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Old 10-12-2010, 12:30 AM   #2
nilshomer
Nils Homer
 
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Location: Boston, MA, USA

Join Date: Nov 2008
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Quote:
Originally Posted by allenday View Post
Trying to use srma for the first time, version 0.1.8. Here's the invocation:

Code:
java -jar ./srma-0.1.8.jar INPUT=x.sam REFERENCE=chr22.fa OUTPUT=x.out
...and the output:

Code:
[Sat Oct 09 05:26:25 UTC 2010] srma.SRMA REFERENCE=chr22.fa    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 NUM_THREADS=1 TMP_DIR=/tmp/ec2-user VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false
java.lang.IllegalArgumentException: Cannot check readability of null file.
	at net.sf.picard.io.IoUtil.assertFileIsReadable(IoUtil.java:48)
	at net.sf.picard.reference.FastaSequenceIndex.<init>(FastaSequenceIndex.java:54)
	at net.sf.picard.reference.IndexedFastaSequenceFile.<init>(IndexedFastaSequenceFile.java:95)
	at srma.SRMA.doWork(SRMA.java:125)
	at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:160)
	at srma.SRMA.main(SRMA.java:92)
Please report bugs to srma-help@lists.sourceforge.net
... and yes, the inputs exist:

Code:
ls -l x.sam chr22.fa 
-rw-rw-r-- 1 ec2-user ec2-user 50685268 Oct  9 05:23 chr22.fa
-rw-rw-r-- 1 ec2-user ec2-user    25181 Oct  9 05:32 x.sam
Help appreciated.
There is a potential bug in Picard that I am investigating right now giving this cryptic error message. Try running "samtools faidx chr22.fa". You need to index the reference FASTA file.
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