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
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