Stalling Issue in rMATS Analysis

[veryqun]

Hello,

I’m using rMATS to analyze alternative splicing based on paired-end fastq files. My data includes two groups with 194 samples each, and I’m running the following command:

python /rmats/rmats.py --s1 S1.txt --s2 S2.txt --gtf gencode.v46.primary_assembly.basic.annotation.gtf --bi STAR_binary_index_GRCh38_primary_assembly -t paired --readLength 150 --nthread 13 --variable-read-length --od /result --tmp /result/tmp

The process ran smoothly until sample 93, where it suddenly stalled. The Log.progress.out file of sample 93 in the tmp directory shows the following output:

Is this normal behavior, and is there any way to continue the analysis from this point if I stop the process?

           Time    Speed        Read     Read   Mapped   Mapped   Mapped   Mapped Unmapped Unmapped Unmapped Unmapped
                    M/hr      number   length   unique   length   MMrate    multi   multi+       MM    short    other
Nov 07 07:57:09	Started 1st pass mapping
Nov 07 07:57:23     10.8       41911      300    67.8%    300.0     0.2%     3.6%     0.0%    19.1%     9.2%     0.4%
Nov 07 07:58:27    127.5     2761665      300    68.1%    300.0     0.2%     3.8%     0.0%    18.4%     9.2%     0.3%
Nov 07 07:59:29    140.9     5478413      300    68.4%    300.0     0.2%     3.9%     0.0%    18.2%     9.2%     0.3%
Nov 07 08:00:30    146.8     8195166      300    68.4%    300.0     0.2%     3.9%     0.0%    18.1%     9.2%     0.3%
Nov 07 08:01:32    149.3    10909373      300    68.4%    300.0     0.2%     3.9%     0.0%    18.1%     9.2%     0.3%
Nov 07 08:02:33    151.3    13618512      300    68.3%    300.0     0.2%     3.9%     0.0%    18.2%     9.2%     0.3%
Nov 07 08:03:35    152.3    16327654      300    68.4%    300.0     0.2%     3.9%     0.0%    18.2%     9.3%     0.3%
Nov 07 08:04:37    153.0    19036792      300    68.4%    300.0     0.2%     3.9%     0.0%    18.1%     9.3%     0.3%
Nov 07 08:05:39    153.5    21745947      300    68.4%    300.0     0.2%     3.9%     0.0%    18.1%     9.3%     0.3%
Nov 07 08:06:40    154.2    24460956      300    68.4%    300.0     0.2%     3.9%     0.0%    18.1%     9.2%     0.3%
Nov 07 08:07:41    154.8    27177686      300    68.5%    300.0     0.2%     3.9%     0.0%    18.0%     9.2%     0.3%
Nov 07 08:08:53	Finished 1st pass mapping
Nov 07 08:13:22      1.1       41962      300    61.6%    300.0     0.2%     9.2%     0.1%    19.0%     8.7%     1.4%
Nov 07 08:15:41      7.6      587105      300    61.8%    300.0     0.2%     9.5%     0.1%    18.6%     8.6%     1.4%
Nov 07 08:17:54      9.9     1131622      300    62.1%    300.0     0.2%     9.5%     0.1%    18.4%     8.6%     1.4%
Nov 07 08:20:06     11.1     1674967      300    62.2%    300.0     0.2%     9.5%     0.1%    18.2%     8.6%     1.4%
Nov 07 08:21:06     12.0     2009342      300    62.2%    300.0     0.2%     9.6%     0.1%    18.2%     8.6%     1.4%
Nov 07 08:22:22     11.8     2218311      300    62.2%    300.0     0.2%     9.6%     0.1%    18.2%     8.6%     1.4%
Nov 07 08:23:24     11.4     2343697      300    62.2%    300.0     0.2%     9.6%     0.1%    18.2%     8.6%     1.4%
Nov 07 08:24:41     12.2     2761665      300    62.2%    300.0     0.2%     9.6%     0.1%    18.1%     8.5%     1.4%
Nov 07 08:25:50     11.7     2887050      300    62.3%    300.0     0.2%     9.6%     0.1%    18.1%     8.5%     1.4%
Nov 07 08:27:00     12.4     3305018      300    62.3%    300.0     0.2%     9.6%     0.1%    18.1%     8.5%     1.4%
Nov 07 08:28:17     11.9     3430406      300    62.3%    300.0     0.2%     9.6%     0.1%    18.0%     8.5%     1.4%
Nov 07 08:29:25     12.6     3848363      300    62.4%    300.0     0.2%     9.6%     0.1%    18.0%     8.5%     1.4%
Nov 07 08:30:45     12.1     3973758      300    62.4%    300.0     0.2%     9.6%     0.1%    18.0%     8.5%     1.4%
Nov 07 08:31:58     12.7     4433518      300    62.4%    300.0     0.2%     9.6%     0.1%    18.0%     8.5%     1.4%
Nov 07 08:33:15     12.2     4517102      300    62.4%    300.0     0.2%     9.6%     0.1%    18.0%     8.5%     1.4%
Nov 07 08:34:16     12.9     4976855      300    62.4%    300.0     0.2%     9.6%     0.1%    18.0%     8.5%     1.4%
Nov 07 08:35:47     12.3     5060457      300    62.4%    300.0     0.2%     9.6%     0.1%    17.9%     8.5%     1.4%
Nov 07 08:36:54     12.9     5562012      300    62.5%    300.0     0.2%     9.6%     0.1%    17.9%     8.5%     1.4%
Nov 07 08:38:15     12.4     5603812      300    62.4%    300.0     0.2%     9.6%     0.1%    17.9%     8.5%     1.4%
Nov 07 08:40:43     12.4     6147151      300    62.4%    300.0     0.2%     9.6%     0.1%    17.9%     8.5%     1.4%
Nov 07 08:41:47     13.0     6648709      300    62.4%    300.0     0.2%     9.6%     0.1%    17.9%     8.5%     1.4%
Nov 07 08:43:09     12.5     6690509      300    62.4%    300.0     0.2%     9.6%     0.1%    17.9%     8.5%     1.4%
Nov 07 08:44:17     13.0     7192064      300    62.5%    300.0     0.2%     9.7%     0.1%    17.8%     8.5%     1.4%
Nov 07 08:45:29     12.6     7233864      300    62.5%    300.0     0.2%     9.7%     0.1%    17.8%     8.5%     1.4%
Nov 07 08:46:46     13.0     7735405      300    62.5%    300.0     0.2%     9.7%     0.1%    17.8%     8.5%     1.4%
Nov 07 08:47:59     12.7     7819007      300    62.5%    300.0     0.2%     9.7%     0.1%    17.8%     8.5%     1.4%
Nov 07 08:49:00     13.0     8236963      300    62.5%    300.0     0.2%     9.7%     0.1%    17.8%     8.5%     1.4%
Nov 07 08:50:05     12.8     8320564      300    62.5%    300.0     0.2%     9.7%     0.1%    17.8%     8.5%     1.4%
Nov 07 08:51:05     12.9     8613124      300    62.5%    300.0     0.2%     9.7%     0.1%    17.8%     8.5%     1.4%
Nov 07 08:52:29     12.8     8863914      300    62.5%    300.0     0.2%     9.7%     0.1%    17.8%     8.5%     1.4%
Nov 07 08:53:38     13.0     9198277      300    62.5%    300.0     0.2%     9.7%     0.1%    17.8%     8.5%     1.4%
Nov 07 08:54:48     12.9     9407259      300    62.5%    300.0     0.2%     9.7%     0.1%    17.8%     8.5%     1.4%
Nov 07 08:55:51     12.9     9658044      300    62.5%    300.0     0.2%     9.7%     0.1%    17.8%     8.5%     1.4%
Nov 07 08:56:57     13.0     9908813      300    62.5%    300.0     0.2%     9.7%     0.1%    17.8%     8.5%     1.4%
Nov 07 08:57:59     12.9    10117470      300    62.5%    300.0     0.2%     9.7%     0.1%    17.8%     8.5%     1.4%
Nov 07 08:59:20     13.0    10450902      300    62.5%    300.0     0.2%     9.7%     0.1%    17.8%     8.5%     1.4%
Nov 07 09:00:23     13.0    10659300      300    62.5%    300.0     0.2%     9.7%     0.1%    17.8%     8.5%     1.4%
Nov 07 09:01:35     13.1    10992728      300    62.5%    300.0     0.2%     9.7%     0.1%    17.8%     8.5%     1.4%
Nov 07 09:02:35     12.9    11117773      300    62.5%    300.0     0.2%     9.7%     0.1%    17.8%     8.5%     1.4%
Nov 07 09:03:36     13.0    11409521      300    62.5%    300.0     0.2%     9.7%     0.1%    17.8%     8.5%     1.4%
Nov 07 09:04:38     13.0    11617919      300    62.5%    300.0     0.2%     9.7%     0.1%    17.8%     8.5%     1.4%
Nov 07 09:05:47     13.0    11826313      300    62.5%    300.0     0.2%     9.7%     0.1%    17.8%     8.5%     1.4%
Nov 07 09:07:05     13.0    12159736      300    62.4%    300.0     0.2%     9.7%     0.1%    17.9%     8.5%     1.4%
Nov 07 09:08:16     13.0    12368129      300    62.4%    300.0     0.2%     9.7%     0.1%    17.9%     8.5%     1.4%
Nov 07 09:09:16     13.1    12701561      300    62.4%    300.0     0.2%     9.7%     0.1%    17.9%     8.5%     1.4%
Nov 07 09:10:23     13.0    12826610      300    62.4%    300.0     0.2%     9.7%     0.1%    17.9%     8.5%     1.4%
Nov 07 09:11:32     13.1    13243392      300    62.4%    300.0     0.2%     9.7%     0.1%    17.9%     8.6%     1.4%
Nov 07 09:12:46     13.0    13326759      300    62.4%    300.0     0.2%     9.7%     0.1%    17.9%     8.6%     1.4%
Nov 07 09:13:47     13.1    13743544      300    62.4%    300.0     0.2%     9.7%     0.1%    17.9%     8.5%     1.4%
Nov 07 09:15:12     13.0    13868582      300    62.4%    300.0     0.2%     9.7%     0.1%    17.9%     8.5%     1.4%
Nov 07 09:16:14     13.1    14243695      300    62.4%    300.0     0.2%     9.7%     0.1%    17.9%     8.5%     1.4%
Nov 07 09:17:18     13.0    14368729      300    62.4%    300.0     0.2%     9.7%     0.1%    17.9%     8.5%     1.4%
Nov 07 09:18:20     13.1    14702161      300    62.4%    300.0     0.2%     9.7%     0.1%    17.9%     8.5%     1.4%
Nov 07 09:19:53     13.0    14910561      300    62.4%    300.0     0.2%     9.7%     0.1%    17.9%     8.5%     1.4%
Nov 07 09:20:53     13.1    15285675      300    62.4%    300.0     0.2%     9.7%     0.1%    17.9%     8.5%     1.4%
Nov 07 09:22:23     13.0    15452389      300    62.4%    300.0     0.2%     9.7%     0.1%    17.9%     8.5%     1.4%
Nov 07 09:23:24     13.2    15869175      300    62.4%    300.0     0.2%     9.7%     0.1%    17.9%     8.6%     1.4%
Nov 07 09:24:47     13.0    15994222      300    62.4%    300.0     0.2%     9.7%     0.1%    17.9%     8.6%     1.4%
Nov 07 09:25:50     13.1    16369335      300    62.4%    300.0     0.2%     9.7%     0.1%    17.9%     8.6%     1.4%
Nov 07 09:27:05     13.0    16536045      300    62.4%    300.0     0.2%     9.7%     0.1%    17.9%     8.6%     1.4%
Nov 07 09:28:08     13.1    16869481      300    62.4%    300.0     0.2%     9.7%     0.1%    17.9%     8.6%     1.4%
Nov 07 09:29:17     13.1    17077878      300    62.4%    300.0     0.2%     9.7%     0.1%    17.9%     8.6%     1.4%
Nov 07 09:30:18     13.1    17327956      300    62.4%    300.0     0.2%     9.7%     0.1%    17.9%     8.6%     1.4%
Nov 07 09:31:22     13.1    17578027      300    62.4%    300.0     0.2%     9.7%     0.1%    17.9%     8.6%     1.4%
Nov 07 09:32:25     13.1    17703070      300    62.4%    300.0     0.2%     9.7%     0.1%    17.9%     8.6%     1.4%
Nov 07 09:33:54     13.1    18119845      300    62.4%    300.0     0.2%     9.7%     0.1%    17.9%     8.6%     1.4%
Nov 07 09:34:55     13.1    18328243      300    62.4%    300.0     0.2%     9.7%     0.1%    17.8%     8.6%     1.4%
Nov 07 09:35:56     13.2    18620008      300    62.5%    300.0     0.2%     9.7%     0.1%    17.8%     8.5%     1.4%
Nov 07 09:37:11     13.1    18786711      300    62.5%    300.0     0.2%     9.7%     0.1%    17.8%     8.6%     1.4%
Nov 07 09:38:23     13.2    19161826      300    62.4%    300.0     0.2%     9.7%     0.1%    17.8%     8.6%     1.4%
Nov 07 09:39:31     13.1    19328559      300    62.4%    300.0     0.2%     9.7%     0.1%    17.8%     8.6%     1.4%
Nov 07 09:40:39     13.2    19661993      300    62.4%    300.0     0.2%     9.7%     0.1%    17.8%     8.6%     1.4%
Nov 07 09:41:55     13.1    19870376      300    62.5%    300.0     0.2%     9.7%     0.1%    17.8%     8.6%     1.4%
Nov 07 09:43:00     13.2    20203811      300    62.5%    300.0     0.2%     9.7%     0.1%    17.8%     8.6%     1.4%
Nov 07 09:44:13     13.1    20412211      300    62.5%    300.0     0.2%     9.7%     0.1%    17.8%     8.6%     1.4%
Nov 07 09:45:13     13.2    20662277      300    62.5%    300.0     0.2%     9.7%     0.1%    17.8%     8.6%     1.4%
Nov 07 09:46:32     13.2    20954040      300    62.5%    300.0     0.2%     9.7%     0.1%    17.8%     8.6%     1.4%
Nov 07 09:47:38     13.2    21204112      300    62.5%    300.0     0.2%     9.7%     0.1%    17.8%     8.6%     1.4%
Nov 07 09:48:51     13.2    21495862      300    62.5%    300.0     0.2%     9.7%     0.1%    17.8%     8.6%     1.4%
Nov 07 09:49:54     13.1    21620902      300    62.5%    300.0     0.2%     9.7%     0.1%    17.8%     8.6%     1.4%
Nov 07 09:50:58     13.2    21954334      300    62.5%    300.0     0.2%     9.7%     0.1%    17.8%     8.6%     1.4%
Nov 07 09:52:05     13.1    22121060      300    62.5%    300.0     0.2%     9.7%     0.1%    17.8%     8.6%     1.4%
Nov 07 09:53:19     13.2    22454751      300    62.5%    300.0     0.2%     9.7%     0.1%    17.8%     8.6%     1.4%
Nov 07 09:54:20     13.1    22621936      300    62.5%    300.0     0.2%     9.7%     0.1%    17.8%     8.6%     1.4%
Nov 07 09:55:21     13.2    22956304      300    62.5%    300.0     0.2%     9.7%     0.1%    17.8%     8.5%     1.4%
Nov 07 09:56:50     13.1    23165282      300    62.5%    300.0     0.2%     9.7%     0.1%    17.8%     8.5%     1.4%
Nov 07 09:57:56     13.2    23499647      300    62.5%    300.0     0.2%     9.7%     0.1%    17.8%     8.5%     1.4%
Nov 07 09:59:10     13.2    23708627      300    62.5%    300.0     0.2%     9.7%     0.1%    17.8%     8.5%     1.4%
Nov 07 10:00:12     13.2    24042997      300    62.5%    300.0     0.2%     9.7%     0.1%    17.8%     8.5%     1.4%
Nov 07 10:01:12     13.2    24210179      300    62.5%    300.0     0.2%     9.7%     0.1%    17.8%     8.5%     1.4%
Nov 07 10:02:12     13.2    24377364      300    62.5%    300.0     0.2%     9.7%     0.1%    17.8%     8.5%     1.4%
Nov 07 10:03:33     13.2    24711729      300    62.5%    300.0     0.2%     9.7%     0.1%    17.8%     8.5%     1.4%
Nov 07 10:04:35     13.1    24878911      300    62.5%    300.0     0.2%     9.7%     0.1%    17.8%     8.5%     1.4%
Nov 07 10:06:02     13.2    25255079      300    62.5%    300.0     0.2%     9.7%     0.1%    17.7%     8.5%     1.4%
Nov 07 10:07:02     13.2    25464054      300    62.5%    300.0     0.2%     9.7%     0.1%    17.7%     8.5%     1.4%
Nov 07 10:08:05     13.2    25756629      300    62.5%    300.0     0.2%     9.7%     0.1%    17.7%     8.5%     1.4%
Nov 07 10:09:12     13.2    25923812      300    62.5%    300.0     0.2%     9.7%     0.1%    17.7%     8.5%     1.4%
Nov 07 10:10:26     13.2    26258179      300    62.5%    300.0     0.2%     9.7%     0.1%    17.7%     8.5%     1.4%
Nov 07 10:11:33     13.2    26467156      300    62.5%    300.0     0.2%     9.7%     0.1%    17.7%     8.5%     1.4%
Nov 07 10:12:44     13.2    26801523      300    62.5%    300.0     0.2%     9.7%     0.1%    17.7%     8.5%     1.4%
Nov 07 10:13:51     13.2    27010506      300    62.5%    300.0     0.2%     9.7%     0.1%    17.7%     8.5%     1.4%
Nov 07 10:14:53     13.2    27219482      300    62.5%    300.0     0.2%     9.7%     0.1%    17.7%     8.5%     1.4%
Nov 07 10:16:09     13.2    27470258      300    62.5%    300.0     0.2%     9.7%     0.1%    17.7%     8.5%     1.4%
Nov 07 10:17:15     13.2    27762827      300    62.6%    300.0     0.2%     9.7%     0.1%    17.7%     8.5%     1.4%
Nov 07 10:18:37     13.2    28013598      300    62.6%    300.0     0.2%     9.7%     0.1%    17.7%     8.5%     1.4%
Nov 07 10:19:39     13.2    28264374      300    62.6%    300.0     0.2%     9.7%     0.1%    17.7%     8.5%     1.4%
Nov 07 10:21:05     13.2    28556943      300    62.6%    300.0     0.2%     9.7%     0.1%    17.7%     8.5%     1.4%
Nov 07 10:22:07     13.2    28807718      300    62.6%    300.0     0.2%     9.7%     0.1%    17.7%     8.5%     1.4%

Thank you very much for your assistance!

[EricKutschera]

The Log.progress.out is from STAR. Based on the log it looks like it may have finished the 2nd pass mapping step and it might be on a sorting step. I'm not sure why STAR would stop making progress without giving an error message

You can find the .bam files from the completed STAR runs in the --tmp dir with names like [datetime]_bam[sample_num]_[replicate_num]/Aligned.sortedByCoord.out.bam. To avoid redoing the alignment for those files you could run STAR directly to get the .bam files for the remaining samples or you could update your --s1 and --s2 files to only have the samples where STAR hasn't been run yet. Then after you have all the .bam files you can use --b1 and --b2 to provide the .bam files to rMATS