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FilterSAMReads ReadID pattern in Read_LIST_FILE
I am running FilterSamReads in picardtools with the following command:
java -jar /bioinf/software/picard/picard-1.133/picard.jar FilterSamReads I=20100518_vs_20100518_Bin_42_1-contigs.fa.sorted.bam O=20100518_Bin42_1_unique_reads.bam READ_LIST_FILE=Read_ID.txt FILTER=includeReadList
picard.sam.FilterSamReads INPUT=20100518_vs_20100518_Bin_42_1-contigs.fa.sorted.bam FILTER=includeReadList [OUTPUT SAM/BAM will contain reads that are supplied in the READ_LIST_FILE file] READ_LIST_FILE=Read_ID.txt OUTPUT=20100518_Bin42_1_unique_reads.bam WRITE_READS_FILES=true 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
Executing as [email protected] on Linux 3.0.101-0.35-default amd64; Java HotSpot(TM) 64-Bit Server VM 1.6.0_30-b12; Picard version: 1.133(95818b6e611725775e29d3b4acbaa23747eb3e94_1433169311) IntelDeflater
INFO 2018-02-07 17:23:56 FilterSamReads Filtering [presorted=true] 20100518_vs_20100518_Bin_42_1-contigs.fa.sorted.bam -> OUTPUT=20100518_Bin42_1_unique_reads.bam [sortorder=coordinate]
INFO 2018-02-07 17:23:56 FilterSamReads 0 SAMRecords written to 20100518_Bin42_1_unique_reads.bam
picard.sam.FilterSamReads done. Elapsed time: 0.13 minutes.
but my output .bam file is empty. As far as I figure out, the readIDs in the read list file could not be detected.
In the read list file, I have the read IDs in the following pattern:
Picard gave another output file with *.reads extension. It contains the all read IDs in the input file and the pattern in this file is:
HISEQ04:245:C21W7ACXX:5:2307:9359:64216 1:N:0:CTTGTA BH:ok 2/2 149b aligned read.
My question is the following: what is the correct read ID pattern which should be provided in read list file?
Thanks in advance for your help!