Also through toolshed, version 0.5.9-r16. An example error on our part is
(SamToBam):
Error extracting alignments from
(/galaxy/galaxy-dist/database/files/067/dataset_67090.dat), [samopen] SAM
header is present: 25 sequences.
Parse error at line 261924: sequence and quality are inconsistent
Aborted
That line in the sam does show sequence/qual inconsistency in length:
HWI-1KL167:27:D1NADACXX:4:2315:10415:96156 0 chr1 152187281
0 99M * 0 0
CTGGAAGACTGACCTGTGCTAGATCCCTCCTGGTCAAAGGTTGATGACTGTCCTGATGTAGAACCATGCTGTCCTTGGCTACAGAAGTGCCCTGAGCCA
BBBFFBFFFFFFFFIFFFBFFBBFBFFFFFBBB XT:A:U NM:i:1 X0:i:1 X1:i:0
XM:i:1 XO:i:0 XG:i:0 MD:Z:33A65
fastq file fed to BWA holds the correct info:
@HWI-1KL167:27:D1NADACXX:4:2315:10415:96156 1:N:0:GTGGCC
CTGGAAGACTGACCTGTGCTAGATCCCTCCTGGTCAAAGGTTGATGACTGTCCTGATGTAGAACCATGCTGTCCTTGGCTACAGAAGTGCCCTGAGCCA
+
BBBFFBFFFFFFFFIFFFIIIIIFIIIIIIFFFIIIIFIIFFFFIIIIFFIIIFFFFFFIIIIBFFBFIFFFFBFBBBFFFFFFFFFB<BBFFFB<<B<
Best,
Geert
________________________________________
Van: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu]
namens Moritz Juchler [juch...@stud.uni-heidelberg.de]
Verzonden: woensdag 14 augustus 2013 12:59
Aan: Bjoern Gruening
CC: galaxy-...@bx.psu.edu
Onderwerp: Re: [galaxy-dev] Fwd: Map with BWA results in correpted SAM file
Through toolshed.
On 14 August 2013 12:50, Bjoern Gruening
<bjoern.gruen...@gmail.com<mailto:bjoern.gruen...@gmail.com>> wrote:
Hi Moritz,
do you installed bwa through the toolshed or manually?
Cheers,
Bjoern
> Hey Folks,
>
>
> Is there really nobody that can help Geert and me? Thats quite
> important to me right now.
> This is obviously not something specific to me, as Geert has the exact
> same error.
> I meanwhile tried to replace the id with "1" but it still doesnt work.
>
>
> Best
> Moritz
>
> ______________________________
> Von: galaxy-dev-boun...@lists.bx.psu.eduIm Auftrag vonGeert Vandeweyer
> Gesendet: Donnerstag, 8. August 2013 17:18:59 (UTC+01:00) Amsterdam,
> Berlin, Bern, Rom, Stockholm, Wien
> An: galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu>
> Betreff: Re: [galaxy-dev] Map with BWA results in correpted SAM file
>
> to add on this :
>
> we have similar issues (sam-to-bam conversion fails with similar
> errors). it seems to be related to the BWA output getting messed up,
> with (part of) columns missing or duplicated on some lines.
>
> I have not found a systematic pattern in the errors, they seem to
> happen rather random.
>
>
>
> On 08/08/2013 05:06 PM, Moritz Juchler wrote:
> Dear Galaxy Community,
>
> I have a local instance and installed 0.5.9-r16 BWA and the toolshed
> wrapper. The mapping is successful. I then use the Filter Sam Tool on
> the sam file from the alignment, but it spits out this error:
>
> Dataset 26: Filter SAM on data 24
>
> Tool execution generated the following error message:
>
> Traceback (most recent call last):
> File
> "/home/trr/galaxy-dist/tools/samtools/sam_bitwise_flag_filter.py",
> line 148, in <module>
> if __name__ == "__main__": main()
>
> File
> "/home/trr/galaxy-dist/tools/samtools/sam_bitwise_flag_filter.py",
> line 137, in main
> flags = int( fields[flag_col] )
> ValueError: invalid literal for int() with base 10:
> 'RG:Z:lane712s006433'
>
>
>
>
> I have the same workflow online and did the exact same steps on the
> same fastq files.
> Is there anything I am missing? Is there any information I can provide
> to answer this question?
>
> Best
> Moritz
>
>
>
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
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>
>
>
> --
>
> Geert Vandeweyer, Ph.D.
> Department of Medical Genetics
> University of Antwerp
> Prins Boudewijnlaan 43
> 2650 Edegem
> Belgium
> Tel: +32 (0)3 275 97 56
> E-mail:
> geert.vandewe...@ua.ac.be<mailto:geert.vandewe...@ua.ac.be><mailto:geert.vandewe...@ua.ac.be<mailto:geert.vandewe...@ua.ac.be>>
> http://ua.ac.be/cognitivegenetics
> http://www.linkedin.com/pub/geert-vandeweyer/26/457/726
>
>
>
>
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client. To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
> http://lists.bx.psu.edu/
>
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___________________________________________________________
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