From commits-noreply@bitbucket.org Mon May 9 11:07:26 2011 From: Bitbucket To: galaxy-commits@lists.galaxyproject.org Subject: [galaxy-commits] commit/galaxy-central: fubar: Grrrr. Must have index - trying hg19 to see if that pleases the buildbot on picard asmetrics Date: Mon, 09 May 2011 15:07:19 +0000 Message-ID: <20110509150719.15204.27088@bitbucket01.managed.contegix.com> MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="===============6239936259246672148==" --===============6239936259246672148== Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: quoted-printable 1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/6690fe6f5e1c/ changeset: r5520:6690fe6f5e1c user: fubar date: 2011-05-09 17:07:01 summary: Grrrr. Must have index - trying hg19 to see if that pleases the = buildbot on picard asmetrics affected #: 3 files (1.3 KB) --- a/test-data/picard_output_AsMetrics_indexed_hg18_sorted_pair.html Mon May= 09 10:57:14 2011 -0400 +++ b/test-data/picard_output_AsMetrics_indexed_hg18_sorted_pair.html Mon May= 09 11:07:01 2011 -0400 @@ -1,35 +1,34 @@ + tr.d0 td {background-color: oldlace; color: black;} + tr.d1 td {background-color: aliceblue; color: black;} + - +
-

Rgenetics tool rgPicardASMetrics.py= run at 09/05/2011 10:53:44

Your job produced the following output fil= es.
- - +Galaxy tool wrapper picard_wrapper at 09/05/2011 11:03:57
The fol= lowing output files were created (click the filename to view/download a copy)= :
AsMetricsIndexed.log
+
CollectAlignmentSumma= ryMetrics.log

-No Picard output found - please consult the Picard log above for an expla= nationPicard log

-
[Mon May 09 10:53:44 EDT 2011] net.sf.picard.analysis.CollectAlignmentS=
ummaryMetrics MAX_INSERT_SIZE=3D100000 ADAPTER_SEQUENCE=3D[AATGATACGGCGACCACC=
GAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG,=
 AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGT=
TCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACT=
CTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTC=
GTATGCCGTCTTCTGCTTG, IS_BISULFITE_SEQUENCED=3Dfalse] INPUT=3D/export/tmp/tmpp=
-lP_s/database/files/000/dataset_4.dat OUTPUT=3D/share/shared/galaxy/database=
/job_working_directory/5/dataset_5_files/rgPicardASMetrics.out REFERENCE_SEQU=
ENCE=3D/share/shared/data/genomes/hg18/hg18.fasta ASSUME_SORTED=3Dtrue TMP_DI=
R=3D/tmp VALIDATION_STRINGENCY=3DLENIENT    IS_BISULFITE_SEQUENCED=3Dfalse ST=
OP_AFTER=3D0 VERBOSITY=3DINFO QUIET=3Dfalse COMPRESSION_LEVEL=3D5 MAX_RECORDS=
_IN_RAM=3D500000 CREATE_INDEX=3Dfalse CREATE_MD5_FILE=3Dfalse
-[Mon May 09 10:53:44 EDT 2011] net.sf.picard.analysis.CollectAlignmentSummar=
yMetrics done.
-Runtime.totalMemory()=3D9109504
-Exception in thread "main" net.sf.samtools.util.SequenceUtil$SequenceListsDi=
fferException: Sequence dictionaries are not the same size (3, 45)
-	at net.sf.samtools.util.SequenceUtil.assertSequenceListsEqual(SequenceUtil.=
java:93)
-	at net.sf.samtools.util.SequenceUtil.assertSequenceDictionariesEqual(Sequen=
ceUtil.java:135)
-	at net.sf.picard.analysis.SinglePassSamProgram.makeItSo(SinglePassSamProgra=
m.java:78)
+Picard log

+
## executing java -Xmx2g -jar /udd/rerla/galaxy-central/tool-data/share=
d/jars/CollectAlignmentSummaryMetrics.jar VALIDATION_STRINGENCY=3DLENIENT ASS=
UME_SORTED=3Dtrue  ADAPTER_SEQUENCE=3D IS_BISULFITE_SEQUENCED=3Dfalse MAX_INS=
ERT_SIZE=3D100000 OUTPUT=3D/udd/rerla/galaxy-central/database/job_working_dir=
ectory/5/dataset_5_files/CollectAlignmentSummaryMetrics.metrics.txt R=3D/udd/=
rerla/galaxy-central/database/job_working_directory/5/dataset_5_files/hg19.fa=
sta_fake.fasta TMP_DIR=3D/tmp INPUT=3D/export/tmp/tmpBrCiH5/database/files/00=
0/dataset_4.dat returned status 1 and stderr:=20
+[Mon May 09 11:03:51 EDT 2011] net.sf.picard.analysis.CollectAlignmentSummar=
yMetrics MAX_INSERT_SIZE=3D100000 ADAPTER_SEQUENCE=3D[AATGATACGGCGACCACCGAGAT=
CTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATG=
ATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGC=
AGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTC=
CCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATG=
CCGTCTTCTGCTTG, IS_BISULFITE_SEQUENCED=3Dfalse] INPUT=3D/export/tmp/tmpBrCiH5=
/database/files/000/dataset_4.dat OUTPUT=3D/udd/rerla/galaxy-central/database=
/job_working_directory/5/dataset_5_files/CollectAlignmentSummaryMetrics.metri=
cs.txt REFERENCE_SEQUENCE=3D/udd/rerla/galaxy-central/database/job_working_di=
rectory/5/dataset_5_files/hg19.fasta_fake.fasta ASSUME_SORTED=3Dtrue TMP_DIR=
=3D/tmp VALIDATION_STRINGENCY=3DLENIENT    IS_BISULFITE_SEQUENCED=3Dfalse STO=
P_AFTER=3D0 VERBOSITY=3DINFO QUIET=3Dfalse COMPRESSION_LEVEL=3D5 MAX_RECORDS_=
IN_RAM=3D500000 CREATE_INDEX=3Dfalse CREATE_MD5_FILE=3Dfalse
+[Mon May 09 11:03:57 EDT 2011] net.sf.picard.analysis.CollectAlignmentSummar=
yMetrics done.
+Runtime.totalMemory()=3D912588800
+Exception in thread "main" net.sf.picard.PicardException: Requesting earlier=
 reference sequence: 0 < 1
+	at net.sf.picard.reference.ReferenceSequenceFileWalker.get(ReferenceSequenc=
eFileWalker.java:78)
+	at net.sf.picard.analysis.SinglePassSamProgram.makeItSo(SinglePassSamProgra=
m.java:115)
 	at net.sf.picard.analysis.SinglePassSamProgram.doWork(SinglePassSamProgram.=
java:54)
 	at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram=
.java:157)
 	at net.sf.picard.cmdline.CommandLineProgram.instanceMainWithExit(CommandLin=
eProgram.java:117)
 	at net.sf.picard.analysis.CollectAlignmentSummaryMetrics.main(CollectAlignm=
entSummaryMetrics.java:106)
+
+
 
The freely available Picard software=20
-generated all outputs reported here, using this command line:

-
java -Xmx2g -jar /share/shared/galaxy/tool-data/shared/jars/CollectAlig=
nmentSummaryMetrics.jar REFERENCE_SEQUENCE=3D/share/shared/data/genomes/hg18/=
hg18.fasta ASSUME_SORTED=3Dtrue ADAPTER_SEQUENCE=3D IS_BISULFITE_SEQUENCED=3D=
false MAX_INSERT_SIZE=3D100000 INPUT=3D/export/tmp/tmpp-lP_s/database/files/0=
00/dataset_4.dat OUTPUT=3D/share/shared/galaxy/database/job_working_directory=
/5/dataset_5_files/rgPicardASMetrics.out VALIDATION_STRINGENCY=3DLENIENT TMP_=
DIR=3D/tmp

-
+generated all outputs reported here running as a Galaxy tool =20 --- a/test-data/picard_output_alignment_summary_metrics.html Mon May 09 10:57= :14 2011 -0400 +++ b/test-data/picard_output_alignment_summary_metrics.html Mon May 09 11:07= :01 2011 -0400 @@ -1,56 +1,62 @@ + tr.d0 td {background-color: oldlace; color: black;} + tr.d1 td {background-color: aliceblue; color: black;} + - +
-

Rgenetics tool rgPicardASMetrics.py= run at 09/05/2011 10:53:32

Your job produced the following output fil= es.
- - - +Galaxy tool wrapper picard_wrapper at 09/05/2011 11:03:41
The fol= lowing output files were created (click the filename to view/download a copy)= :
rgPicardASMetrics.out
AsMetrics.log
+ +
CollectAlignmentSumma= ryMetrics.log
CollectAlignm= entSummaryMetrics.metrics.txt

-Picard on line resources

+generated all outputs reported here running as a Galaxy tool =20 --- a/tools/picard/rgPicardASMetrics.xml Mon May 09 10:57:14 2011 -0400 +++ b/tools/picard/rgPicardASMetrics.xml Mon May 09 11:07:01 2011 -0400 @@ -70,7 +70,8 @@ - + + Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email. --===============6239936259246672148==--