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 chr1152187281
0 99M * 0 0
CTGGAAGACTGACCTGTGCTAGATCCCTCCTGGTCAAAGGTTGATGACTGTCCTGATGTAGAACCATGCTGTCCTTGGCTACAGAAGTGCCCTGAGCCA
BBBFFBIFFFBFFBBFBFBBB 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
+
BBBFFBIFFFIFIIFFFFIIFFIIIFFBFFBFIBFBBBFBBBFFFBB
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.commailto: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.edumailto: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
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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.bemailto:geert.vandewe...@ua.ac.bemailto:geert.vandewe...@ua.ac.bemailto:geert.vandewe...@ua.ac.be
http://ua.ac.be/cognitivegenetics
http://www.linkedin.com/pub/geert-vandeweyer/26/457/726
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