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Very long run-time - GATK HaplotypeCaller GVCF with Ion proton reads

HyunminHyunmin Seoul, KoreaMember

I analyzing the proton reads using GATK Haplotypecaller.

but I have an very long run-time to analyze this data with below command.

gatk -Xmx48g -T HaplotypeCaller -nct 8 -R hg19.fasta -I IonXpress_022_R_2014_03_25_00_24_38_user_PRO-28-20140325_TS13217-070A-WD_1_Auto_user_PRO-28-20140325_TS13217-070A-WD_1_54.bam --genotyping_mode DISCOVERY -stand_emit_conf 10 -stand_call_conf 30 --emitRefConfidence GVCF -L /BiO/BioPeople/brandon/test_nextflow/proton_multisample/ref/AmpliSeqExome.20131001.designed.bed -o IonXpress_022_R_2014_03_25_00_24_38_user_PRO-28-20140325_TS13217-070A-WD_1_Auto_user_PRO-28-20140325_TS13217-070A-WD_1_54.g.vcf

The stderr message is..

INFO 13:23:53,732 ProgressMeter - chr1:11141303 2.29214957E8 3.3 h 51.0 s 0.7% 19.1 d 19.0 d
INFO 13:24:53,734 ProgressMeter - chr1:11142957 2.29627629E8 3.3 h 51.0 s 0.7% 19.2 d 19.1 d
INFO 13:25:53,736 ProgressMeter - chr1:11151689 2.30454171E8 3.3 h 51.0 s 0.7% 19.2 d 19.1 d
INFO 13:26:53,738 ProgressMeter - chr1:11173128 2.33360023E8 3.3 h 51.0 s 0.7% 19.2 d 19.1 d
INFO 13:27:53,740 ProgressMeter - chr1:11177210 2.35026772E8 3.3 h 51.0 s 0.7% 19.3 d 19.1 d

I think 19 day is abnormal time with targeted exome data.

Is it normal? or any suggestion?

Thanks in advance!

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by Sheila

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