.github.com/users/loeblab/followers","following_url":"https://api.github.com/users/loeblab/following{/other_user}","gists_url":"https://api.github.com/users/loeblab/gists{/gist_id}","starred_url":"https://api.github.com/users/loeblab/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/loeblab/subscriptions","organizations_url":"https://api.github.com/users/loeblab/orgs","repos_url":"https://api.github.com/users/loeblab/repos","events_url":"https://api.github.com/users/loeblab/events{/privacy}","received_events_url":"https://api.github.com/users/loeblab/received_events","type":"User","site_admin":false},"created_at":"2015-12-03T03:47:49Z","updated_at":"2015-12-03T03:47:49Z","body":"Well, either you don't have uniform read lengths like you think you do, \nor you're telling the consensus maker the wrong read length using the \n--readlength option.\n\nScott\n\nOn 12/2/15 9:03 AM, KonstantinosC wrote:\n> Hi guys,\n>\n> I trimmed my reads down to 70 and also filtered anything else that \n> could be\n> shorter than 70 so I have all my reads 100% the same length (I visually\n> inspected 2000 lines). I used FastX to trim down to 70 and then flexbar\n> trimmer to filter out anything bellow 70bp (paired end mode)\n> But, I'm getting a similar error...\n>\n> What could be the issue this time?\n>\n> Thank you in advance. Bellow is the error and I attached the log file.\n>\n> [bwa_sai2sam_pe_core] 9959777 sequences have been processed.\n> [main] Version: 0.7.5a-r405\n> [main] CMD: bwa sampe -s /media/kostas/OS/indexes/human_g1k_v37.fasta\n> 001.seq1.aln 001.seq2.aln 001.seq1.smi.fq 001.seq2.smi.fq\n> [main] Real time: 918.264 sec; CPU: 859.537 sec\n> Reads processed:0\n> Reads processed:1000000\n> Reads processed:2000000\n> Reads processed:3000000\n> Reads processed:4000000\n> Reads processed:5000000\n> Reads processed:6000000\n> Reads processed:7000000\n> Reads processed:8000000\n> Reads processed:9000000\n> Traceback (most recent call last):\n> File \"ConsensusMaker.py\", line 430, in <module>\n> main()\n> File \"ConsensusMaker.py\", line 349, in main\n> a.qual = qualScore\n> File \"csamtools.pyx\", line 2438, in\n> pysam.csamtools.AlignedRead.qual.__set__ (pysam/csamtools.c:23669)\n> ValueError: quality and sequence mismatch: 53 != 57\n>\n> On Tue, Nov 24, 2015 at 5:16 PM, Konstantinos Charizanis <\n> charizanisk@gmail.com> wrote:\n>\n> > Thank you. I'll trim to 70bp and go from there.\n> >\n> > On Tue, Nov 24, 2015 at 5:05 PM, S. Kennedy <notifications@github.com>\n> > wrote:\n> >\n> >> Yes, we enforce a defined read size. The reason is because if the two\n> >> reads differ in length, then you can't make a double-stranded \n> consensus in\n> >> the noncomplementary regions. This would likely exhibit some sort of\n> >> undefined behavior and/or throw an exception. It's easier to just \n> trim to\n> >> the smallest read size to make everything uniform in length.\n> >>\n> >> Scott\n> >> --\n> >> Scott R. Kennedy, Ph.D.\n> >> HSB K-058, Box 357705\n> >> Dept. of Pathology\n> >> University of Washington-Seattle\n> >> Seattle, WA 98195-7705\n> >>\n> >> Phone: (206)543-0557\n> >>\n> >>\n> >> On Tue, 24 Nov 2015, KonstantinosC wrote:\n> >>\n> >> > Thank you for all the input, I have run most of the scripts by \n> removing\n> >> the\n> >> > \"unnecessary\" strings but I have one problem.\n> >> >\n> >> > This is also highlighted in the following thread\n> >> >\n> >> >\n> >> \n> https://github.com/loeblab/Duplex-Sequencing/pull/15#issuecomment-138168260\n> >> >\n> >> > I do 2x75 NextSeq runs and of course not all reads in my fastq files\n> >> have\n> >> > 75 bases read length. There is some variation. So at the\n> >> consencus_maker.py\n> >> > step I'm getting a similar error. Is there any fix around this?\n> >> > Should I trim down to 70bp and then keep only the reads with 70bp\n> >> length?\n> >> > Here is the error\n> >> >\n> >> > File \"csamtools.pyx\", line 2438, in\n> >> > pysam.csamtools.AlignedRead.qual.__set__ (pysam/csamtools.c:23669)\n> >> > ValueError: quality and sequence mismatch: 58 != 57\n> >> >\n> >> > and here is few lines of my R1.fastq\n> >> >\n> >> > @NS500501:93:HLFJFBGXX:2:13210:18911:18275 1:N:0:10\n> >> >\n> >> \n> TAACTTTCAGTAGCTCACCTACTCCACCAATGGGCAGACCTTCTCCCTGCAGTATGGCAGTGGCAGCCTCACCGG\n> >> > +\n> >> >\n> >> \n> AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEE\n> >> > @NS500501:93:HLFJFBGXX:2:13210:20147:18275 1:N:0:10\n> >> >\n> >> \n> CTACCCGTAGCTCAGAATGACCTTGAGCATAATTTAAGCTTCTCTTTGTGATTCAGTCATTTTTATGCATGTC\n> >> > +\n> >> >\n> >> \n> AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE\n> >> > @NS500501:93:HLFJFBGXX:2:13210:7654:18276 1:N:0:10\n> >> >\n> >> \n> TATAGGGTAGCTCACCTTAGTTGGTGTTCGATACCAGCAAAGCAGTGGTATCCACTGTTTCTTCTGATTGATGA\n> >> > +\n> >> >\n> >> \n> AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE\n> >> > @NS500501:93:HLFJFBGXX:2:13210:11140:18279 1:N:0:10\n> >> >\n> >> \n> ATTGCACAGTAGCTCAGTGGCCCTGTTGGGTCACTTCCCCTAAGGGCCACAGCCACTGCCTGGAGCTGGTGGACT\n> >> > +\n> >> >\n> >> \n> AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE/EEEEAEEE/EEEEEEEEEE<\n> >> >\n> >> >\n> >> > Thank you again for your help.\n> >> >\n> >> > Kostas\n> >> >\n> >> > On Tue, Nov 24, 2015 at 9:23 AM, bkohrn <notifications@github.com>\n> >> wrote:\n> >> >\n> >> > > If I recall correctly, spath is designed to point to the default\n> >> template\n> >> > > (which should be in the same directory as PE_BASH_MAKER.py, and \n> which\n> >> I\n> >> > > assumed when writing the script would be a different directory than\n> >> the one\n> >> > > you were running the script in). Spath is created by taking the \n> path\n> >> to\n> >> > > the script and removing the string \"/PE_BASH_MAKER.py\". The \n> error is\n> >> > > happening because the path you give doesn't include the pattern the\n> >> script\n> >> > > is looking for.\n> >> > >\n> >> > > Brendan\n> >> > >\n> >> > > On Tue, Nov 24, 2015 at 5:53 AM, KonstantinosC <\n> >> notifications@github.com>\n> >> > >\n> >> > > wrote:\n> >> > >\n> >> > > > python PE_BASH_MAKER.py --ref /media/kostas/OS/indexes/hg19.fa\n> >> --r1src\n> >> > > > /media/kostas/OS/NGS_Data/YB8R1.fastq --r2src\n> >> > > > /media/kostas/OS/NGS_Data/YB8R2.fastq --rlength 75 --blength 6\n> >> --slength\n> >> > > > 11 --runIdentifier 001\n> >> > > >\n> >> > > > Also I have another comment.\n> >> > > > When I run the ./001.script.sh 3>&1 1>&2 2>&3 | tee -a\n> >> 001.se.log.txt\"\n> >> > > it\n> >> > > > gave me a similar error\n> >> > > > python: can't open file 'PE_BASH_MAKER.py/tag_to_header.py': \n> [Errno\n> >> 20]\n> >> > > Not\n> >> > > > a directory\n> >> > > > and I had to do the same, go and erase the PE_BASH_MAKER.py/ in\n> >> front of\n> >> > > > the tag_to_header.py.\n> >> > > >\n> >> > > > I'm running ubuntu 14.04 but that should not have any impact \n> on the\n> >> > > script.\n> >> > > > Also, Even though I told the script barcode lenght (blength) \n> 6 and\n> >> stem\n> >> > > > length 11, it did the oposite. it grabbed the first 11 and append\n> >> them on\n> >> > > > the header per read and then erased 6 as stem hahah. easy fix for\n> >> me but\n> >> > > I\n> >> > > > just had to let you know just in case a)I'm doing something wrong\n> >> b)you\n> >> > > > accidentally swapped something in your script.\n> >> > > > I didn't have time to go dig :)\n> >> > > >\n> >> > > > Thanks for you super prompt response!\n> >> > > >\n> >> > > > Kostas\n> >> > > >\n> >> > > > On Mon, Nov 23, 2015 at 11:34 PM, S. Kennedy <\n> >> notifications@github.com>\n> >> > > > wrote:\n> >> > > >\n> >> > > > > What was the precise command you used to invoke \n> PE_BASH_MAKER.py?\n> >> > > > >\n> >> > > > > On 11/23/15 2:36 PM, KonstantinosC wrote:\n> >> > > > > >\n> >> > > > > > I was getting this error when running the PE_BASH_MAKER.py\n> >> > > > > >\n> >> > > > > > Traceback (most recent call last):\n> >> > > > > > File \"PE_BASH_MAKER.py\", line 183, in\n> >> > > > > > main()\n> >> > > > > > File \"PE_BASH_MAKER.py\", line 131, in main\n> >> > > > > > inBash = open(spath + \"/bash_template.sh\", \"r\")\n> >> > > > > > IOError: [Errno 20] Not a directory:\n> >> > > > 'PE_BASH_MAKER.py/bash_template.sh'\n> >> > > > > >\n> >> > > > > > I changed the line 131 by erasing the \"spath +\" and it run\n> >> fine. Let\n> >> > > > > > me know if by doing that I messed anything up.\n> >> > > > > >\n> >> > > > > > Thank you\n> >> > > > > >\n> >> > > > > > —\n> >> > > > > > Reply to this email directly or view it on GitHub\n> >> > > > > > <https://github.com/loeblab/Duplex-Sequencing/issues/18>.\n> >> > > > > >\n> >> > > > >\n> >> > > > > —\n> >> > > > > Reply to this email directly or view it on GitHub\n> >> > > > > <\n> >> > > >\n> >> > >\n> >> \n> https://github.com/loeblab/Duplex-Sequencing/issues/18#issuecomment-159147365\n> >> > > > >\n> >> > > > > .\n> >> > > >\n> >> > > > >\n> >> > > >\n> >> > > > —\n> >> > > > Reply to this email directly or view it on GitHub\n> >> > > > <\n> >> > >\n> >> \n> https://github.com/loeblab/Duplex-Sequencing/issues/18#issuecomment-159274232\n> >> > > >\n> >> > >\n> >> > > > .\n> >> > > >\n> >> > >\n> >> > > —\n> >> > > Reply to this email directly or view it on GitHub\n> >> > > <\n> >> \n> https://github.com/loeblab/Duplex-Sequencing/issues/18#issuecomment-159281510\n> >> >\n> >> > > .\n> >> > >\n> >> >\n> >> > —\n> >> > Reply to this email directly or view it on\n> >> GitHub.[AB8PUBIVP40jc4K2GCHUIEGwHtHPrVSKks5pJNEcgaJpZM4Gn70O.gif]\n> >>\n> >> >\n> >> >\n> >> >\n> >>\n> >> —\n> >> Reply to this email directly or view it on GitHub\n> >> \n> <https://github.com/loeblab/Duplex-Sequencing/issues/18#issuecomment-159419771>\n> >> .\n> >>\n> >\n> >\n>\n> 001.script.sh: command not found\n> 001.script.sh: command not found\n> python: can't open file 'PE_BASH_MAKER.py/tag_to_header.py': [Errno \n> 20] Not a directory\n> Total sequences processed: 1000000\n> Sequences with passing tags: 996341\n> Missing spacers: 0\n> Bad tags: 3659\n> Total sequences processed: 2000000\n> Sequences with passing tags: 1992918\n> Missing spacers: 0\n> Bad tags: 7082\n> Total sequences processed: 3000000\n> Sequences with passing tags: 2989978\n> Missing spacers: 0\n> Bad tags: 10022\n> Total sequences processed: 4000000\n> Sequences with passing tags: 3987639\n> Missing spacers: 0\n> Bad tags: 12361\n> Total sequences processed: 5000000\n> Sequences with passing tags: 4984749\n> Missing spacers: 0\n> Bad tags: 15251\n> Total sequences processed: 6000000\n> Sequences with passing tags: 5982278\n> Missing spacers: 0\n> Bad tags: 17722\n> Total sequences processed: 7000000\n> Sequences with passing tags: 6979679\n> Missing spacers: 0\n> Bad tags: 20321\n> Total sequences processed: 8000000\n> Sequences with passing tags: 7977354\n> Missing spacers: 0\n> Bad tags: 22646\n> Total sequences processed: 9000000\n> Sequences with passing tags: 8974670\n> Missing spacers: 0\n> Bad tags: 25330\n> Total sequences processed: 10000000\n> Sequences with passing tags: 9972443\n> Missing spacers: 0\n> Bad tags: 27557\n> Total sequences processed: 10000000\n> Sequences with passing tags: 9972443\n> Missing spacers: 0\n> Bad tags: 27557\n> [bwa_aln] 17bp reads: max_diff = 2\n> [bwa_aln] 38bp reads: max_diff = 3\n> [bwa_aln] 64bp reads: max_diff = 4\n> [bwa_aln] 93bp reads: max_diff = 5\n> [bwa_aln] 124bp reads: max_diff = 6\n> [bwa_aln] 157bp reads: max_diff = 7\n> [bwa_aln] 190bp reads: max_diff = 8\n> [bwa_aln] 225bp reads: max_diff = 9\n> [bwa_aln] fail to locate the index\n> Total sequences processed: 1000000\n> Sequences with passing tags: 996341\n> Missing spacers: 0\n> Bad tags: 3659\n> Total sequences processed: 2000000\n> Sequences with passing tags: 1992918\n> Missing spacers: 0\n> Bad tags: 7082\n> Total sequences processed: 3000000\n> Sequences with passing tags: 2989978\n> Missing spacers: 0\n> Bad tags: 10022\n> Total sequences processed: 4000000\n> Sequences with passing tags: 3987639\n> Missing spacers: 0\n> Bad tags: 12361\n> Total sequences processed: 5000000\n> Sequences with passing tags: 4984749\n> Missing spacers: 0\n> Bad tags: 15251\n> Total sequences processed: 6000000\n> Sequences with passing tags: 5982278\n> Missing spacers: 0\n> Bad tags: 17722\n> Total sequences processed: 7000000\n> Sequences with passing tags: 6979679\n> Missing spacers: 0\n> Bad tags: 20321\n> Total sequences processed: 8000000\n> Sequences with passing tags: 7977354\n> Missing spacers: 0\n> Bad tags: 22646\n> Total sequences processed: 9000000\n> Sequences with passing tags: 8974670\n> Missing spacers: 0\n> Bad tags: 25330\n> Total sequences processed: 10000000\n> Sequences with passing tags: 9972443\n> Missing spacers: 0\n> Bad tags: 27557\n> Total sequences processed: 10000000\n> Sequences with passing tags: 9972443\n> Missing spacers: 0\n> Bad tags: 27557\n> [bwa_aln] 17bp reads: max_diff = 2\n> [bwa_aln] 38bp reads: max_diff = 3\n> [bwa_aln] 64bp reads: max_diff = 4\n> [bwa_aln] 93bp reads: max_diff = 5\n> [bwa_aln] 124bp reads: max_diff = 6\n> [bwa_aln] 157bp reads: max_diff = 7\n> [bwa_aln] 190bp reads: max_diff = 8\n> [bwa_aln] 225bp reads: max_diff = 9\n> [bwa_aln] fail to locate the index\n> Total sequences processed: 1000000\n> Sequences with passing tags: 996341\n> Missing spacers: 0\n> Bad tags: 3659\n> Total sequences processed: 2000000\n> Sequences with passing tags: 1992918\n> Missing spacers: 0\n> Bad tags: 7082\n> Total sequences processed: 3000000\n> Sequences with passing tags: 2989978\n> Missing spacers: 0\n> Bad tags: 10022\n> Total sequences processed: 4000000\n> Sequences with passing tags: 3987639\n> Missing spacers: 0\n> Bad tags: 12361\n> Total sequences processed: 5000000\n> Sequences with passing tags: 4984749\n> Missing spacers: 0\n> Bad tags: 15251\n> Total sequences processed: 6000000\n> Sequences with passing tags: 5982278\n> Missing spacers: 0\n> Bad tags: 17722\n> Total sequences processed: 7000000\n> Sequences with passing tags: 6979679\n> Missing spacers: 0\n> Bad tags: 20321\n> Total sequences processed: 8000000\n> Sequences with passing tags: 7977354\n> Missing spacers: 0\n> Bad tags: 22646\n> Total sequences processed: 9000000\n> Sequences with passing tags: 8974670\n> Missing spacers: 0\n> Bad tags: 25330\n> Total sequences processed: 10000000\n> Sequences with passing tags: 9972443\n> Missing spacers: 0\n> Bad tags: 27557\n> Total sequences processed: 10000000\n> Sequences with passing tags: 9972443\n> Missing spacers: 0\n> Bad tags: 27557\n> [bwa_aln] 17bp reads: max_diff = 2\n> [bwa_aln] 38bp reads: max_diff = 3\n> [bwa_aln] 64bp reads: max_diff = 4\n> [bwa_aln] 93bp reads: max_diff = 5\n> [bwa_aln] 124bp reads: max_diff = 6\n> [bwa_aln] 157bp reads: max_diff = 7\n> [bwa_aln] 190bp reads: max_diff = 8\n> [bwa_aln] 225bp reads: max_diff = 9\n> [bwa_aln_core] calculate SA coordinate... 32.11 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 262144 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 33.00 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 524288 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 33.88 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 786432 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 32.55 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 1048576 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 32.38 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 1310720 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 33.09 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 1572864 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 33.18 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 1835008 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 34.01 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 2097152 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 32.57 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 2359296 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 34.42 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 2621440 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 33.29 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 2883584 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 33.41 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 3145728 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 31.97 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 3407872 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 32.32 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 3670016 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 32.33 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 3932160 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 32.06 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 4194304 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 33.86 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 4456448 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 32.89 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 4718592 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 32.91 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 4980736 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 33.56 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 5242880 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 33.17 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 5505024 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 32.81 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 5767168 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 31.87 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 6029312 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 32.65 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 6291456 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 32.40 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 6553600 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 33.19 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 6815744 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 32.98 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 7077888 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 32.99 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 7340032 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 32.41 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 7602176 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 33.65 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 7864320 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 33.71 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 8126464 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... Total sequences processed: \n> 1000000\n> Sequences with passing tags: 996343\n> Missing spacers: 0\n> Bad tags: 3657\n> Total sequences processed: 2000000\n> Sequences with passing tags: 1992920\n> Missing spacers: 0\n> Bad tags: 7080\n> Total sequences processed: 3000000\n> Sequences with passing tags: 2989982\n> Missing spacers: 0\n> Bad tags: 10018\n> Total sequences processed: 4000000\n> Sequences with passing tags: 3987645\n> Missing spacers: 0\n> Bad tags: 12355\n> Total sequences processed: 5000000\n> Sequences with passing tags: 4984755\n> Missing spacers: 0\n> Bad tags: 15245\n> Total sequences processed: 6000000\n> Sequences with passing tags: 5982287\n> Missing spacers: 0\n> Bad tags: 17713\n> Total sequences processed: 7000000\n> Sequences with passing tags: 6979688\n> Missing spacers: 0\n> Bad tags: 20312\n> Total sequences processed: 8000000\n> Sequences with passing tags: 7977363\n> Missing spacers: 0\n> Bad tags: 22637\n> Total sequences processed: 9000000\n> Sequences with passing tags: 8974679\n> Missing spacers: 0\n> Bad tags: 25321\n> Total sequences processed: 10000000\n> Sequences with passing tags: 9972452\n> Missing spacers: 0\n> Bad tags: 27548\n> Total sequences processed: 10000000\n> Sequences with passing tags: 9972452\n> Missing spacers: 0\n> Bad tags: 27548\n> [bwa_aln] 17bp reads: max_diff = 2\n> [bwa_aln] 38bp reads: max_diff = 3\n> [bwa_aln] 64bp reads: max_diff = 4\n> [bwa_aln] 93bp reads: max_diff = 5\n> [bwa_aln] 124bp reads: max_diff = 6\n> [bwa_aln] 157bp reads: max_diff = 7\n> [bwa_aln] 190bp reads: max_diff = 8\n> [bwa_aln] 225bp reads: max_diff = 9\n> [bwa_aln_core] calculate SA coordinate... 32.57 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 262144 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 32.55 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 524288 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 33.33 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 786432 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 32.03 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 1048576 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 31.80 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 1310720 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 32.91 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 1572864 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 32.10 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 1835008 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 32.82 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 2097152 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 32.49 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 2359296 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 33.02 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 2621440 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 32.40 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 2883584 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 32.93 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 3145728 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 32.36 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 3407872 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 31.68 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 3670016 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 31.70 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 3932160 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 31.52 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 4194304 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 32.48 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 4456448 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 31.97 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 4718592 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 32.40 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 4980736 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 32.79 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 5242880 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 31.87 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 5505024 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 31.96 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 5767168 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 31.28 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 6029312 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 31.77 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 6291456 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 31.89 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 6553600 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 32.20 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 6815744 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 31.45 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 7077888 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 32.43 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 7340032 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 32.06 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 7602176 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 32.83 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 7864320 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 33.88 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 8126464 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 33.43 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 8388608 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 33.72 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 8650752 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 32.49 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 8912896 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 33.07 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 9175040 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 32.95 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 9437184 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 32.86 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 9699328 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 31.99 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 9961472 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 1.39 sec\n> [bwa_aln_core] write to the disk... 0.00 sec\n> [bwa_aln_core] 9972452 sequences have been processed.\n> [main] Version: 0.7.5a-r405\n> [main] CMD: bwa aln /media/kostas/OS/indexes/human_g1k_v37.fasta \n> 001.seq1.smi.fq\n> [main] Real time: 1269.759 sec; CPU: 1245.217 sec\n> [bwa_aln] 17bp reads: max_diff = 2\n> [bwa_aln] 38bp reads: max_diff = 3\n> [bwa_aln] 64bp reads: max_diff = 4\n> [bwa_aln] 93bp reads: max_diff = 5\n> [bwa_aln] 124bp reads: max_diff = 6\n> [bwa_aln] 157bp reads: max_diff = 7\n> [bwa_aln] 190bp reads: max_diff = 8\n> [bwa_aln] 225bp reads: max_diff = 9\n> [bwa_aln_core] calculate SA coordinate... 29.82 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 262144 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 29.71 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 524288 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 29.24 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 786432 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 29.76 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 1048576 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 29.65 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 1310720 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 29.56 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 1572864 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 29.90 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 1835008 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 29.43 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 2097152 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 29.67 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 2359296 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 29.34 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 2621440 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 29.80 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 2883584 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 30.72 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 3145728 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 29.20 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 3407872 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 29.39 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 3670016 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 29.26 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 3932160 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 30.19 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 4194304 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 30.45 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 4456448 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 30.32 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 4718592 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 29.78 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 4980736 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 29.53 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 5242880 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 29.87 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 5505024 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 28.88 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 5767168 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 28.38 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 6029312 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 30.55 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 6291456 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 29.94 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 6553600 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 30.68 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 6815744 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 29.70 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 7077888 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 30.39 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 7340032 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 30.91 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 7602176 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 30.24 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 7864320 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 30.44 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 8126464 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 30.32 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 8388608 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 29.95 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 8650752 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 29.93 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 8912896 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 30.40 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 9175040 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 29.94 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 9437184 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 29.58 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 9699328 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 30.26 sec\n> [bwa_aln_core] write to the disk... 0.02 sec\n> [bwa_aln_core] 9961472 sequences have been processed.\n> [bwa_aln_core] calculate SA coordinate... 1.28 sec\n> [bwa_aln_core] write to the disk... 0.00 sec\n> [bwa_aln_core] 9972452 sequences have been processed.\n> [main] Version: 0.7.5a-r405\n> [main] CMD: bwa aln /media/kostas/OS/indexes/human_g1k_v37.fasta \n> 001.seq2.smi.fq\n> [main] Real time: 1161.202 sec; CPU: 1146.200 sec\n> [bwa_sai2sam_pe_core] convert to sequence coordinate...\n> [infer_isize] (25, 50, 75) percentile: (154, 165, 178)\n> [infer_isize] low and high boundaries: 106 and 226 for estimating avg \n> and std\n> [infer_isize] inferred external isize from 190166 pairs: 163.334 +/- \n> 18.662\n> [infer_isize] skewness: 0.014; kurtosis: 0.761; ap_prior: 7.30e-04\n> [infer_isize] inferred maximum insert size: 295 (7.05 sigma)\n> [bwa_sai2sam_pe_core] time elapses: 14.49 sec\n> [bwa_sai2sam_pe_core] changing coordinates of 8456 alignments.\n> [bwa_sai2sam_pe_core] align unmapped mate...\n> [bwa_sai2sam_pe_core] time elapses: 0.31 sec\n> [bwa_sai2sam_pe_core] refine gapped alignments... 0.30 sec\n> [bwa_sai2sam_pe_core] print alignments... 0.85 sec\n> [bwa_sai2sam_pe_core] 262144 sequences have been processed.\n> [bwa_sai2sam_pe_core] convert to sequence coordinate...\n> [infer_isize] (25, 50, 75) percentile: (154, 165, 178)\n> [infer_isize] low and high boundaries: 106 and 226 for estimating avg \n> and std\n> [infer_isize] inferred external isize from 190837 pairs: 163.389 +/- \n> 18.649\n> [infer_isize] skewness: 0.031; kurtosis: 0.754; ap_prior: 7.18e-04\n> [infer_isize] inferred maximum insert size: 295 (7.05 sigma)\n> [bwa_sai2sam_pe_core] time elapses: 15.42 sec\n> [bwa_sai2sam_pe_core] changing coordinates of 8561 alignments.\n> [bwa_sai2sam_pe_core] align unmapped mate...\n> [bwa_sai2sam_pe_core] time elapses: 0.38 sec\n> [bwa_sai2sam_pe_core] refine gapped alignments... 0.24 sec\n> [bwa_sai2sam_pe_core] print alignments... 0.86 sec\n> [bwa_sai2sam_pe_core] 524288 sequences have been processed.\n> [bwa_sai2sam_pe_core] convert to sequence coordinate...\n> [infer_isize] (25, 50, 75) percentile: (154, 165, 178)\n> [infer_isize] low and high boundaries: 106 and 226 for estimating avg \n> and std\n> [infer_isize] inferred external isize from 191166 pairs: 163.359 +/- \n> 18.643\n> [infer_isize] skewness: 0.009; kurtosis: 0.749; ap_prior: 7.12e-04\n> [infer_isize] inferred maximum insert size: 295 (7.05 sigma)\n> [bwa_sai2sam_pe_core] time elapses: 14.88 sec\n> [bwa_sai2sam_pe_core] changing coordinates of 8508 alignments.\n> [bwa_sai2sam_pe_core] align unmapped mate...\n> [bwa_sai2sam_pe_core] time elapses: 0.15 sec\n> [bwa_sai2sam_pe_core] refine gapped alignments... 0.23 sec\n> [bwa_sai2sam_pe_core] print alignments... 0.86 sec\n> [bwa_sai2sam_pe_core] 786432 sequences have been processed.\n> [bwa_sai2sam_pe_core] convert to sequence coordinate...\n> [infer_isize] (25, 50, 75) percentile: (154, 165, 178)\n> [infer_isize] low and high boundaries: 106 and 226 for estimating avg \n> and std\n> [infer_isize] inferred external isize from 190979 pairs: 163.354 +/- \n> 18.658\n> [infer_isize] skewness: -0.003; kurtosis: 0.745; ap_prior: 6.99e-04\n> [infer_isize] inferred maximum insert size: 295 (7.05 sigma)\n> [bwa_sai2sam_pe_core] time elapses: 15.49 sec\n> [bwa_sai2sam_pe_core] changing coordinates of 8315 alignments.\n> [bwa_sai2sam_pe_core] align unmapped mate...\n> [bwa_sai2sam_pe_core] time elapses: 0.15 sec\n> [bwa_sai2sam_pe_core] refine gapped alignments... 0.24 sec\n> [bwa_sai2sam_pe_core] print alignments... 0.86 sec\n> [bwa_sai2sam_pe_core] 1048576 sequences have been processed.\n> [bwa_sai2sam_pe_core] convert to sequence coordinate...\n> [infer_isize] (25, 50, 75) percentile: (154, 165, 178)\n> [infer_isize] low and high boundaries: 106 and 226 for estimating avg \n> and std\n> [infer_isize] inferred external isize from 191260 pairs: 163.464 +/- \n> 18.660\n> [infer_isize] skewness: 0.023; kurtosis: 0.763; ap_prior: 7.28e-04\n> [infer_isize] inferred maximum insert size: 295 (7.05 sigma)\n> [bwa_sai2sam_pe_core] time elapses: 13.85 sec\n> [bwa_sai2sam_pe_core] changing coordinates of 8448 alignments.\n> [bwa_sai2sam_pe_core] align unmapped mate...\n> [bwa_sai2sam_pe_core] time elapses: 0.16 sec\n> [bwa_sai2sam_pe_core] refine gapped alignments... 0.23 sec\n> [bwa_sai2sam_pe_core] print alignments... 0.86 sec\n> [bwa_sai2sam_pe_core] 1310720 sequences have been processed.\n> [bwa_sai2sam_pe_core] convert to sequence coordinate...\n> [infer_isize] (25, 50, 75) percentile: (154, 165, 178)\n> [infer_isize] low and high boundaries: 106 and 226 for estimating avg \n> and std\n> [infer_isize] inferred external isize from 191063 pairs: 163.339 +/- \n> 18.661\n> [infer_isize] skewness: 0.019; kurtosis: 0.758; ap_prior: 7.06e-04\n> [infer_isize] inferred maximum insert size: 295 (7.05 sigma)\n> [bwa_sai2sam_pe_core] time elapses: 14.59 sec\n> [bwa_sai2sam_pe_core] changing coordinates of 8366 alignments.\n> [bwa_sai2sam_pe_core] align unmapped mate...\n> [bwa_sai2sam_pe_core] time elapses: 0.15 sec\n> [bwa_sai2sam_pe_core] refine gapped alignments... 0.23 sec\n> [bwa_sai2sam_pe_core] print alignments... 0.92 sec\n> [bwa_sai2sam_pe_core] 1572864 sequences have been processed.\n> [bwa_sai2sam_pe_core] convert to sequence coordinate...\n> [infer_isize] (25, 50, 75) percentile: (154, 165, 178)\n> [infer_isize] low and high boundaries: 106 and 226 for estimating avg \n> and std\n> [infer_isize] inferred external isize from 190686 pairs: 163.365 +/- \n> 18.634\n> [infer_isize] skewness: 0.017; kurtosis: 0.757; ap_prior: 7.25e-04\n> [infer_isize] inferred maximum insert size: 295 (7.05 sigma)\n> [bwa_sai2sam_pe_core] time elapses: 14.78 sec\n> [bwa_sai2sam_pe_core] changing coordinates of 8508 alignments.\n> [bwa_sai2sam_pe_core] align unmapped mate...\n> [bwa_sai2sam_pe_core] time elapses: 0.15 sec\n> [bwa_sai2sam_pe_core] refine gapped alignments... 0.23 sec\n> [bwa_sai2sam_pe_core] print alignments... 0.86 sec\n> [bwa_sai2sam_pe_core] 1835008 sequences have been processed.\n> [bwa_sai2sam_pe_core] convert to sequence coordinate...\n> [infer_isize] (25, 50, 75) percentile: (154, 165, 178)\n> [infer_isize] low and high boundaries: 106 and 226 for estimating avg \n> and std\n> [infer_isize] inferred external isize from 190813 pairs: 163.333 +/- \n> 18.658\n> [infer_isize] skewness: 0.027; kurtosis: 0.767; ap_prior: 7.32e-04\n> [infer_isize] inferred maximum insert size: 295 (7.05 sigma)\n> [bwa_sai2sam_pe_core] time elapses: 13.85 sec\n> [bwa_sai2sam_pe_core] changing coordinates of 8372 alignments.\n> [bwa_sai2sam_pe_core] align unmapped mate...\n> [bwa_sai2sam_pe_core] time elapses: 0.15 sec\n> [bwa_sai2sam_pe_core] refine gapped alignments... 0.23 sec\n> [bwa_sai2sam_pe_core] print alignments... 0.86 sec\n> [bwa_sai2sam_pe_core] 2097152 sequences have been processed.\n> [bwa_sai2sam_pe_core] convert to sequence coordinate...\n> [infer_isize] (25, 50, 75) percentile: (153, 165, 178)\n> [infer_isize] low and high boundaries: 103 and 228 for estimating avg \n> and std\n> [infer_isize] inferred external isize from 192060 pairs: 163.264 +/- \n> 18.963\n> [infer_isize] skewness: -0.012; kurtosis: 0.854; ap_prior: 6.78e-04\n> [infer_isize] inferred maximum insert size: 297 (7.05 sigma)\n> [bwa_sai2sam_pe_core] time elapses: 13.91 sec\n> [bwa_sai2sam_pe_core] changing coordinates of 8562 alignments.\n> [bwa_sai2sam_pe_core] align unmapped mate...\n> [bwa_sai2sam_pe_core] time elapses: 0.15 sec\n> [bwa_sai2sam_pe_core] refine gapped alignments... 0.23 sec\n> [bwa_sai2sam_pe_core] print alignments... 1.00 sec\n> [bwa_sai2sam_pe_core] 2359296 sequences have been processed.\n> [bwa_sai2sam_pe_core] convert to sequence coordinate...\n> [infer_isize] (25, 50, 75) percentile: (154, 165, 178)\n> [infer_isize] low and high boundaries: 106 and 226 for estimating avg \n> and std\n> [infer_isize] inferred external isize from 190788 pairs: 163.303 +/- \n> 18.569\n> [infer_isize] skewness: 0.015; kurtosis: 0.770; ap_prior: 7.32e-04\n> [infer_isize] inferred maximum insert size: 294 (7.05 sigma)\n> [bwa_sai2sam_pe_core] time elapses: 15.10 sec\n> [bwa_sai2sam_pe_core] changing coordinates of 8595 alignments.\n> [bwa_sai2sam_pe_core] align unmapped mate...\n> [bwa_sai2sam_pe_core] time elapses: 0.15 sec\n> [bwa_sai2sam_pe_core] refine gapped alignments... 0.23 sec\n> [bwa_sai2sam_pe_core] print alignments... 0.87 sec\n> [bwa_sai2sam_pe_core] 2621440 sequences have been processed.\n> [bwa_sai2sam_pe_core] convert to sequence coordinate...\n> [infer_isize] (25, 50, 75) percentile: (154, 165, 178)\n> [infer_isize] low and high boundaries: 106 and 226 for estimating avg \n> and std\n> [infer_isize] inferred external isize from 190737 pairs: 163.418 +/- \n> 18.640\n> [infer_isize] skewness: 0.017; kurtosis: 0.755; ap_prior: 7.32e-04\n> [infer_isize] inferred maximum insert size: 295 (7.05 sigma)\n> [bwa_sai2sam_pe_core] time elapses: 14.16 sec\n> [bwa_sai2sam_pe_core] changing coordinates of 8522 alignments.\n> [bwa_sai2sam_pe_core] align unmapped mate...\n> [bwa_sai2sam_pe_core] time elapses: 0.15 sec\n> [bwa_sai2sam_pe_core] refine gapped alignments... 0.23 sec\n> [bwa_sai2sam_pe_core] print alignments... 0.87 sec\n> [bwa_sai2sam_pe_core] 2883584 sequences have been processed.\n> [bwa_sai2sam_pe_core] convert to sequence coordinate...\n> [infer_isize] (25, 50, 75) percentile: (154, 165, 178)\n> [infer_isize] low and high boundaries: 106 and 226 for estimating avg \n> and std\n> [infer_isize] inferred external isize from 190765 pairs: 163.391 +/- \n> 18.597\n> [infer_isize] skewness: 0.025; kurtosis: 0.752; ap_prior: 7.39e-04\n> [infer_isize] inferred maximum insert size: 294 (7.05 sigma)\n> [bwa_sai2sam_pe_core] time elapses: 14.16 sec\n> [bwa_sai2sam_pe_core] changing coordinates of 8525 alignments.\n> [bwa_sai2sam_pe_core] align unmapped mate...\n> [bwa_sai2sam_pe_core] time elapses: 0.15 sec\n> [bwa_sai2sam_pe_core] refine gapped alignments... 0.24 sec\n> [bwa_sai2sam_pe_core] print alignments... 0.87 sec\n> [bwa_sai2sam_pe_core] 3145728 sequences have been processed.\n> [bwa_sai2sam_pe_core] convert to sequence coordinate...\n> [infer_isize] (25, 50, 75) percentile: (154, 165, 178)\n> [infer_isize] low and high boundaries: 106 and 226 for estimating avg \n> and std\n> [infer_isize] inferred external isize from 190644 pairs: 163.494 +/- \n> 18.641\n> [infer_isize] skewness: 0.033; kurtosis: 0.765; ap_prior: 7.30e-04\n> [infer_isize] inferred maximum insert size: 295 (7.05 sigma)\n> [bwa_sai2sam_pe_core] time elapses: 14.17 sec\n> [bwa_sai2sam_pe_core] changing coordinates of 8441 alignments.\n> [bwa_sai2sam_pe_core] align unmapped mate...\n> [bwa_sai2sam_pe_core] time elapses: 0.15 sec\n> [bwa_sai2sam_pe_core] refine gapped alignments... 0.23 sec\n> [bwa_sai2sam_pe_core] print alignments... 0.87 sec\n> [bwa_sai2sam_pe_core] 3407872 sequences have been processed.\n> [bwa_sai2sam_pe_core] convert to sequence coordinate...\n> [infer_isize] (25, 50, 75) percentile: (154, 165, 178)\n> [infer_isize] low and high boundaries: 106 and 226 for estimating avg \n> and std\n> [infer_isize] inferred external isize from 190407 pairs: 163.436 +/- \n> 18.643\n> [infer_isize] skewness: 0.014; kurtosis: 0.752; ap_prior: 7.47e-04\n> [infer_isize] inferred maximum insert size: 295 (7.05 sigma)\n> [bwa_sai2sam_pe_core] time elapses: 14.01 sec\n> [bwa_sai2sam_pe_core] changing coordinates of 8377 alignments.\n> [bwa_sai2sam_pe_core] align unmapped mate...\n> [bwa_sai2sam_pe_core] time elapses: 0.16 sec\n> [bwa_sai2sam_pe_core] refine gapped alignments... 0.24 sec\n> [bwa_sai2sam_pe_core] print alignments... 0.87 sec\n> [bwa_sai2sam_pe_core] 3670016 sequences have been processed.\n> [bwa_sai2sam_pe_core] convert to sequence coordinate...\n> [infer_isize] (25, 50, 75) percentile: (154, 165, 178)\n> [infer_isize] low and high boundaries: 106 and 226 for estimating avg \n> and std\n> [infer_isize] inferred external isize from 191453 pairs: 163.336 +/- \n> 18.700\n> [infer_isize] skewness: 0.025; kurtosis: 0.748; ap_prior: 7.20e-04\n> [infer_isize] inferred maximum insert size: 295 (7.05 sigma)\n> [bwa_sai2sam_pe_core] time elapses: 13.71 sec\n> [bwa_sai2sam_pe_core] changing coordinates of 8226 alignments.\n> [bwa_sai2sam_pe_core] align unmapped mate...\n> [bwa_sai2sam_pe_core] time elapses: 0.16 sec\n> [bwa_sai2sam_pe_core] refine gapped alignments... 0.23 sec\n> [bwa_sai2sam_pe_core] print alignments... 0.87 sec\n> [bwa_sai2sam_pe_core] 3932160 sequences have been processed.\n> [bwa_sai2sam_pe_core] convert to sequence coordinate...\n> [infer_isize] (25, 50, 75) percentile: (154, 165, 178)\n> [infer_isize] low and high boundaries: 106 and 226 for estimating avg \n> and std\n> [infer_isize] inferred external isize from 190751 pairs: 163.415 +/- \n> 18.625\n> [infer_isize] skewness: 0.007; kurtosis: 0.756; ap_prior: 7.58e-04\n> [infer_isize] inferred maximum insert size: 295 (7.05 sigma)\n> [bwa_sai2sam_pe_core] time elapses: 13.60 sec\n> [bwa_sai2sam_pe_core] changing coordinates of 8528 alignments.\n> [bwa_sai2sam_pe_core] align unmapped mate...\n> [bwa_sai2sam_pe_core] time elapses: 0.16 sec\n> [bwa_sai2sam_pe_core] refine gapped alignments... 0.23 sec\n> [bwa_sai2sam_pe_core] print alignments... 0.86 sec\n> [bwa_sai2sam_pe_core] 4194304 sequences have been processed.\n> [bwa_sai2sam_pe_core] convert to sequence coordinate...\n> [infer_isize] (25, 50, 75) percentile: (154, 165, 178)\n> [infer_isize] low and high boundaries: 106 and 226 for estimating avg \n> and std\n> [infer_isize] inferred external isize from 191015 pairs: 163.377 +/- \n> 18.658\n> [infer_isize] skewness: 0.014; kurtosis: 0.730; ap_prior: 7.13e-04\n> [infer_isize] inferred maximum insert size: 295 (7.05 sigma)\n> [bwa_sai2sam_pe_core] time elapses: 13.98 sec\n> [bwa_sai2sam_pe_core] changing coordinates of 8590 alignments.\n> [bwa_sai2sam_pe_core] align unmapped mate...\n> [bwa_sai2sam_pe_core] time elapses: 0.15 sec\n> [bwa_sai2sam_pe_core] refine gapped alignments... 0.23 sec\n> [bwa_sai2sam_pe_core] print alignments... [vfprintf(stdout)] No space \n> left on device\n> [bwa_sai2sam_pe_core] convert to sequence coordinate...\n> [infer_isize] (25, 50, 75) percentile: (154, 165, 178)\n> [infer_isize] low and high boundaries: 106 and 226 for estimating avg \n> and std\n> [infer_isize] inferred external isize from 190166 pairs: 163.334 +/- \n> 18.662\n> [infer_isize] skewness: 0.014; kurtosis: 0.761; ap_prior: 7.30e-04\n> [infer_isize] inferred maximum insert size: 295 (7.05 sigma)\n> [bwa_sai2sam_pe_core] time elapses: 13.97 sec\n> [bwa_sai2sam_pe_core] changing coordinates of 8456 alignments.\n> [bwa_sai2sam_pe_core] align unmapped mate...\n> [bwa_sai2sam_pe_core] time elapses: 0.15 sec\n> [bwa_sai2sam_pe_core] refine gapped alignments... 0.23 sec\n> [bwa_sai2sam_pe_core] print alignments... 0.86 sec\n> [bwa_sai2sam_pe_core] 262144 sequences have been processed.\n> [bwa_sai2sam_pe_core] convert to sequence coordinate...\n> [infer_isize] (25, 50, 75) percentile: (154, 165, 178)\n> [infer_isize] low and high boundaries: 106 and 226 for estimating avg \n> and std\n> [infer_isize] inferred external isize from 190837 pairs: 163.389 +/- \n> 18.649\n> [infer_isize] skewness: 0.031; kurtosis: 0.754; ap_prior: 7.18e-04\n> [infer_isize] inferred maximum insert size: 295 (7.05 sigma)\n> [bwa_sai2sam_pe_core] time elapses: 14.31 sec\n> [bwa_sai2sam_pe_core] changing coordinates of 8561 alignments.\n> [bwa_sai2sam_pe_core] align unmapped mate...\n> [bwa_sai2sam_pe_core] time elapses: 0.17 sec\n> [bwa_sai2sam_pe_core] refine gapped alignments... 0.24 sec\n> [bwa_sai2sam_pe_core] print alignments... 0.88 sec\n> [bwa_sai2sam_pe_core] 524288 sequences have been processed.\n> [bwa_sai2sam_pe_core] convert to sequence coordinate...\n> [infer_isize] (25, 50, 75) percentile: (154, 165, 178)\n> [infer_isize] low and high boundaries: 106 and 226 for estimating avg \n> and std\n> [infer_isize] inferred external isize from 191166 pairs: 163.359 +/- \n> 18.643\n> [infer_isize] skewness: 0.009; kurtosis: 0.749; ap_prior: 7.12e-04\n> [infer_isize] inferred maximum insert size: 295 (7.05 sigma)\n> [bwa_sai2sam_pe_core] time elapses: 14.52 sec\n> [bwa_sai2sam_pe_core] changing coordinates of 8508 alignments.\n> [bwa_sai2sam_pe_core] align unmapped mate...\n> [bwa_sai2sam_pe_core] time elapses: 0.15 sec\n> [bwa_sai2sam_pe_core] refine gapped alignments... 0.23 sec\n> [bwa_sai2sam_pe_core] print alignments... 0.86 sec\n> [bwa_sai2sam_pe_core] 786432 sequences have been processed.\n> [bwa_sai2sam_pe_core] convert to sequence coordinate...\n> [infer_isize] (25, 50, 75) percentile: (154, 165, 178)\n> [infer_isize] low and high boundaries: 106 and 226 for estimating avg \n> and std\n> [infer_isize] inferred external isize from 190979 pairs: 163.354 +/- \n> 18.658\n> [infer_isize] skewness: -0.003; kurtosis: 0.745; ap_prior: 6.99e-04\n> [infer_isize] inferred maximum insert size: 295 (7.05 sigma)\n> [bwa_sai2sam_pe_core] time elapses: 14.57 sec\n> [bwa_sai2sam_pe_core] changing coordinates of 8315 alignments.\n> [bwa_sai2sam_pe_core] align unmapped mate...\n> [bwa_sai2sam_pe_core] time elapses: 0.15 sec\n> [bwa_sai2sam_pe_core] refine gapped alignments... 0.24 sec\n> [bwa_sai2sam_pe_core] print alignments... 0.87 sec\n> [bwa_sai2sam_pe_core] 1048576 sequences have been processed.\n> [bwa_sai2sam_pe_core] convert to sequence coordinate...\n> [infer_isize] (25, 50, 75) percentile: (154, 165, 178)\n> [infer_isize] low and high boundaries: 106 and 226 for estimating avg \n> and std\n> [infer_isize] inferred external isize from 191260 pairs: 163.464 +/- \n> 18.660\n> [infer_isize] skewness: 0.023; kurtosis: 0.763; ap_prior: 7.28e-04\n> [infer_isize] inferred maximum insert size: 295 (7.05 sigma)\n> [bwa_sai2sam_pe_core] time elapses: 14.20 sec\n> [bwa_sai2sam_pe_core] changing coordinates of 8448 alignments.\n> [bwa_sai2sam_pe_core] align unmapped mate...\n> [bwa_sai2sam_pe_core] time elapses: 0.16 sec\n> [bwa_sai2sam_pe_core] refine gapped alignments... 0.23 sec\n> [bwa_sai2sam_pe_core] print alignments... 0.86 sec\n> [bwa_sai2sam_pe_core] 1310720 sequences have been processed.\n> [bwa_sai2sam_pe_core] convert to sequence coordinate...\n> [infer_isize] (25, 50, 75) percentile: (154, 165, 178)\n> [infer_isize] low and high boundaries: 106 and 226 for estimating avg \n> and std\n> [infer_isize] inferred external isize from 191063 pairs: 163.339 +/- \n> 18.661\n> [infer_isize] skewness: 0.019; kurtosis: 0.758; ap_prior: 7.06e-04\n> [infer_isize] inferred maximum insert size: 295 (7.05 sigma)\n> [bwa_sai2sam_pe_core] time elapses: 14.07 sec\n> [bwa_sai2sam_pe_core] changing coordinates of 8366 alignments.\n> [bwa_sai2sam_pe_core] align unmapped mate...\n> [bwa_sai2sam_pe_core] time elapses: 0.15 sec\n> [bwa_sai2sam_pe_core] refine gapped alignments... 0.23 sec\n> [bwa_sai2sam_pe_core] print alignments... 0.86 sec\n> [bwa_sai2sam_pe_core] 1572864 sequences have been processed.\n> [bwa_sai2sam_pe_core] convert to sequence coordinate...\n> [infer_isize] (25, 50, 75) percentile: (154, 165, 178)\n> [infer_isize] low and high boundaries: 106 and 226 for estimating avg \n> and std\n> [infer_isize] inferred external isize from 190686 pairs: 163.365 +/- \n> 18.634\n> [infer_isize] skewness: 0.017; kurtosis: 0.757; ap_prior: 7.25e-04\n> [infer_isize] inferred maximum insert size: 295 (7.05 sigma)\n> [bwa_sai2sam_pe_core] time elapses: 14.66 sec\n> [bwa_sai2sam_pe_core] changing coordinates of 8508 alignments.\n> [bwa_sai2sam_pe_core] align unmapped mate...\n> [bwa_sai2sam_pe_core] time elapses: 0.15 sec\n> [bwa_sai2sam_pe_core] refine gapped alignments... 0.23 sec\n> [bwa_sai2sam_pe_core] print alignments... 0.87 sec\n> [bwa_sai2sam_pe_core] 1835008 sequences have been processed.\n> [bwa_sai2sam_pe_core] convert to sequence coordinate...\n> [infer_isize] (25, 50, 75) percentile: (154, 165, 178)\n> [infer_isize] low and high boundaries: 106 and 226 for estimating avg \n> and std\n> [infer_isize] inferred external isize from 190813 pairs: 163.333 +/- \n> 18.658\n> [infer_isize] skewness: 0.027; kurtosis: 0.767; ap_prior: 7.32e-04\n> [infer_isize] inferred maximum insert size: 295 (7.05 sigma)\n> [bwa_sai2sam_pe_core] time elapses: 14.13 sec\n> [bwa_sai2sam_pe_core] changing coordinates of 8372 alignments.\n> [bwa_sai2sam_pe_core] align unmapped mate...\n> [bwa_sai2sam_pe_core] time elapses: 0.15 sec\n> [bwa_sai2sam_pe_core] refine gapped alignments... 0.23 sec\n> [bwa_sai2sam_pe_core] print alignments... 0.87 sec\n> [bwa_sai2sam_pe_core] 2097152 sequences have been processed.\n> [bwa_sai2sam_pe_core] convert to sequence coordinate...\n> [infer_isize] (25, 50, 75) percentile: (153, 165, 178)\n> [infer_isize] low and high boundaries: 103 and 228 for estimating avg \n> and std\n> [infer_isize] inferred external isize from 192060 pairs: 163.264 +/- \n> 18.963\n> [infer_isize] skewness: -0.012; kurtosis: 0.854; ap_prior: 6.78e-04\n> [infer_isize] inferred maximum insert size: 297 (7.05 sigma)\n> [bwa_sai2sam_pe_core] time elapses: 13.34 sec\n> [bwa_sai2sam_pe_core] changing coordinates of 8562 alignments.\n> [bwa_sai2sam_pe_core] align unmapped mate...\n> [bwa_sai2sam_pe_core] time elapses: 0.15 sec\n> [bwa_sai2sam_pe_core] refine gapped alignments... 0.23 sec\n> [bwa_sai2sam_pe_core] print alignments... 0.87 sec\n> [bwa_sai2sam_pe_core] 2359296 sequences have been processed.\n> [bwa_sai2sam_pe_core] convert to sequence coordinate...\n> [infer_isize] (25, 50, 75) percentile: (154, 165, 178)\n> [infer_isize] low and high boundaries: 106 and 226 for estimating avg \n> and std\n> [infer_isize] inferred external isize from 190788 pairs: 163.303 +/- \n> 18.569\n> [infer_isize] skewness: 0.015; kurtosis: 0.770; ap_prior: 7.32e-04\n> [infer_isize] inferred maximum insert size: 294 (7.05 sigma)\n> [bwa_sai2sam_pe_core] time elapses: 13.60 sec\n> [bwa_sai2sam_pe_core] changing coordinates of 8595 alignments.\n> [bwa_sai2sam_pe_core] align unmapped mate...\n> [bwa_sai2sam_pe_core] time elapses: 0.15 sec\n> [bwa_sai2sam_pe_core] refine gapped alignments... 0.23 sec\n> [bwa_sai2sam_pe_core] print alignments... 0.87 sec\n> [bwa_sai2sam_pe_core] 2621440 sequences have been processed.\n> [bwa_sai2sam_pe_core] convert to sequence coordinate...\n> [infer_isize] (25, 50, 75) percentile: (154, 165, 178)\n> [infer_isize] low and high boundaries: 106 and 226 for estimating avg \n> and std\n> [infer_isize] inferred external isize from 190737 pairs: 163.418 +/- \n> 18.640\n> [infer_isize] skewness: 0.017; kurtosis: 0.755; ap_prior: 7.32e-04\n> [infer_isize] inferred maximum insert size: 295 (7.05 sigma)\n> [bwa_sai2sam_pe_core] time elapses: 13.78 sec\n> [bwa_sai2sam_pe_core] changing coordinates of 8522 alignments.\n> [bwa_sai2sam_pe_core] align unmapped mate...\n> [bwa_sai2sam_pe_core] time elapses: 0.15 sec\n> [bwa_sai2sam_pe_core] refine gapped alignments... 0.23 sec\n> [bwa_sai2sam_pe_core] print alignments... 0.87 sec\n> [bwa_sai2sam_pe_core] 2883584 sequences have been processed.\n> [bwa_sai2sam_pe_core] convert to sequence coordinate...\n> [infer_isize] (25, 50, 75) percentile: (154, 165, 178)\n> [infer_isize] low and high boundaries: 106 and 226 for estimating avg \n> and std\n> [infer_isize] inferred external isize from 190765 pairs: 163.391 +/- \n> 18.597\n> [infer_isize] skewness: 0.025; kurtosis: 0.752; ap_prior: 7.39e-04\n> [infer_isize] inferred maximum insert size: 294 (7.05 sigma)\n> [bwa_sai2sam_pe_core] time elapses: 13.85 sec\n> [bwa_sai2sam_pe_core] changing coordinates of 8525 alignments.\n> [bwa_sai2sam_pe_core] align unmapped mate...\n> [bwa_sai2sam_pe_core] time elapses: 0.15 sec\n> [bwa_sai2sam_pe_core] refine gapped alignments... 0.23 sec\n> [bwa_sai2sam_pe_core] print alignments... 0.87 sec\n> [bwa_sai2sam_pe_core] 3145728 sequences have been processed.\n> [bwa_sai2sam_pe_core] convert to sequence coordinate...\n> [infer_isize] (25, 50, 75) percentile: (154, 165, 178)\n> [infer_isize] low and high boundaries: 106 and 226 for estimating avg \n> and std\n> [infer_isize] inferred external isize from 190644 pairs: 163.494 +/- \n> 18.641\n> [infer_isize] skewness: 0.033; kurtosis: 0.765; ap_prior: 7.30e-04\n> [infer_isize] inferred maximum insert size: 295 (7.05 sigma)\n> [bwa_sai2sam_pe_core] time elapses: 13.30 sec\n> [bwa_sai2sam_pe_core] changing coordinates of 8441 alignments.\n> [bwa_sai2sam_pe_core] align unmapped mate...\n> [bwa_sai2sam_pe_core] time elapses: 0.16 sec\n> [bwa_sai2sam_pe_core] refine gapped alignments... 0.23 sec\n> [bwa_sai2sam_pe_core] print alignments... 0.87 sec\n> [bwa_sai2sam_pe_core] 3407872 sequences have been processed.\n> [bwa_sai2sam_pe_core] convert to sequence coordinate...\n> [infer_isize] (25, 50, 75) percentile: (154, 165, 178)\n> [infer_isize] low and high boundaries: 106 and 226 for estimating avg \n> and std\n> [infer_isize] inferred external isize from 190407 pairs: 163.436 +/- \n> 18.643\n> [infer_isize] skewness: 0.014; kurtosis: 0.752; ap_prior: 7.47e-04\n> [infer_isize] inferred maximum insert size: 295 (7.05 sigma)\n> [bwa_sai2sam_pe_core] time elapses: 14.22 sec\n> [bwa_sai2sam_pe_core] changing coordinates of 8377 alignments.\n> [bwa_sai2sam_pe_core] align unmapped mate...\n> [bwa_sai2sam_pe_core] time elapses: 0.15 sec\n> [bwa_sai2sam_pe_core] refine gapped alignments... 0.23 sec\n> [bwa_sai2sam_pe_core] print alignments... 0.87 sec\n> [bwa_sai2sam_pe_core] 3670016 sequences have been processed.\n> [bwa_sai2sam_pe_core] convert to sequence coordinate...\n> [infer_isize] (25, 50, 75) percentile: (154, 165, 178)\n> [infer_isize] low and high boundaries: 106 and 226 for estimating avg \n> and std\n> [infer_isize] inferred external isize from 191453 pairs: 163.336 +/- \n> 18.700\n> [infer_isize] skewness: 0.025; kurtosis: 0.748; ap_prior: 7.20e-04\n> [infer_isize] inferred maximum insert size: 295 (7.05 sigma)\n> [bwa_sai2sam_pe_core] time elapses: 13.56 sec\n> [bwa_sai2sam_pe_core] changing coordinates of 8226 alignments.\n> [bwa_sai2sam_pe_core] align unmapped mate...\n> [bwa_sai2sam_pe_core] time elapses: 0.15 sec\n> [bwa_sai2sam_pe_core] refine gapped alignments... 0.23 sec\n> [bwa_sai2sam_pe_core] print alignments... 0.87 sec\n> [bwa_sai2sam_pe_core] 3932160 sequences have been processed.\n> [bwa_sai2sam_pe_core] convert to sequence coordinate...\n> [infer_isize] (25, 50, 75) percentile: (154, 165, 178)\n> [infer_isize] low and high boundaries: 106 and 226 for estimating avg \n> and std\n> [infer_isize] inferred external isize from 190751 pairs: 163.415 +/- \n> 18.625\n> [infer_isize] skewness: 0.007; kurtosis: 0.756; ap_prior: 7.58e-04\n> [infer_isize] inferred maximum insert size: 295 (7.05 sigma)\n> [bwa_sai2sam_pe_core] time elapses: 13.89 sec\n> [bwa_sai2sam_pe_core] changing coordinates of 8528 alignments.\n> [bwa_sai2sam_pe_core] align unmapped mate...\n> [bwa_sai2sam_pe_core] time elapses: 0.15 sec\n> [bwa_sai2sam_pe_core] refine gapped alignments... 0.23 sec\n> [bwa_sai2sam_pe_core] print alignments... 0.87 sec\n> [bwa_sai2sam_pe_core] 4194304 sequences have been processed.\n> [bwa_sai2sam_pe_core] convert to sequence coordinate...\n> [infer_isize] (25, 50, 75) percentile: (154, 165, 178)\n> [infer_isize] low and high boundaries: 106 and 226 for estimating avg \n> and std\n> [infer_isize] inferred external isize from 191015 pairs: 163.377 +/- \n> 18.658\n> [infer_isize] skewness: 0.014; kurtosis: 0.730; ap_prior: 7.13e-04\n> [infer_isize] inferred maximum insert size: 295 (7.05 sigma)\n> [bwa_sai2sam_pe_core] time elapses: 14.39 sec\n> [bwa_sai2sam_pe_core] changing coordinates of 8590 alignments.\n> [bwa_sai2sam_pe_core] align unmapped mate...\n> [bwa_sai2sam_pe_core] time elapses: 0.16 sec\n> [bwa_sai2sam_pe_core] refine gapped alignments... 0.24 sec\n> [bwa_sai2sam_pe_core] print alignments... 0.90 sec\n> [bwa_sai2sam_pe_core] 4456448 sequences have been processed.\n> [bwa_sai2sam_pe_core] convert to sequence coordinate...\n> [infer_isize] (25, 50, 75) percentile: (154, 165, 178)\n> [infer_isize] low and high boundaries: 106 and 226 for estimating avg \n> and std\n> [infer_isize] inferred external isize from 190828 pairs: 163.348 +/- \n> 18.623\n> [infer_isize] skewness: 0.017; kurtosis: 0.766; ap_prior: 7.15e-04\n> [infer_isize] inferred maximum insert size: 295 (7.05 sigma)\n> [bwa_sai2sam_pe_core] time elapses: 13.08 sec\n> [bwa_sai2sam_pe_core] changing coordinates of 8396 alignments.\n> [bwa_sai2sam_pe_core] align unmapped mate...\n> [bwa_sai2sam_pe_core] time elapses: 0.15 sec\n> [bwa_sai2sam_pe_core] refine gapped alignments... 0.24 sec\n> [bwa_sai2sam_pe_core] print alignments... 0.88 sec\n> [bwa_sai2sam_pe_core] 4718592 sequences have been processed.\n> [bwa_sai2sam_pe_core] convert to sequence coordinate...\n> [infer_isize] (25, 50, 75) percentile: (154, 165, 178)\n> [infer_isize] low and high boundaries: 106 and 226 for estimating avg \n> and std\n> [infer_isize] inferred external isize from 191429 pairs: 163.312 +/- \n> 18.625\n> [infer_isize] skewness: 0.020; kurtosis: 0.747; ap_prior: 7.16e-04\n> [infer_isize] inferred maximum insert size: 295 (7.05 sigma)\n> [bwa_sai2sam_pe_core] time elapses: 12.45 sec\n> [bwa_sai2sam_pe_core] changing coordinates of 8376 alignments.\n> [bwa_sai2sam_pe_core] align unmapped mate...\n> [bwa_sai2sam_pe_core] time elapses: 0.15 sec\n> [bwa_sai2sam_pe_core] refine gapped alignments... 0.23 sec\n> [bwa_sai2sam_pe_core] print alignments... 0.88 sec\n> [bwa_sai2sam_pe_core] 4980736 sequences have been processed.\n> [bwa_sai2sam_pe_core] convert to sequence coordinate...\n> [infer_isize] (25, 50, 75) percentile: (153, 165, 178)\n> [infer_isize] low and high boundaries: 103 and 228 for estimating avg \n> and std\n> [infer_isize] inferred external isize from 192585 pairs: 163.262 +/- \n> 18.939\n> [infer_isize] skewness: 0.011; kurtosis: 0.844; ap_prior: 6.81e-04\n> [infer_isize] inferred maximum insert size: 297 (7.05 sigma)\n> [bwa_sai2sam_pe_core] time elapses: 12.50 sec\n> [bwa_sai2sam_pe_core] changing coordinates of 8479 alignments.\n> [bwa_sai2sam_pe_core] align unmapped mate...\n> [bwa_sai2sam_pe_core] time elapses: 0.15 sec\n> [bwa_sai2sam_pe_core] refine gapped alignments... 0.23 sec\n> [bwa_sai2sam_pe_core] print alignments... 0.88 sec\n> [bwa_sai2sam_pe_core] 5242880 sequences have been processed.\n> [bwa_sai2sam_pe_core] convert to sequence coordinate...\n> [infer_isize] (25, 50, 75) percentile: (154, 165, 178)\n> [infer_isize] low and high boundaries: 106 and 226 for estimating avg \n> and std\n> [infer_isize] inferred external isize from 190979 pairs: 163.379 +/- \n> 18.609\n> [infer_isize] skewness: 0.021; kurtosis: 0.768; ap_prior: 7.08e-04\n> [infer_isize] inferred maximum insert size: 295 (7.05 sigma)\n> [bwa_sai2sam_pe_core] time elapses: 12.30 sec\n> [bwa_sai2sam_pe_core] changing coordinates of 8416 alignments.\n> [bwa_sai2sam_pe_core] align unmapped mate...\n> [bwa_sai2sam_pe_core] time elapses: 0.15 sec\n> [bwa_sai2sam_pe_core] refine gapped alignments... 0.23 sec\n> [bwa_sai2sam_pe_core] print alignments... 0.87 sec\n> [bwa_sai2sam_pe_core] 5505024 sequences have been processed.\n> [bwa_sai2sam_pe_core] convert to sequence coordinate...\n> [infer_isize] (25, 50, 75) percentile: (153, 165, 178)\n> [infer_isize] low and high boundaries: 103 and 228 for estimating avg \n> and std\n> [infer_isize] inferred external isize from 192456 pairs: 163.209 +/- \n> 18.969\n> [infer_isize] skewness: -0.011; kurtosis: 0.849; ap_prior: 6.93e-04\n> [infer_isize] inferred maximum insert size: 297 (7.05 sigma)\n> [bwa_sai2sam_pe_core] time elapses: 12.21 sec\n> [bwa_sai2sam_pe_core] changing coordinates of 8389 alignments.\n> [bwa_sai2sam_pe_core] align unmapped mate...\n> [bwa_sai2sam_pe_core] time elapses: 0.16 sec\n> [bwa_sai2sam_pe_core] refine gapped alignments... 0.23 sec\n> [bwa_sai2sam_pe_core] print alignments... 0.88 sec\n> [bwa_sai2sam_pe_core] 5767168 sequences have been processed.\n> [bwa_sai2sam_pe_core] convert to sequence coordinate...\n> [infer_isize] (25, 50, 75) percentile: (154, 165, 178)\n> [infer_isize] low and high boundaries: 106 and 226 for estimating avg \n> and std\n> [infer_isize] inferred external isize from 190576 pairs: 163.332 +/- \n> 18.695\n> [infer_isize] skewness: 0.014; kurtosis: 0.745; ap_prior: 7.64e-04\n> [infer_isize] inferred maximum insert size: 295 (7.05 sigma)\n> [bwa_sai2sam_pe_core] time elapses: 12.63 sec\n> [bwa_sai2sam_pe_core] changing coordinates of 8422 alignments.\n> [bwa_sai2sam_pe_core] align unmapped mate...\n> [bwa_sai2sam_pe_core] time elapses: 0.15 sec\n> [bwa_sai2sam_pe_core] refine gapped alignments... 0.23 sec\n> [bwa_sai2sam_pe_core] print alignments... 0.88 sec\n> [bwa_sai2sam_pe_core] 6029312 sequences have been processed.\n> [bwa_sai2sam_pe_core] convert to sequence coordinate...\n> [infer_isize] (25, 50, 75) percentile: (154, 165, 178)\n> [infer_isize] low and high boundaries: 106 and 226 for estimating avg \n> and std\n> [infer_isize] inferred external isize from 190651 pairs: 163.360 +/- \n> 18.665\n> [infer_isize] skewness: 0.015; kurtosis: 0.758; ap_prior: 7.15e-04\n> [infer_isize] inferred maximum insert size: 295 (7.05 sigma)\n> [bwa_sai2sam_pe_core] time elapses: 12.90 sec\n> [bwa_sai2sam_pe_core] changing coordinates of 8477 alignments.\n> [bwa_sai2sam_pe_core] align unmapped mate...\n> [bwa_sai2sam_pe_core] time elapses: 0.15 sec\n> [bwa_sai2sam_pe_core] refine gapped alignments... 0.24 sec\n> [bwa_sai2sam_pe_core] print alignments... 0.89 sec\n> [bwa_sai2sam_pe_cor"}}