From commits-noreply@bitbucket.org Sun May 8 21:22:39 2011 From: Bitbucket To: galaxy-commits@lists.galaxyproject.org Subject: [galaxy-commits] commit/galaxy-central: fubar: picard as metrics test outputs and test tweaks to try to get around buildbot Date: Mon, 09 May 2011 01:22:31 +0000 Message-ID: <20110509012231.21794.98112@bitbucket02.managed.contegix.com> MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="===============3551792240318212367==" --===============3551792240318212367== 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/9644cbed297c/ changeset: r5516:9644cbed297c user: fubar date: 2011-05-09 03:21:51 summary: picard as metrics test outputs and test tweaks to try to get aro= und buildbot affected #: 2 files (992 bytes) --- a/test-data/picard_output_alignment_summary_metrics.html Sun May 08 19:31= :13 2011 -0400 +++ b/test-data/picard_output_alignment_summary_metrics.html Sun May 08 21:21= :51 2011 -0400 @@ -6,53 +6,56 @@ - +
-Galaxy Rgenetics tool output rgPicar= dASMetrics.py run at 10/04/2011 14:49:13Your job produced the followin= g output files.
- - +Galaxy tool wrapper run picard_wrapper at 08/05/2011 21:08:01
The= following output files were created (click the filename to view/download a c= opy):
picardAlignSumMetrics_out.= txt
+
CollectAlignm= entSummaryMetrics.metrics.txt

-Picard on line resources

    +Picard on line resources:
    Picard output (transposed to= make it easier to see)
    -## METRICS CLASS net.sf.picard.analysis.AlignmentSummaryMetrics + - - - - - - - + + + + + + + - - - - + + + +<= td>PCT_CHIMERAS
    ## net.sf.picard.metrics.StringHeader
    # net.sf.picard.analysis.CollectAlignmentSummaryMetrics MAX_INSE= RT_SIZE=3D100000 ADAPTER_SEQUENCE=3D[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTAC= ACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAG= ATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGA= TCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTC= CGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, I= S_BISULFITE_SEQUENCED=3Dfalse] INPUT=3D/export/tmp/tmpBfU1Um/database/files/0= 00/dataset_89.dat OUTPUT=3D/udd/rerla/rgalaxy/database/job_working_directory/= 88/dataset_90_files/picardAlignSumMetrics_out.txt 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
    ## net.sf.picard.metrics.StringHeader
    # Started on: Sun Apr 10 14:49:13 EDT 2011
    CATEGORYFIRST_OF_PAIR
    ## net.sf.picard.metrics.StringHeader
    # net.sf.picard.analysis.CollectAlignmentSummaryMetrics MAX_INSE= RT_SIZE=3D100000 ADAPTER_SEQUENCE=3D[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTAC= ACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAG= ATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGA= TCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTC= CGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, I= S_BISULFITE_SEQUENCED=3Dfalse] INPUT=3D/export/tmp/tmpNfOoN9/database/files/0= 00/dataset_2.dat OUTPUT=3D/udd/rerla/galaxy-central/database/job_working_dire= ctory/3/dataset_3_files/CollectAlignmentSummaryMetrics.metrics.txt REFERENCE_= SEQUENCE=3D/udd/rerla/galaxy-central/database/job_working_directory/3/dataset= _3_files/CollectAlignmentSummaryMetrics2ZaS1j.fasta_fake.fasta ASSUME_SORTED= =3Dtrue TMP_DIR=3D/tmp VALIDATION_STRINGENCY=3DLENIENT IS_BISULFITE_SEQUEN= CED=3Dfalse STOP_AFTER=3D0 VERBOSITY=3DINFO QUIET=3Dfalse COMPRESSION_LEVEL= =3D5 MAX_RECORDS_IN_RAM=3D500000 CREATE_INDEX=3Dfalse CREATE_MD5_FILE=3Dfalse=
    ## net.sf.picard.metrics.StringHeader
    # Started on: Sun May 08 21:08:00 EDT 2011
    ## METRICS CLASS net.sf.picard.analysis.AlignmentSummaryMet= rics
    CATEGORYFIRST_OF_PAIR
    TOTAL_READS4
    PF_REA= DS4
    PCT_PF_READS1
    PF_NOISE_READS0
    PF_READS_ALIGNED0
    PCT_PF_READS_ALIGNED0
    PF_HQ_ALIGNED_READS0
    PF_HQ_ALIGNED_BASES0
    PF_HQ_ALIGNED_Q20_BASES0
    PF_HQ_MEDIAN_MISMATCHES0
    PF_HQ_ERROR_RATE0
    PF_READS_ALIGNED4
    PCT_PF_READS_ALIGNED1
    PF_HQ_ALIGNED_READS4
    PF_HQ_ALIGNED_BASES404
    PF_HQ_ALIGNED_Q20_BASES28
    PF_HQ_MEDIAN_MISMATCHES78
    PF_HQ_ERROR_RATE0.777228
    MEAN_READ_LENGTH101
    READS_ALIGNED_IN_PAIRS0
    PCT_READS_ALIGNED_IN_PAIRS0
    BAD_CYCLES2
    STRAND_BALANCE0
    READS_ALIGNED_IN_PAIRS3
    PCT_READS_ALIGNED_IN_PAIRS0.75
    BAD_CYCLES63
    STRAND_BALANCE0.25
    0
    PCT_ADAPTER 0
    Picard log
    -
    ## executing java -Xmx2g  -jar /udd/rerla/rgalaxy/tool-data/shared/jars=
/CollectAlignmentSummaryMetrics.jar MAX_INSERT_SIZE=3D100000 OUTPUT=3D/udd/re=
rla/rgalaxy/database/job_working_directory/88/dataset_90_files/picardAlignSum=
Metrics_out.txt  ADAPTER_SEQUENCE=3D  IS_BISULFITE_SEQUENCED=3Dfalse VALIDATI=
ON_STRINGENCY=3DLENIENT INPUT=3D/export/tmp/tmpBfU1Um/database/files/000/data=
set_89.dat ASSUME_SORTED=3Dtrue TMP_DIR=3D/tmp returned status 0 and log (std=
out/stderr) records:=20
-[Sun Apr 10 14:49:13 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/tmpBfU1Um=
/database/files/000/dataset_89.dat OUTPUT=3D/udd/rerla/rgalaxy/database/job_w=
orking_directory/88/dataset_90_files/picardAlignSumMetrics_out.txt ASSUME_SOR=
TED=3Dtrue TMP_DIR=3D/tmp VALIDATION_STRINGENCY=3DLENIENT    IS_BISULFITE_SEQ=
UENCED=3Dfalse STOP_AFTER=3D0 VERBOSITY=3DINFO QUIET=3Dfalse COMPRESSION_LEVE=
L=3D5 MAX_RECORDS_IN_RAM=3D500000 CREATE_INDEX=3Dfalse CREATE_MD5_FILE=3Dfalse
-WARNING	2011-04-10 14:49:13	SinglePassSamProgram	File reports sort order 'qu=
eryname', assuming it's coordinate sorted anyway.
-[Sun Apr 10 14:49:13 EDT 2011] net.sf.picard.analysis.CollectAlignmentSummar=
yMetrics done.
+
    ## executing java -Xmx2g -jar /udd/rerla/galaxy-central/tool-data/share=
d/jars/CreateSequenceDictionary.jar REFERENCE=3D/tmp/CollectAlignmentSummaryM=
etrics2ZaS1j.fasta OUTPUT=3D/tmp/CollectAlignmentSummaryMetrics2ZaS1j.dict UR=
I=3Ddataset_1.dat TRUNCATE_NAMES_AT_WHITESPACE=3DNone returned status 0 and s=
tderr:=20
+[Sun May 08 21:08:00 EDT 2011] net.sf.picard.sam.CreateSequenceDictionary RE=
FERENCE=3D/tmp/CollectAlignmentSummaryMetrics2ZaS1j.fasta OUTPUT=3D/tmp/Colle=
ctAlignmentSummaryMetrics2ZaS1j.dict URI=3Ddataset_1.dat TRUNCATE_NAMES_AT_WH=
ITESPACE=3Dfalse    NUM_SEQUENCES=3D2147483647 TMP_DIR=3D/tmp/rerla VERBOSITY=
=3DINFO QUIET=3Dfalse VALIDATION_STRINGENCY=3DSTRICT COMPRESSION_LEVEL=3D5 MA=
X_RECORDS_IN_RAM=3D500000 CREATE_INDEX=3Dfalse CREATE_MD5_FILE=3Dfalse
+[Sun May 08 21:08:00 EDT 2011] net.sf.picard.sam.CreateSequenceDictionary do=
ne.
 Runtime.totalMemory()=3D9109504
=20
=20
+## executing java -Xmx2g -jar /udd/rerla/galaxy-central/tool-data/shared/jar=
s/CollectAlignmentSummaryMetrics.jar VALIDATION_STRINGENCY=3DLENIENT ASSUME_S=
ORTED=3Dtrue  ADAPTER_SEQUENCE=3D IS_BISULFITE_SEQUENCED=3Dfalse MAX_INSERT_S=
IZE=3D100000 OUTPUT=3D/udd/rerla/galaxy-central/database/job_working_director=
y/3/dataset_3_files/CollectAlignmentSummaryMetrics.metrics.txt R=3D/udd/rerla=
/galaxy-central/database/job_working_directory/3/dataset_3_files/CollectAlign=
mentSummaryMetrics2ZaS1j.fasta_fake.fasta TMP_DIR=3D/tmp INPUT=3D/export/tmp/=
tmpNfOoN9/database/files/000/dataset_2.dat returned status 0 and stderr:=20
+[Sun May 08 21:08:00 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/tmpNfOoN9=
/database/files/000/dataset_2.dat OUTPUT=3D/udd/rerla/galaxy-central/database=
/job_working_directory/3/dataset_3_files/CollectAlignmentSummaryMetrics.metri=
cs.txt REFERENCE_SEQUENCE=3D/udd/rerla/galaxy-central/database/job_working_di=
rectory/3/dataset_3_files/CollectAlignmentSummaryMetrics2ZaS1j.fasta_fake.fas=
ta ASSUME_SORTED=3Dtrue TMP_DIR=3D/tmp VALIDATION_STRINGENCY=3DLENIENT    IS_=
BISULFITE_SEQUENCED=3Dfalse STOP_AFTER=3D0 VERBOSITY=3DINFO QUIET=3Dfalse COM=
PRESSION_LEVEL=3D5 MAX_RECORDS_IN_RAM=3D500000 CREATE_INDEX=3Dfalse CREATE_MD=
5_FILE=3Dfalse
+WARNING	2011-05-08 21:08:00	SinglePassSamProgram	File reports sort order 'qu=
eryname', assuming it's coordinate sorted anyway.
+[Sun May 08 21:08:01 EDT 2011] net.sf.picard.analysis.CollectAlignmentSummar=
yMetrics done.
+Runtime.totalMemory()=3D9109504
+
+
 
    The freely available Picard software=20
-generated all outputs reported here, using this command line:
    
-
    java -Xmx2g  -jar /udd/rerla/rgalaxy/tool-data/shared/jars/CollectAlign=
mentSummaryMetrics.jar MAX_INSERT_SIZE=3D100000 OUTPUT=3D/udd/rerla/rgalaxy/d=
atabase/job_working_directory/88/dataset_90_files/picardAlignSumMetrics_out.t=
xt  ADAPTER_SEQUENCE=3D  IS_BISULFITE_SEQUENCED=3Dfalse VALIDATION_STRINGENCY=
=3DLENIENT INPUT=3D/export/tmp/tmpBfU1Um/database/files/000/dataset_89.dat AS=
SUME_SORTED=3Dtrue TMP_DIR=3D/tmp
    
-
+generated all outputs reported here running as a Galaxy tool =20 --- a/tools/picard/rgPicardASMetrics.xml Sun May 08 19:31:13 2011 -0400 +++ b/tools/picard/rgPicardASMetrics.xml Sun May 08 21:21:51 2011 -0400 @@ -61,7 +61,7 @@ - + @@ -69,7 +69,6 @@ - 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. --===============3551792240318212367==--