srma-0.1.8 error - Cannot check readability of null file.

[allenday]

Trying to use srma for the first time, version 0.1.8. Here's the invocation:

java -jar ./srma-0.1.8.jar INPUT=x.sam REFERENCE=chr22.fa OUTPUT=x.out

...and the output:

[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 [email protected]

... and yes, the inputs exist:

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.

[nilshomer]

Trying to use srma for the first time, version 0.1.8. Here's the invocation:

java -jar ./srma-0.1.8.jar INPUT=x.sam REFERENCE=chr22.fa OUTPUT=x.out

...and the output:

[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 [email protected]

... and yes, the inputs exist:

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.