Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

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

    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 [email protected]
    ... 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.

  • #2
    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 [email protected]
    ... 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.

    Comment

    Latest Articles

    Collapse

    • seqadmin
      Strategies for Sequencing Challenging Samples
      by seqadmin


      Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
      03-22-2024, 06:39 AM
    • seqadmin
      Techniques and Challenges in Conservation Genomics
      by seqadmin



      The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

      Avian Conservation
      Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
      03-08-2024, 10:41 AM

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by seqadmin, Yesterday, 06:37 PM
    0 responses
    12 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, Yesterday, 06:07 PM
    0 responses
    10 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-22-2024, 10:03 AM
    0 responses
    51 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-21-2024, 07:32 AM
    0 responses
    68 views
    0 likes
    Last Post seqadmin  
    Working...
    X