Hi all,
I have a small problem :
java -jar ~/Downloads/picard/picard.jar IlluminaBasecallsToFastq BASECALLS_DIR=./raw/19854859/Data/Intensities/BaseCalls/ LANE=1 OUTPUT_PREFIX=1111 RUN_BARCODE=19854859 MACHINE_NAME=M00911 READ_STRUCTURE=151T6M151T FIRST_TILE=1111 TILE_LIMIT=1 FLOWCELL_BARCODE=AR4JF
[Tue Feb 28 04:10:29 EST 2017] picard.illumina.IlluminaBasecallsToFastq BASECALLS_DIR=./raw/19854859/Data/Intensities/BaseCalls LANE=1 OUTPUT_PREFIX=1111 RUN_BARCODE=19854859 MACHINE_NAME=M00911 FLOWCELL_BARCODE=AR4JF READ_STRUCTURE=151T6M151T FIRST_TILE=1111 TILE_LIMIT=1 ADAPTERS_TO_CHECK=[INDEXED, DUAL_INDEXED, NEXTERA_V2, FLUIDIGM] NUM_PROCESSORS=0 APPLY_EAMSS_FILTER=true FORCE_GC=true MAX_READS_IN_RAM_PER_TILE=1200000 MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false 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 GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Feb 28 04:10:29 EST 2017] Executing as root@debian on Linux 3.16.0-4-amd64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_121-b13; Picard version: 2.9.0-9-gb9978f5-SNAPSHOT
[Tue Feb 28 04:10:29 EST 2017] picard.illumina.IlluminaBasecallsToFastq done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=32440320
To get help, see http://broadinstitute.github.io/pica...ml#GettingHelp
Exception in thread "main" picard.PicardException: Could not find a format with available files for the following data types: BaseCalls, PF, Position, QualityScores
at picard.illumina.parser.IlluminaDataProviderFactory.<init>(IlluminaDataProviderFactory.java:173)
at picard.illumina.IlluminaBasecallsConverter.<init>(IlluminaBasecallsConverter.java:250)
at picard.illumina.IlluminaBasecallsToFastq.initialize(IlluminaBasecallsToFastq.java:276)
at picard.illumina.IlluminaBasecallsToFastq.doWork(IlluminaBasecallsToFastq.java:219)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:205)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:94)
at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:104)
What is wrong here ? I can see this but how i can get skip this 3 data types ? or how can i can get a list with all data types and put let`s say null on that 3 ?
root@debian:# java -version
java version "1.8.0_121"
Java(TM) SE Runtime Environment (build 1.8.0_121-b13)
Java HotSpot(TM) 64-Bit Server VM (build 25.121-b13, mixed mode)
root@debian:#
Picard version: 2.9.0-9-gb9978f5-SNAPSHOT
Thank you in advance !
I have a small problem :
java -jar ~/Downloads/picard/picard.jar IlluminaBasecallsToFastq BASECALLS_DIR=./raw/19854859/Data/Intensities/BaseCalls/ LANE=1 OUTPUT_PREFIX=1111 RUN_BARCODE=19854859 MACHINE_NAME=M00911 READ_STRUCTURE=151T6M151T FIRST_TILE=1111 TILE_LIMIT=1 FLOWCELL_BARCODE=AR4JF
[Tue Feb 28 04:10:29 EST 2017] picard.illumina.IlluminaBasecallsToFastq BASECALLS_DIR=./raw/19854859/Data/Intensities/BaseCalls LANE=1 OUTPUT_PREFIX=1111 RUN_BARCODE=19854859 MACHINE_NAME=M00911 FLOWCELL_BARCODE=AR4JF READ_STRUCTURE=151T6M151T FIRST_TILE=1111 TILE_LIMIT=1 ADAPTERS_TO_CHECK=[INDEXED, DUAL_INDEXED, NEXTERA_V2, FLUIDIGM] NUM_PROCESSORS=0 APPLY_EAMSS_FILTER=true FORCE_GC=true MAX_READS_IN_RAM_PER_TILE=1200000 MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false 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 GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Feb 28 04:10:29 EST 2017] Executing as root@debian on Linux 3.16.0-4-amd64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_121-b13; Picard version: 2.9.0-9-gb9978f5-SNAPSHOT
[Tue Feb 28 04:10:29 EST 2017] picard.illumina.IlluminaBasecallsToFastq done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=32440320
To get help, see http://broadinstitute.github.io/pica...ml#GettingHelp
Exception in thread "main" picard.PicardException: Could not find a format with available files for the following data types: BaseCalls, PF, Position, QualityScores
at picard.illumina.parser.IlluminaDataProviderFactory.<init>(IlluminaDataProviderFactory.java:173)
at picard.illumina.IlluminaBasecallsConverter.<init>(IlluminaBasecallsConverter.java:250)
at picard.illumina.IlluminaBasecallsToFastq.initialize(IlluminaBasecallsToFastq.java:276)
at picard.illumina.IlluminaBasecallsToFastq.doWork(IlluminaBasecallsToFastq.java:219)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:205)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:94)
at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:104)
What is wrong here ? I can see this but how i can get skip this 3 data types ? or how can i can get a list with all data types and put let`s say null on that 3 ?
root@debian:# java -version
java version "1.8.0_121"
Java(TM) SE Runtime Environment (build 1.8.0_121-b13)
Java HotSpot(TM) 64-Bit Server VM (build 25.121-b13, mixed mode)
root@debian:#
Picard version: 2.9.0-9-gb9978f5-SNAPSHOT
Thank you in advance !
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