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ProgressMeter 100% but the computation won't stop

zhenlizhenli Menlo ParkMember

Hi, I'm using chr21.fa as a reference genome to run the genomic pipeline so I can test my pipeline more quickly. The alignment ran smoothly but when I started to use GATK to do the realignment and base recalibration, when the ProgressMeter get 100%, it won't stop. It just repeat in the same position like this.

INFO 23:09:49,973 ProgressMeter - chr21:48119895 2.920136E7 15.7 h 32.2 m 100.0% 15.7 h 11.0 s
INFO 23:10:49,974 ProgressMeter - chr21:48119895 2.920136E7 15.7 h 32.3 m 100.0% 15.7 h 11.0 s
INFO 23:11:49,976 ProgressMeter - chr21:48119895 2.920136E7 15.7 h 32.3 m 100.0% 15.7 h 11.0 s
INFO 23:12:49,977 ProgressMeter - chr21:48119895 2.920136E7 15.7 h 32.4 m 100.0% 15.7 h 11.0 s
INFO 23:13:50,110 ProgressMeter - chr21:48119895 2.920136E7 15.8 h 32.4 m 100.0% 15.8 h 11.0 s
INFO 23:14:50,111 ProgressMeter - chr21:48119895 2.920136E7 15.8 h 32.4 m 100.0% 15.8 h 11.0 s
INFO 23:15:50,113 ProgressMeter - chr21:48119895 2.920136E7 15.8 h 32.5 m 100.0% 15.8 h 11.0 s
INFO 23:16:50,115 ProgressMeter - chr21:48119895 2.920136E7 15.8 h 32.5 m 100.0% 15.8 h 11.0 s
INFO 23:17:50,116 ProgressMeter - chr21:48119895 2.920136E7 15.8 h 32.5 m 100.0% 15.8 h 11.0 s
INFO 23:18:50,118 ProgressMeter - chr21:48119895 2.920136E7 15.8 h 32.6 m 100.0% 15.8 h 11.0 s
INFO 23:19:50,119 ProgressMeter - chr21:48119895 2.920136E7 15.9 h 32.6 m 100.0% 15.9 h 11.0 s
INFO 23:20:50,121 ProgressMeter - chr21:48119895 2.920136E7 15.9 h 32.6 m 100.0% 15.9 h 11.0 s
INFO 23:21:50,122 ProgressMeter - chr21:48119895 2.920136E7 15.9 h 32.7 m 100.0% 15.9 h 11.0 s
INFO 23:22:50,124 ProgressMeter - chr21:48119895 2.920136E7 15.9 h 32.7 m 100.0% 15.9 h 11.0 s
INFO 23:23:50,125 ProgressMeter - chr21:48119895 2.920136E7 15.9 h 32.7 m 100.0% 15.9 h 11.0 s
INFO 23:24:50,127 ProgressMeter - chr21:48119895 2.920136E7 15.9 h 32.8 m 100.0% 15.9 h 11.0 s
INFO 23:25:50,128 ProgressMeter - chr21:48119895 2.920136E7 16.0 h 32.8 m 100.0% 16.0 h 11.0 s
INFO 23:26:50,130 ProgressMeter - chr21:48119895 2.920136E7 16.0 h 32.8 m 100.0% 16.0 h 11.0 s
INFO 23:27:50,131 ProgressMeter - chr21:48119895 2.920136E7 16.0 h 32.9 m 100.0% 16.0 h 11.0 s

Can someone help to resolve this?

Best Answer

Answers

  • zhenlizhenli Menlo ParkMember

    Thanks for your advice. I think you are right. I will try this. Another question is does the alignment tools like bwa has similar flag as "-L" to specify the regions?

  • pdexheimerpdexheimer Member ✭✭✭✭

    I've never seen such a flag on an aligner. The critical thing here is to keep all of the sequence dictionaries associated with each file consistent, and the only safe way to do that is to maintain consistency in the reference used at every step. In my mind, at least, that safety is worth the extra runtime to align to the full reference

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