Hi,
First time using SRMA and right the way into error... typical.
Anyhow, here it is:
hmm...
help would be appreciated!
thanks
First time using SRMA and right the way into error... typical.
Anyhow, here it is:
Code:
java -jar -Xmx2g ../srma-0.1.15.jar I=sorted.bam O=SRMA.bam R=chr17.fasta [Tue Aug 09 14:42:24 CEST 2011] srma.SRMA INPUT=[sorted.bam] OUTPUT=[SRMA.bam] REFERENCE=chr17.fasta 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/ VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT 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: 1 (last 17:3217-3266)java.lang.Exception: Error. Soft clipping with color-space data not currently supported. at srma.Align.align(Align.java:134) at srma.SRMA$AlignThread.run(SRMA.java:659) Please report bugs to [email][email protected][/email]
help would be appreciated!
thanks
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