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SplitNCigarReads take a long time

Hi, GATK team:
I got in trouble while using SplitNCigarReads in GATK.

INFO 12:57:51,153 ProgressMeter - chrM:16557 5.8048662E7 88.2 m 91.0 s 98.7% 89.3 m 70.0 s
INFO 12:58:21,164 ProgressMeter - chrM:16557 5.8352949E7 88.7 m 91.0 s 98.7% 89.8 m 71.0 s
INFO 12:58:51,305 ProgressMeter - chrM:16557 5.9379541E7 89.2 m 90.0 s 98.7% 90.4 m 71.0 s
INFO 12:59:21,317 ProgressMeter - chrM:16557 6.0129818E7 89.7 m 89.0 s 98.7% 90.9 m 72.0 s
INFO 12:59:51,328 ProgressMeter - chrM:16557 6.0608243E7 90.2 m 89.0 s 98.7% 91.4 m 72.0 s
INFO 13:00:21,338 ProgressMeter - chrM:16557 6.0883019E7 90.7 m 89.0 s 98.7% 91.9 m 72.0 s
INFO 13:05:07,709 ProgressMeter - chrM:16557 6.0883019E7 95.4 m 94.0 s 98.7% 96.7 m 76.0 s
INFO 13:05:46,225 ProgressMeter - chrM:16557 6.1509252E7 95.9 m 93.0 s 98.7% 97.2 m 77.0 s
INFO 13:06:16,236 ProgressMeter - chrM:16557 6.200168E7 96.6 m 93.0 s 98.7% 97.9 m 77.0 s
INFO 13:06:46,246 ProgressMeter - chrM:16557 6.200168E7 97.1 m 93.0 s 98.7% 98.4 m 78.0 s
INFO 13:07:54,627 ProgressMeter - chrM:16557 6.200168E7 98.2 m 95.0 s 98.7% 99.5 m 78.0 s
INFO 13:10:39,906 ProgressMeter - chrM:16557 6.200168E7 101.0 m 97.0 s 98.7% 102.3 m 81.0 s
INFO 13:11:10,129 ProgressMeter - chrM:16557 6.200168E7 101.5 m 98.0 s 98.7% 102.8 m 81.0 s
INFO 13:11:40,288 ProgressMeter - chrM:16557 6.200168E7 102.0 m 98.0 s 98.7% 103.3 m 81.0 s
INFO 13:13:13,893 ProgressMeter - chrM:16557 6.200168E7 103.5 m 100.0 s 98.7% 104.9 m 83.0 s

the logs show that it seems stopped at 13:13:13 ,after a long time (7days~~~), still no update.
I' ve search for this , it seems that there are a lot of reads map to this area(chrM:16557 nearby).
how can i solve this?

sincerely,
Xin

Answers

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