Hello,
I need your help on using Mutect2. I tried to call somatic mutations using mutect2_multi_sample.wdl in tumor-only mode with make_bamout = true and scatter_count = 50.
It was failed for a small fraction of samples during the task, MergeBamOuts. It appears that, for those samples, a gathered bam file was not sorted and it failed to index the unsorted bam file.
Below is from stderr of a failed sample. Thank you!
[Mon Feb 19 22:57:09 CST 2018] picard.sam.GatherBamFiles done. Elapsed time: 0.29 minutes.
Runtime.totalMemory()=1533542400
Using GATK jar mutect2-gatk4.0.1.2/wgs/tumor-only/cromwell-executions/Mutect2_Multi/5a39fcf2-c68d-4a03-b868-648c0e307351/call-Mutect2/shard-68/Mutect2/ccb28ebf-07b7-40e6-b9ef-0ae57a399b36/call-MergeBamOuts/inputs/software/GATK/gatk-4.0.1.2/gatk-package-4.0.1.2-local.jar defined in environment variable GATK_LOCAL_JAR
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=1 -Xmx6000m -jar gatk-package-4.0.1.2-local.jar GatherBamFiles -I {shard-0.bamout} -I {shard-1.bamout} ... -I {shard-49.bamout} -O unfiltered.vcf.gz.out.bam
-R reference.fasta
[bam_index_core] the alignment is not sorted (K00000:00:H50000000:1:1105:27438:36024): 4613952 > 4613923 in 7-th chr
[bam_index_build2] fail to index the BAM file.
