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problem with variant calling

Ahmed_AljumailiAhmed_Aljumaili UKMember
edited December 2016 in Ask the GATK team

Hi All,
I am calling variants by using HaplotypeCaller, it runs with no error untill now, but the problem is the progress still on the percentage 44.6% from more than 30 hours until now. I have pasted what appears on my screen below. I can see the time change and the hours on the right. Thanks

NFO 15:34:23,411 ProgressMeter - 4:91282656 4.57065401E8 27.6 h 3.6 m 44.6% 61.9 h 34.3 h
INFO 15:35:23,412 ProgressMeter - 4:91282656 4.57065401E8 27.6 h 3.6 m 44.6% 62.0 h 34.3 h
INFO 15:36:23,413 ProgressMeter - 4:91282656 4.57065401E8 27.6 h 3.6 m 44.6% 62.0 h 34.4 h
INFO 15:37:23,414 ProgressMeter - 4:91282656 4.57065401E8 27.6 h 3.6 m 44.6% 62.0 h 34.4 h
INFO 15:38:23,415 ProgressMeter - 4:91282656 4.57065401E8 27.7 h 3.6 m 44.6% 62.1 h 34.4 h
INFO 15:39:23,416 ProgressMeter - 4:91282656 4.57065401E8 27.7 h 3.6 m 44.6% 62.1 h 34.4 h
INFO 15:40:23,417 ProgressMeter - 4:91282656 4.57065401E8 27.7 h 3.6 m 44.6% 62.1 h 34.4 h
INFO 15:41:23,418 ProgressMeter - 4:91282656 4.57065401E8 27.7 h 3.6 m 44.6% 62.2 h 34.5 h
INFO 15:42:23,419 ProgressMeter - 4:91282656 4.57065401E8 27.7 h 3.6 m 44.6% 62.2 h 34.5 h
INFO 15:43:23,420 ProgressMeter - 4:91282656 4.57065401E8 27.7 h 3.6 m 44.6% 62.3 h 34.5 h
INFO 15:44:23,421 ProgressMeter - 4:91282656 4.57065401E8 27.8 h 3.6 m 44.6% 62.3 h 34.5 h
INFO 15:45:23,423 ProgressMeter - 4:91282656 4.57065401E8 27.8 h 3.6 m 44.6% 62.3 h 34.5 h
INFO 15:46:23,424 ProgressMeter - 4:91282656 4.57065401E8 27.8 h 3.6 m 44.6% 62.4 h 34.6 h
INFO 15:47:23,425 ProgressMeter - 4:91282656 4.57065401E8 27.8 h 3.7 m 44.6% 62.4 h 34.6 h
INFO 15:48:23,426 ProgressMeter - 4:91282656 4.57065401E8 27.8 h 3.7 m 44.6% 62.4 h 34.6 h
INFO 15:49:23,427 ProgressMeter - 4:91282656 4.57065401E8 27.8 h 3.7 m 44.6% 62.5 h 34.6 h
INFO 15:50:23,428 ProgressMeter - 4:91282656 4.57065401E8 27.9 h 3.7 m 44.6% 62.5 h 34.7 h
INFO 15:51:23,429 ProgressMeter - 4:91282656 4.57065401E8 27.9 h 3.7 m 44.6% 62.6 h 34.7

Best Answers

Answers

  • shleeshlee CambridgeMember, Broadie ✭✭✭✭✭

    Hi @Ahmed_Aljumaili,

    I deleted your earlier post because it appears to be a duplicate of this one. Can you help me understand what exactly is the problem? The output you've posted above is the ProgressMeter and contains no errors. I believe the progress times that are given are estimates of progress and so they are not necessarily exact.

  • Dear Shlee,
    Thanks for replying, there is no error but also no progress. The progress stays on 44.6%
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