Using CRAM files in Picard SamToFastq with Queue


I'm trying to convert CRAM files to FASTQ format with SamToFastq as part of a pipeline I have written in a Queue script. Is there any parameter for passing a reference file in the SamToFastq Queue module? I didn't see any such parameter in SamToFastq.scala, PicardBamFunction.scala, or JavaCommandLineFunction.scala. I couldn't find anything on the forum, and I tried a bunch of different things by guessing, but didn't have any luck. If there is no parameter to use a reference file in a Queue script for Picard tools, is there any sort of workaround (e.g., environment variable that Picard will pick up on)?



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by Sheila

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  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    CRAM support is still patchy in Picard tools -- each tool has to be modified individually to support CRAM and this has not yet been done across the board. I second @shlee's recommendation to convert to BAM first.

  • @Geraldine_VdAuwera
    Thanks to you both for the responses. I did try to input CRAM files but I got an error message referring to a reference file as input, hence my question about how to supply the reference file. Here's the command that was sent to the cluster by Queue, and the accompanying error message I received:

    'java'  '-Xmx4480m'  '-XX:+UseParallelOldGC'  '-XX:ParallelGCThreads=4'  '-XX:GCTimeLimit=100'  '-XX:GCHeapFreeLimit=2'  ''  '-cp' '/software/Queue/3.5-0-Java-1.8.0_45/Queue.jar'  'picard.sam.SamToFastq'  'INPUT=/data/1514768.cram'  'TMP_DIR=/data/.queue/tmp'  'VALIDATION_STRINGENCY=SILENT'  'CREATE_INDEX=true'  'FASTQ=/data/1514768.cram_R1.fastq'  'SECOND_END_FASTQ=/data/1514768.cram_R2.fastq'
        [Wed Feb 22 12:18:04 EST 2017] picard.sam.SamToFastq INPUT=/data/1514768.cram FASTQ=/data/1514768.cram_R1.fastq SECOND_END_FASTQ=/data/1514768.cram_R2.fastq TMP_DIR=[/data/.queue/tmp] VALIDATION_STRINGENCY=SILENT CREATE_INDEX=true    OUTPUT_PER_RG=false RG_TAG=PU RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
        [Wed Feb 22 12:18:04 EST 2017] Executing as on Linux 3.10.0-327.36.1.el7.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_45-b14; Picard version: null JdkDeflater
        [Wed Feb 22 12:18:05 EST 2017] picard.sam.SamToFastq done. Elapsed time: 0.01 minutes.
        To get help, see
        Exception in thread "main" htsjdk.samtools.cram.CRAMException: Contig chr1 not found in the reference file.
            at htsjdk.samtools.CRAMIterator.nextContainer(
            at htsjdk.samtools.CRAMIterator.hasNext(
            at htsjdk.samtools.SamReader$AssertingIterator.hasNext(
            at picard.sam.SamToFastq.doWork(
            at picard.cmdline.CommandLineProgram.instanceMain(
            at picard.sam.SamToFastq.main(

    The error message mentioned that 'chr1' was not found in the reference file. I wasn't sure if there was some default reference it looks for but I assumed this error was because I had not provided a reference fasta file. I can manually run Picard and add the parameter REFERENCE_SEQUENCE=hg19.fa, which works, but I couldn't find a way to add that parameter to the SamToFastq object in my Queue script. I think I'm limited to the options that Queue allows me to specify (for example,
    The solution you mentioned is what I came up with as well, which is to convert to BAM and then run SamToFastq. I was hoping to go straight from CRAM to FASTQ but this works.

    Thanks for mentioning WDL as well. It appears that GridEngine is supported now so I will probably try to move our pipelines to WDL in the near future.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    It should be possible to add an argument setting for REFERENCE_SEQUENCE in Queue but to be honest I forget how it's done. I definitely encourage you to consider migrating to WDL; we're starting to share and support full workflow scripts, which should help.

  • shleeshlee CambridgeMember, Broadie, Moderator

    @andrewo, The error sounds like you are mistakenly using the wrong reference set. Be sure the contig naming matches between your data and the reference, e.g. chr1 vs just 1.

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