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Old 07-05-2011, 01:04 AM   #5
gavin.oliver
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Location: uk

Join Date: Jan 2010
Posts: 110
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Hi Nils,

The input file is a 916MB BAM file. Is there anywhere I could deposit it by FTP?

On the issue of running the file per chromosome, without specifying a numerical range, I tried the following "RANGE=chr1" but got an error:

[Tue Jul 05 09:00:03 BST 2011] srma.SRMA INPUT=[reads_sort.bam] OUTPUT=[reads_sort_realigned] REFERENCE=../../hg19/hg19_all_but_haps.fa RANGE=chr1 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 VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
java.lang.Exception: BAM files and BAM indexes when using the RANGE or RANGES option
at srma.SAMRecordIO.<init>(SAMRecordIO.java:53)
at srma.SRMA.doWork(SRMA.java:159)
at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:156)
at srma.SRMA.main(SRMA.java:98)
Please report bugs to srma-help@lists.sourceforge.net
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