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Old 07-04-2011, 12:52 AM   #3
gavin.oliver
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Location: uk

Join Date: Jan 2010
Posts: 110
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Quote:
Originally Posted by nilshomer View Post
What version are you using? Could you display the output error?
I am using version 0.1.15 Nils.

The screen output on program death looks like this:

[Fri Jul 01 10:07:16 BST 2011] srma.SRMA INPUT=[reads_sort.bam] OUTPUT=[reads_sort_realigned] REFERENCE=../hg19/hg19_all_but_haps.fa VALIDATION_STRINGENCY=SILENT OFFSET=20 MIN_MAPQ=0 MINIMUM_ALLELE_PROBABILITY=0.1 MINIMUM_ALLELE_COVERAGE=3 MAXIMUM_TOTAL_COVERAGE=100 CORRECT_BASES=false USE_SEQUENCE_QUALITIES=true QUIET_STDERR=false MAX_HEAP_SIZE=8192 MAX_QUEUE_SIZE=65536 GRAPH_PRUNING=false NUM_THREADS=1 TMP_DIR=/tmp/goliver VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
Allele coverage cutoffs:
coverage: 1 minimum allele coverage: 0
coverage: 2 minimum allele coverage: 0
coverage: 3 minimum allele coverage: 0
coverage: 4 minimum allele coverage: 1
coverage: 5 minimum allele coverage: 1
coverage: 6 minimum allele coverage: 1
coverage: 7 minimum allele coverage: 2
coverage: 8 minimum allele coverage: 2
coverage: 9 minimum allele coverage: 3
coverage: >9 minimum allele coverage: 3
Records processsed: 105356 (last chr10:135518316-135518416)java.lang.Exception: SAMRecord contig does not match the current reference sequence contig
at srma.Graph.addSAMRecord(Graph.java:54)
at srma.SRMA$GraphThread.run(SRMA.java:708)
Please report bugs to srma-help@lists.sourceforge.net
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