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Thread | Thread Starter | Forum | Replies | Last Post |
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#1 |
Junior Member
Location: Montana Join Date: Jun 2010
Posts: 7
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Greetings, I am a novice user with little experience running command line software. I am enjoying learning, though error messages leave me at a loss.
Background: I used bwa to create my SAM file. When I attempt to use the "view" option to convert to BAM I receive the following: [samopen] SAM header is present: 100 sequences. Parse error at line 18750817: unmatched CIGAR operation Aborted I am unclear as to what the problem is. Any guidance? -Chris |
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#2 | |
Nils Homer
Location: Boston, MA, USA Join Date: Nov 2008
Posts: 1,285
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#3 |
Junior Member
Location: Montana Join Date: Jun 2010
Posts: 7
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Thank you for getting back to me. I don't know how to get text from the terminal and paste it into these forum windows. I did, however, look at the offending line. It is missing the actual nucleotide and associated Illumina information. Is there an easy way to explain how I can get terminal screen printout into a form I can "cut/paste"? I could then show you exactly what I'm seeing.
Based on your comments, it appears that bwa perhaps introduced an error in creating the SAM file ...or there may be something off in the datafiles I'm feeding into bwa? Again, I appreciate your willingness to help. There is a steep learning curve for me as I've never had any Unix training. I just learned the "sed" function to look at the offending line and see what was wrong. -Chris |
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#4 |
Senior Member
Location: Boston Join Date: Feb 2008
Posts: 693
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is it the last line in output? i guess it is truncated.
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#5 |
Junior Member
Location: Montana Join Date: Jun 2010
Posts: 7
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No, it's not the last line in output. I'm not sure of the line's exact position in the SAM file, but I printed out the lines prior and after the offending line and they are intact with a nucleotide string followed by what I understand to be Illumina information (perhaps pertaining to quality of the nucleotide call?)
I would show you what I'm seeing but I don't know how to get output from my terminal window into a form that I can post, other than typing verbatim what I'm seeing into these chat windows. There must be an easier way. At this point I don't know if this offending line is the only one in my SAM file or if there are others. It just appears to be the first and thus aborts the SAM --> BAM conversion. Thanks for you help. |
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#6 |
Junior Member
Location: Montana Join Date: Jun 2010
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Figured out my terminal to chat cut/paste. So, here are three lines from my .sam file. The middle line is the offending line that brings up the "unmatched CIGAR operation".
output/ chriswall@ubuntu:/host/Users/chris.wall/Desktop/Mastigo-genomics/bwa_cw$ sed '18750816,18750818!d' WC.sam ILLUMINA-2F52BD:6:50:1169:1446#0 163 NODE_37776_length_48465_cov_160.191483\par 35442 29 59M = 35600 217 TTTTATCGGTGTGTATCGGTGTGTATCGGTGGGCGAGTTTTCAACAAGATTATGGGGCA gggfggggfdae[_aee_eeZ_^]_`aaeS]\FY\`dWZ]_^`_`WcSZXg`dgfcbYV XT:A:U NM:i:2 SM:i:0 AM:i:0 X0:i:1 X1:i:2 XM:i:2 XO:i:0 XG:i:0 MD:Z:7T27G23 ILLUMINA-2F52BD:6:50:1169:1947#0 83 NODE_51983_length_172857_cov_173.044144\par 119160 60 5 XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:39C19 ILLUMINA-2F52BD:6:50:1178:417#0 83 NODE_43256_length_74978_cov_171.684830\par 68201 60 59M = 67821 -439 CAGAGAAAAGACAGGTGATTATCAGACAACCTACGGATTGATAGGAATTTTGAACCGCA bgdgbgfgf^dddddgdfgffggfbaggZefeae\ggggbfgggegfggggcg`feffe XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:59 /output Can this offending line and perhaps any subsequent offending lines be deleted from the .sam file and not introduce a problem? |
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#7 |
Nils Homer
Location: Boston, MA, USA Join Date: Nov 2008
Posts: 1,285
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The sequence and qualities are also missing along with the CIGAR. What program generated the SAM file?
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#8 |
Junior Member
Location: Montana Join Date: Jun 2010
Posts: 7
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bwa 0.5.5 package from Ubuntu
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#9 |
Nils Homer
Location: Boston, MA, USA Join Date: Nov 2008
Posts: 1,285
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#10 |
Senior Member
Location: Boston Join Date: Feb 2008
Posts: 693
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actually 0.5.5 is more stable than the latest release. 1KG has been using it to map >20TB of data and it never fails.
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#11 |
Nils Homer
Location: Boston, MA, USA Join Date: Nov 2008
Posts: 1,285
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Any suggestions for the missing CIGAR?
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#12 |
Senior Member
Location: Boston Join Date: Feb 2008
Posts: 693
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I guess this is a disk error or input error. It is quite unlikely to happen if you read the source code on printing alignments. It has never happened before.
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#13 | |
Junior Member
Location: USA Join Date: Oct 2012
Posts: 5
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I am having trouble converting the sam files to bam using samtools. I used this cmd to convert my sam to bam - samtools view -bT hg19.fa s_chip2.sam > s_chip2.bam I got this error. Parse error at line 7707082: sequence and quality are inconsistent Aborted I ran ValidateSamFile.jar, a picard tool and got the following error, hundreds of them - WARNING: Read name HWI-ST798R:82: D18MUACXX:2:1101:2025:1987, A record is missing a read group ERROR: Record 5, Read name HWI-ST798R:82: D18MUACXX:2:1101:8625:1992, Empty sequence dictionary. I am not sure how to fix this, any help is appreciated. |
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