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Indel Realignment stops but gives no error
It's not the first time I run NEXT-seq pipeline on fastq files. It works for me several times and I never got a problem. But it's only one sample which drives me crazy because during the indel realignment via GATK, the processes ends in chromosome 9 but gives no error, here is the tail of the log
INFO 10:57:36,310 ProgressMeter - 7:57136589 3.7736356E7 16.5 m 26.0 s 41.7% 39.6 m 23.1 m INFO 10:58:06,312 ProgressMeter - 7:94166979 3.8936404E7 17.0 m 26.0 s 42.9% 39.6 m 22.6 m INFO 10:58:36,313 ProgressMeter - 7:116838457 3.9836497E7 17.5 m 26.0 s 43.6% 40.1 m 22.6 m INFO 10:59:06,315 ProgressMeter - 7:152055822 4.1036547E7 18.0 m 26.0 s 44.8% 40.2 m 22.2 m INFO 10:59:36,316 ProgressMeter - 8:31716097 4.2233863E7 18.5 m 26.0 s 46.0% 40.2 m 21.7 m INFO 11:00:06,423 ProgressMeter - 8:85353783 4.3434018E7 19.0 m 26.0 s 47.7% 39.8 m 20.8 m INFO 11:00:36,425 ProgressMeter - 8:104075325 4.4434162E7 19.5 m 26.0 s 48.4% 40.3 m 20.8 m INFO 11:01:06,426 ProgressMeter - 9:6600457 4.5663137E7 20.0 m 26.0 s 49.9% 40.1 m 20.1 m INFO 11:01:36,428 ProgressMeter - 9:67965301 4.6863186E7 20.5 m 26.0 s 51.9% 39.5 m 19.0 m INFO 11:02:04,323 GATKRunReport - Uploaded run statistics report to AWS S3
Of course the out bam file here is truncated at chromosome 9, but the input sorted bam file isn't. Also the indel target interval which was created in the previous step via GATK RealignerTargetCreator include all chromosomes not just the first 9. How do I solve this problem ? I tried re-aligning reads and reprocess it several time but nothing change I keep getting a truncation. It's only happening with this sample.
Here is my command
nohup /usr/bin/jre1.7.0_51/bin/java -jar /usr/bin/GenomeAnalysisTK.jar -T IndelRealigner --log_to_file families/BP/log/$filename.indelrealigner.log -I families/BP/bam/$filename.dedup.bam -R $maindir/genome/hg19.fa -targetIntervals families/BP/bam/$filename.target_intervals.list -o families/BP/bam/$filename.realigned.bam -known $maindir/databases/Mills_and_1000G_gold_standard.indels.hg19.vcf &