To celebrate the release of GATK 4.0, we are giving away free credits for running the GATK4 Best Practices pipelines in FireCloud, our secure online analysis portal. It’s first come first serve, so sign up now to claim your free credits worth $250. Sponsored by Google Cloud. Learn more at https://software.broadinstitute.org/firecloud/documentation/freecredits

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 -Djava.io.tmpdir=./ -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!

Issue · Github
by Sheila

Issue Number
1162
State
closed
Last Updated
Assignee
Array
Milestone
Array
Closed By
vdauwera

Best Answer

Answers

Sign In or Register to comment.