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I am using GATK for resequencing data of cattle genome
Right now I am using BaseRecalibration and after recalibration I have my GATK report file
For recalibrated bam file my commandline is -
Sample]$ java -Xmx30g -jar GenomeAnalysisTK.jar -T PrintReads -I Sample_realigned.bam -R reference/umd3.1_genome.fa -BQSR Sample_rcal.grp -o Sample_rcal.bam -S LENIENT
But getting problem after processing of 11.8% data, The error message is follows
INFO 20:11:01,971 ProgressMeter - Chr3:12544311 9.15e+07 12.1 h 7.9 m 11.5% 4.4 d 92.8 h INFO 20:12:08,586 ProgressMeter - Chr3:14795199 9.24e+07 12.1 h 7.9 m 11.6% 4.3 d 92.2 h INFO 20:13:12,670 ProgressMeter - Chr3:18812278 9.32e+07 12.1 h 7.8 m 11.8% 4.3 d 91.0 h INFO 20:31:46,929 ProgressMeter - Chr3:19688330 9.34e+07 12.4 h 8.0 m 11.8% 4.4 d 93.0 h INFO 20:31:48,283 GATKRunReport - Uploaded run statistics report to AWS S3
but I tried the same command with intervals and it worked , I have my output bam file with following command
Sample]$ java -Xmx30g -jar GenomeAnalysisTK.jar -T PrintReads -I Sample_realigned.bam -L Chr25 -R reference/umd3.1_genome.fa -BQSR Sample_rcal.grp -o Sample_rcal.bam -S LENIENT
Plaese, could you help me?