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/CollectAlignmentSummaryMetrics.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=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, 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_2672529_files/CollectAlignmentSummaryMetrics.metrics.txt REFERENCE_SEQUENCE=/galaxy/main_pool/pool5/tmp/job_working_directory/2368774/dataset_2672529_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(SinglePassSamProgram.java:85)

  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(CommandLineProgram.java:117)

  at net.sf.picard.analysis.CollectAlignmentSummaryMetrics.main(CollectAlignmentSummaryMetrics.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