Hey Brad,
it looks like someone or something stopped the execution midstream. Is
there a time limit on your job, or some other resource manager that would
shut this down? This tool supports NextSeq data so the machine type should
not be an issue.
N
On Mon, Nov 10, 2014 at 3:56 PM, Langhorst, Brad <langho...@neb.com> wrote:
> [Mon Nov 10 11:07:48 EST 2014] picard.illumina.IlluminaBasecallsToFastq
> BASECALLS_DIR=/mnt/ngswork/langhorst/141029_NS500355_0002_AH15U8BGXX/Data/Intensities/BaseCalls
> LANE=2 RUN_BARCODE=141029_NS500355_0002_AH15U8BGXX MACHINE_NAME=NS500355
> FLOWCELL_BARCODE=H15U8BGXX READ_STRUCTURE=151T7B151T
> MULTIPLEX_PARAMS=/mnt/ngswork/langhorst/141029_NS500355_0002_AH15U8BGXX/lane2_multiplex_params.txt
> NUM_PROCESSORS=32 ADAPTERS_TO_CHECK=[INDEXED, DUAL_INDEXED, NEXTERA_V2,
> FLUIDIGM] APPLY_EAMSS_FILTER=true FORCE_GC=true
> MAX_READS_IN_RAM_PER_TILE=1200000 MINIMUM_QUALITY=2
> INCLUDE_NON_PF_READS=true READ_NAME_FORMAT=CASAVA_1_8
> COMPRESS_OUTPUTS=false VERBOSITY=INFO QUIET=false
> VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000
> CREATE_INDEX=false CREATE_MD5_FILE=false
> [Mon Nov 10 11:07:48 EST 2014] Executing as langhorst@seq-himem01-i on
> Linux 3.13.0-32-generic amd64; OpenJDK 64-Bit Server VM 1.7.0_65-b32;
> Picard version: 1.124(69ecf101f612fdc0f3d555aa2d3cc0b1ea193c68_1415030499)
> IntelDeflater
>
> ...
>
> INFO 2014-11-10 11:25:11 IlluminaBasecallsConverter Write
> 62,000,000 records. Elapsed time: 00:17:15s. Time for last 1,000,000:
> 6s. Last read position: */*
> ERROR 2014-11-10 11:25:11 IlluminaBasecallsConverter Failure
> encountered in worker thread; attempting to shut down remaining worker
> threads and terminate ...
> java.lang.InterruptedException
> at java.lang.Object.wait(Native Method)
> at java.lang.Object.wait(Object.java:503)
> at
> picard.illumina.IlluminaBasecallsConverter$TileReadAggregator.awaitWorkComplete(IlluminaBasecallsConverter.java:695)
> at
> picard.illumina.IlluminaBasecallsConverter.doTileProcessing(IlluminaBasecallsConverter.java:311)
> at
> picard.illumina.IlluminaBasecallsToFastq.doWork(IlluminaBasecallsToFastq.java:186)
> at
> picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:187)
> at
> picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:89)
> at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:99)
>
> Anybody have experience parsing nextseq data will these tools?
> The code does refer to nextseq, but I'm not sure how well tested it is.
>
> Brad
>
>
>
>
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