interrupted ngless run lock1

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Ulrike Löber

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Jan 7, 2021, 6:58:43 AM1/7/21
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Deal all,
I ran an ngless instance with parallel which was somehow interrupted. From the resubmitted jobs I'm not sure whether this is running or not. It seems to stop with:
Does this mean the samples are still locked and how do I resubmit it in a clean way?
Best wishes,
Ulrike

Luis Pedro Coelho

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Jan 11, 2021, 3:55:16 AM1/11/21
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Hi Ulrike,

The locks expire after 1 hour. So, eventually, it should be possible to run them again.

You can, in principle, also just remove the lock files and things will be fine, but just make sure to only remove files with the name xxxx.lock

Best
Luis

Luis Pedro Coelho | Fudan University | http://luispedro.org
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ullo...@googlemail.com

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Mar 3, 2021, 4:22:40 AM3/3/21
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Thanks Luis!
I currently have a "similar" problem with the parallel module. Somehow different ngless-partial dirs are created for the same task, such that the collect function never gets executed. How can I avoid this and why does that happen?
These for example are all gmgc mapping instances and it runs through the same samples over and over again and never finish
-rw-r--r-- 1 uloeber uloeber_usr      3407 Feb 26 01:54 script.ngl
-rw-r--r-- 1 uloeber uloeber_usr 656952776 Feb 26 01:57 partial.S104.tsv.gz
-rw-r--r-- 1 uloeber uloeber_usr 659400070 Feb 26 03:26 partial.S105.tsv.gz
-rw-r--r-- 1 uloeber uloeber_usr 671277624 Feb 26 04:04 partial.S106.tsv.gz
-rw-r--r-- 1 uloeber uloeber_usr 637177155 Feb 27 21:07 partial.S11.tsv.gz
-rw-r--r-- 1 uloeber uloeber_usr 660308610 Feb 28 12:47 partial.S110.tsv.gz
-rw-r--r-- 1 uloeber uloeber_usr 655226100 Feb 28 21:31 partial.S112.tsv.gz
-rw-r--r-- 1 uloeber uloeber_usr 663248091 Mar  1 01:19 partial.S111.tsv.gz
-rw-r--r-- 1 uloeber uloeber_usr 661682719 Mar  1 17:37 partial.S113.tsv.gz
-rw-r--r-- 1 uloeber uloeber_usr 656442568 Mar  2 00:52 partial.S114.tsv.gz
-rw-r--r-- 1 uloeber uloeber_usr 662755489 Mar  2 08:52 partial.S115.tsv.gz
-rw-r--r-- 1 uloeber uloeber_usr 662433570 Mar  2 22:06 partial.S116.tsv.gz
-rw-r--r-- 1 uloeber uloeber_usr 657533419 Mar  3 06:26 partial.S117.tsv.gz
WGS/MOCATstruc] $ ll -tr ngless-partials/7b6bd26d
total 7813313
-rw-r--r-- 1 uloeber uloeber_usr      3407 Feb 26 02:17 script.ngl
-rw-r--r-- 1 uloeber uloeber_usr 665069519 Feb 26 02:20 partial.S104.tsv.gz
-rw-r--r-- 1 uloeber uloeber_usr 665794289 Feb 26 03:53 partial.S105.tsv.gz
-rw-r--r-- 1 uloeber uloeber_usr 683467018 Feb 26 04:31 partial.S106.tsv.gz
-rw-r--r-- 1 uloeber uloeber_usr 637505397 Feb 27 21:19 partial.S11.tsv.gz
-rw-r--r-- 1 uloeber uloeber_usr 668998638 Feb 28 13:23 partial.S110.tsv.gz
-rw-r--r-- 1 uloeber uloeber_usr 661033778 Feb 28 22:06 partial.S112.tsv.gz
-rw-r--r-- 1 uloeber uloeber_usr 673077345 Mar  1 01:47 partial.S111.tsv.gz
-rw-r--r-- 1 uloeber uloeber_usr 670871190 Mar  1 18:05 partial.S113.tsv.gz
-rw-r--r-- 1 uloeber uloeber_usr 666899014 Mar  2 01:23 partial.S114.tsv.gz
-rw-r--r-- 1 uloeber uloeber_usr 672149305 Mar  2 09:16 partial.S115.tsv.gz
-rw-r--r-- 1 uloeber uloeber_usr 670356664 Mar  2 22:34 partial.S116.tsv.gz
-rw-r--r-- 1 uloeber uloeber_usr 665361382 Mar  3 06:50 partial.S117.tsv.gz
WGS/MOCATstruc] $ ll -tr ngless-partials/feade545/
total 114625
-rw-r--r-- 1 uloeber uloeber_usr     3407 Feb 26 11:35 script.ngl
-rw-r--r-- 1 uloeber uloeber_usr 13380823 Feb 26 11:35 partial.S104.tsv.gz
-rw-r--r-- 1 uloeber uloeber_usr  9859061 Feb 28 05:19 partial.S11.tsv.gz
-rw-r--r-- 1 uloeber uloeber_usr 13665744 Feb 28 23:34 partial.S110.tsv.gz
-rw-r--r-- 1 uloeber uloeber_usr 13163441 Mar  1 07:51 partial.S112.tsv.gz
-rw-r--r-- 1 uloeber uloeber_usr 13518044 Mar  1 10:59 partial.S111.tsv.gz
-rw-r--r-- 1 uloeber uloeber_usr 13595413 Mar  2 03:45 partial.S113.tsv.gz
-rw-r--r-- 1 uloeber uloeber_usr 13300816 Mar  2 11:43 partial.S114.tsv.gz
-rw-r--r-- 1 uloeber uloeber_usr 13466349 Mar  2 18:47 partial.S115.tsv.gz
-rw-r--r-- 1 uloeber uloeber_usr 13322513 Mar  3 08:44 partial.S116.tsv.gz
WGS/MOCATstruc] $ ll -tr ngless-partials/66f89a1b/
total 7
-rw-r--r-- 1 uloeber uloeber_usr 3407 Feb 26 04:50 script.ngl
-rw-r--r-- 1 uloeber uloeber_usr  216 Feb 26 04:50 partial.S104.tsv.gz
-rw-r--r-- 1 uloeber uloeber_usr  218 Feb 26 06:32 partial.S105.tsv.gz
-rw-r--r-- 1 uloeber uloeber_usr  217 Feb 26 07:09 partial.S106.tsv.gz
-rw-r--r-- 1 uloeber uloeber_usr  213 Feb 27 23:41 partial.S11.tsv.gz
-rw-r--r-- 1 uloeber uloeber_usr  217 Feb 28 16:16 partial.S110.tsv.gz
-rw-r--r-- 1 uloeber uloeber_usr  219 Mar  1 00:53 partial.S112.tsv.gz
-rw-r--r-- 1 uloeber uloeber_usr  217 Mar  1 04:27 partial.S111.tsv.gz
-rw-r--r-- 1 uloeber uloeber_usr  219 Mar  1 20:42 partial.S113.tsv.gz
-rw-r--r-- 1 uloeber uloeber_usr  217 Mar  2 04:06 partial.S114.tsv.gz
-rw-r--r-- 1 uloeber uloeber_usr  213 Mar  2 11:54 partial.S115.tsv.gz
-rw-r--r-- 1 uloeber uloeber_usr  218 Mar  3 01:30 partial.S116.tsv.gz
-rw-r--r-- 1 uloeber uloeber_usr  216 Mar  3 09:31 partial.S117.tsv.gz

Luis Pedro Coelho

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Mar 5, 2021, 11:29:06 PM3/5/21
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That is strange.

Are the script.ngl files in those directories the same?

Best
Luis

Luis Pedro Coelho | Fudan University | http://luispedro.org


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