[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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