Question: Picard Alignment Summary Metrics Failure
0
Huge, Andreas • 10 wrote:
Hello,
When I use the NGS Picard tool "SAM/BAM alignment summary metrics"
with a BAM file produced with Tophat in Galaxy I get the following
message:
INFO:root:## executing java -Xmx4g -jar
/galaxy/home/g2main/galaxy_main/tool-
data/shared/jars/CollectAlignmentSummaryMetrics.jar
VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true ADAPTER_SEQUENCE=
IS_BISULFITE_SEQUENCED=false MAX_INSERT_SIZE=1000 OUTPUT=/galaxy/main_
pool/pool5/tmp/job_working_directory/2368774/dataset_2672529_files/Col
lectAlignmentSummaryMetrics.metrics.txt R=/galaxy/main_pool/pool5/tmp/
job_working_directory/2368774/dataset_2672529_files/mm9.fa_fake.fasta
TMP_DIR=/tmp
INPUT=/galaxy/main_database/files/002/666/dataset_2666199.dat returned
status 1 and stderr:
[Mon Jul 11 03:27:56 EDT 2011]
net.sf.picard.analysis.CollectAlignmentSummaryMetrics
MAX_INSERT_SIZE=1000 ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTC
TTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG,
AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT,
AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG,
AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT,
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG,
IS_BISULFITE_SEQUENCED=false]
INPUT=/galaxy/main_database/files/002/666/dataset_2666199.dat OUTPUT=/
galaxy/main_pool/pool5/tmp/job_working_directory/2368774/dataset_26725
29_files/CollectAlignmentSummaryMetrics.metrics.txt REFERENCE_SEQUENCE
=/galaxy/main_pool/pool5/tmp/job_working_directory/2368774/dataset_267
2529_files/mm9.fa_fake.fasta ASSUME_SORTED=true TMP_DIR=/tmp
VALIDATION_STRINGENCY=LENIENT IS_BISULFITE_SEQUENCED=false
STOP_AFTER=0 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5
MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
[Mon Jul 11 03:27:57 EDT 2011]
net.sf.picard.analysis.CollectAlignmentSummaryMetrics done.
Runtime.totalMemory()=507379712
Exception in thread "main" java.lang.IllegalArgumentException: No enum
const class net.sf.samtools.SAMFileHeader$SortOrder.sorted
at java.lang.Enum.valueOf(Enum.java:196)
at
net.sf.samtools.SAMFileHeader$SortOrder.valueOf(SAMFileHeader.java:58)
at
net.sf.samtools.SAMFileHeader.getSortOrder(SAMFileHeader.java:239)
at net.sf.picard.analysis.SinglePassSamProgram.makeItSo(SinglePassSa
mProgram.java:85)
at net.sf.picard.analysis.SinglePassSamProgram.doWork(SinglePassSamP
rogram.java:54)
at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLine
Program.java:157)
at net.sf.picard.cmdline.CommandLineProgram.instanceMainWithExit(Com
mandLineProgram.java:117)
at net.sf.picard.analysis.CollectAlignmentSummaryMetrics.main(Collec
tAlignmentSummaryMetrics.java:106)
If I use the NGS: Picard BAM Index Statistics, the script is running
without any failure so I think the BAM format should be okay.
Any help would be gratefully received.
Thanks.
Andreas Huge