RepeatMasker
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rmhubley
FATAL ERROR: RepeatMasker giving up
Hello,
I am attempting to run RepeatMasker on my University's computing cluster. Specifically, I am using your Nexflow pipeline. I have also posted this error on the GitHub page for the Nexflow pipeline.
RepeatMasker finishes successfully when provided with a custom repeat library generated by RepeatModeler. However, when I attempt to annotate the same genome using the Dfam 3.7 database, I encounter the following error for at least one of the Nextflow processes.
FATAL ERROR: RepeatMasker giving up. One or more
batches failed! Unfortunately this type of error
cannot be recovered from. Please submit the following
details to the feedback page at the repeatmasker
website:
http://www.repeatmasker.org
RepeatMasker Version: 4.1.5
Library Version: CONS-Dfam_3.7
Search Engine: ncbi [ 2.14.0+ ]
Command Line: /projects/academic/tkrabben/modules_KrabLab/easybuild/2023.01/software/avx512/MPI/gcc/11.2.0/openmpi/4.1.1/repeatmasker/4.1.5/RepeatMasker-pa 5 -a -engine rmblast -species vertebrata batch-20.fa
Batch Number: 77
Disk Space:
Filesystem 1K-blocks Used Available Use% Mounted on
vast.cbls.ccr.buffalo.edu:/projects 35157227520 32484939776 2672287744 93% /projects
System Memory:
MemTotal: 527869828 kB
MemFree: 310701720 kB
MemAvailable: 318746904 kB
Cached: 11067292 kB
SwapCached: 225168 kB
SwapTotal: 7812092 kB
SwapFree: 5140376 kB
Further details about this problem may be found in
the directory: /projects/academic/tkrabben/MacGuigan/genome_annotations/Mmel_annotation_test_2/Mmel_RepeatMasker/work/23/d917f13ff17f82847233c61f1b4391/RM_3420708.ThuFeb81018352024
The directory that is supposed to contain additional details about the problem is not very informative. Here are the contents of that directory:
$ ls -l /projects/academic/tkrabben/MacGuigan/genome_annotations/Mmel_annotation_test_2/Mmel_RepeatMasker/work/23/d917f13ff17f82847233c61f1b4391/RM_3420708.ThuFeb81018352024
total 332108
-rwx------ 1 dmacguig grp-tkrabben 51000170 Feb 8 10:35 batch-20.fa
-rw-r--r-- 1 dmacguig grp-tkrabben 477528 Feb 8 19:55 batch-20.fa_batch-100.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 544314 Feb 8 19:56 batch-20.fa_batch-101.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 420961 Feb 8 19:54 batch-20.fa_batch-102.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 562524 Feb 8 19:58 batch-20.fa_batch-103.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 477781 Feb 8 19:58 batch-20.fa_batch-104.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 527972 Feb 8 20:00 batch-20.fa_batch-105.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 521687 Feb 8 20:01 batch-20.fa_batch-106.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 439043 Feb 8 20:02 batch-20.fa_batch-107.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 372682 Feb 8 20:03 batch-20.fa_batch-108.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 503546 Feb 8 20:05 batch-20.fa_batch-109.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 454817 Feb 8 20:04 batch-20.fa_batch-110.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 559704 Feb 8 20:07 batch-20.fa_batch-111.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 523691 Feb 8 20:10 batch-20.fa_batch-112.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 504823 Feb 8 20:09 batch-20.fa_batch-113.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 588864 Feb 8 20:12 batch-20.fa_batch-114.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 433995 Feb 8 20:12 batch-20.fa_batch-115.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 528350 Feb 8 20:15 batch-20.fa_batch-116.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 510911 Feb 8 20:25 batch-20.fa_batch-117.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 432411 Feb 8 20:17 batch-20.fa_batch-118.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 499807 Feb 8 20:18 batch-20.fa_batch-119.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 550706 Feb 8 20:21 batch-20.fa_batch-120.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 539879 Feb 8 20:21 batch-20.fa_batch-121.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 476166 Feb 8 20:24 batch-20.fa_batch-122.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 433530 Feb 8 20:24 batch-20.fa_batch-123.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 496448 Feb 8 20:28 batch-20.fa_batch-124.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 419308 Feb 8 20:27 batch-20.fa_batch-125.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 486586 Feb 8 20:28 batch-20.fa_batch-126.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 464393 Feb 8 20:29 batch-20.fa_batch-127.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 521728 Feb 8 20:32 batch-20.fa_batch-128.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 591157 Feb 8 20:32 batch-20.fa_batch-129.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 496090 Feb 8 20:33 batch-20.fa_batch-130.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 486211 Feb 8 20:36 batch-20.fa_batch-131.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 486986 Feb 8 20:36 batch-20.fa_batch-132.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 500724 Feb 8 20:37 batch-20.fa_batch-133.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 447147 Feb 8 20:40 batch-20.fa_batch-134.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 364644 Feb 8 20:40 batch-20.fa_batch-135.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 282362 Feb 8 20:39 batch-20.fa_batch-136.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 335475 Feb 8 20:42 batch-20.fa_batch-137.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 324665 Feb 8 20:43 batch-20.fa_batch-138.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 326885 Feb 8 20:43 batch-20.fa_batch-139.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 288374 Feb 8 20:45 batch-20.fa_batch-140.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 379505 Feb 8 20:45 batch-20.fa_batch-141.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 453085 Feb 8 20:46 batch-20.fa_batch-142.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 436328 Feb 8 20:48 batch-20.fa_batch-143.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 428221 Feb 8 20:48 batch-20.fa_batch-144.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 545934 Feb 8 20:49 batch-20.fa_batch-145.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 439474 Feb 8 20:51 batch-20.fa_batch-146.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 447639 Feb 8 20:51 batch-20.fa_batch-147.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 537102 Feb 8 20:53 batch-20.fa_batch-148.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 415085 Feb 8 20:53 batch-20.fa_batch-149.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 629371 Feb 8 20:58 batch-20.fa_batch-150.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 573071 Feb 8 20:56 batch-20.fa_batch-151.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 490812 Feb 8 20:57 batch-20.fa_batch-152.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 444760 Feb 8 20:59 batch-20.fa_batch-153.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 469728 Feb 8 21:11 batch-20.fa_batch-154.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 491686 Feb 8 21:04 batch-20.fa_batch-155.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 465033 Feb 8 21:02 batch-20.fa_batch-156.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 553263 Feb 8 21:06 batch-20.fa_batch-157.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 493040 Feb 8 21:07 batch-20.fa_batch-158.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 547628 Feb 8 21:10 batch-20.fa_batch-159.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 544035 Feb 8 21:11 batch-20.fa_batch-160.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 508976 Feb 8 21:13 batch-20.fa_batch-161.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 574516 Feb 8 21:16 batch-20.fa_batch-162.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 464460 Feb 8 21:14 batch-20.fa_batch-163.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 619034 Feb 8 21:18 batch-20.fa_batch-164.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 409735 Feb 8 21:16 batch-20.fa_batch-165.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 545554 Feb 8 21:20 batch-20.fa_batch-166.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 402925 Feb 8 21:20 batch-20.fa_batch-167.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 488856 Feb 8 21:21 batch-20.fa_batch-168.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 599798 Feb 8 21:24 batch-20.fa_batch-169.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 485960 Feb 8 21:23 batch-20.fa_batch-170.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 534433 Feb 8 21:25 batch-20.fa_batch-171.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 533330 Feb 8 21:27 batch-20.fa_batch-172.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 434005 Feb 8 21:28 batch-20.fa_batch-173.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 522525 Feb 8 21:29 batch-20.fa_batch-174.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 444578 Feb 8 21:32 batch-20.fa_batch-175.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 462043 Feb 8 21:33 batch-20.fa_batch-176.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 454582 Feb 8 21:31 batch-20.fa_batch-177.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 538179 Feb 8 21:35 batch-20.fa_batch-178.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 466211 Feb 8 21:35 batch-20.fa_batch-179.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 494388 Feb 8 21:36 batch-20.fa_batch-180.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 460022 Feb 8 21:39 batch-20.fa_batch-181.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 491221 Feb 8 21:39 batch-20.fa_batch-182.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 483144 Feb 8 21:40 batch-20.fa_batch-183.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 465671 Feb 8 21:42 batch-20.fa_batch-184.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 517350 Feb 8 21:43 batch-20.fa_batch-185.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 465639 Feb 8 21:46 batch-20.fa_batch-186.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 459125 Feb 8 21:47 batch-20.fa_batch-187.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 528119 Feb 8 21:47 batch-20.fa_batch-188.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 419640 Feb 8 21:49 batch-20.fa_batch-189.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 516466 Feb 8 21:54 batch-20.fa_batch-190.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 489720 Feb 8 21:51 batch-20.fa_batch-191.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 484369 Feb 8 21:53 batch-20.fa_batch-192.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 493968 Feb 8 21:55 batch-20.fa_batch-193.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 518513 Feb 8 21:57 batch-20.fa_batch-194.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 511179 Feb 8 21:58 batch-20.fa_batch-195.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 485018 Feb 8 21:59 batch-20.fa_batch-196.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 564901 Feb 8 22:01 batch-20.fa_batch-197.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 492976 Feb 8 22:01 batch-20.fa_batch-198.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 483488 Feb 8 22:02 batch-20.fa_batch-199.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 496627 Feb 8 22:04 batch-20.fa_batch-200.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 500059 Feb 8 22:06 batch-20.fa_batch-201.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 376803 Feb 8 22:05 batch-20.fa_batch-202.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 444636 Feb 8 22:07 batch-20.fa_batch-203.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 496065 Feb 8 22:09 batch-20.fa_batch-204.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 366960 Feb 8 22:10 batch-20.fa_batch-205.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 470420 Feb 8 22:12 batch-20.fa_batch-206.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 564357 Feb 8 22:13 batch-20.fa_batch-207.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 406812 Feb 8 22:13 batch-20.fa_batch-208.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 519055 Feb 8 22:15 batch-20.fa_batch-209.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 484446 Feb 8 22:16 batch-20.fa_batch-210.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 612766 Feb 8 22:20 batch-20.fa_batch-211.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 485127 Feb 8 22:19 batch-20.fa_batch-212.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 448024 Feb 8 22:20 batch-20.fa_batch-213.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 472864 Feb 8 22:23 batch-20.fa_batch-214.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 524179 Feb 8 22:24 batch-20.fa_batch-215.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 546918 Feb 8 22:41 batch-20.fa_batch-216.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 458999 Feb 8 22:26 batch-20.fa_batch-217.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 516299 Feb 8 22:28 batch-20.fa_batch-218.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 423038 Feb 8 22:29 batch-20.fa_batch-219.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 554505 Feb 8 22:32 batch-20.fa_batch-220.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 618160 Feb 8 22:34 batch-20.fa_batch-221.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 511891 Feb 8 22:36 batch-20.fa_batch-222.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 485291 Feb 8 22:37 batch-20.fa_batch-223.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 467701 Feb 8 22:44 batch-20.fa_batch-224.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 436283 Feb 8 22:41 batch-20.fa_batch-225.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 471086 Feb 8 22:45 batch-20.fa_batch-226.cat
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-rw-r--r-- 1 dmacguig grp-tkrabben 573256 Feb 8 22:48 batch-20.fa_batch-228.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 396368 Feb 8 22:47 batch-20.fa_batch-229.cat
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-rw-r--r-- 1 dmacguig grp-tkrabben 551699 Feb 8 22:53 batch-20.fa_batch-231.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 450422 Feb 8 22:54 batch-20.fa_batch-232.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 452511 Feb 8 22:53 batch-20.fa_batch-233.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 439605 Feb 8 22:56 batch-20.fa_batch-234.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 465804 Feb 8 22:57 batch-20.fa_batch-235.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 360161 Feb 8 22:56 batch-20.fa_batch-236.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 426234 Feb 8 23:01 batch-20.fa_batch-237.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 422614 Feb 8 23:00 batch-20.fa_batch-238.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 474100 Feb 8 23:00 batch-20.fa_batch-239.cat
-rw-r--r-- 1 dmacguig grp-tkrabben 467551 Feb 8 23:03 batch-20.fa_batch-240.cat
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-rw-r--r-- 1 dmacguig grp-tkrabben 481014 Feb 8 23:04 batch-20.fa_batch-242.cat
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-rw-r--r-- 1 dmacguig grp-tkrabben 387168 Feb 8 23:13 batch-20.fa_batch-245.cat
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-rw-r--r-- 1 dmacguig grp-tkrabben 567362 Feb 8 23:17 batch-20.fa_batch-250.cat
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-rw-r--r-- 1 dmacguig grp-tkrabben 512493 Feb 8 23:30 batch-20.fa_batch-257.cat
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-rw-r--r-- 1 dmacguig grp-tkrabben 8355677 Feb 8 19:35 batch-20.fa.cat.all.gz
-rw-r--r-- 1 dmacguig grp-tkrabben 0 Feb 8 18:48 ncResults-1707436083-3425733-3649.75217891455.err
-rw-r--r-- 1 dmacguig grp-tkrabben 0 Feb 8 22:53 ncResults-1707450810-3425707-2092.75157093606.err
-rw-r--r-- 1 dmacguig grp-tkrabben 0 Feb 8 23:28 ncResults-1707452923-3432572-1446.57419806876.err
-rw-r--r-- 1 dmacguig grp-tkrabben 0 Feb 9 09:05 ncResults-1707487557-3440948-1064.00195411942.err
-rw-r--r-- 1 dmacguig grp-tkrabben 0 Feb 9 11:56 ncResults-1707497805-3449007-841.496685040823.err
-rw-r--r-- 1 dmacguig grp-tkrabben 0 Feb 9 12:14 ncResults-1707498871-3449176-675.490412847779.err
-rw-r--r-- 1 dmacguig grp-tkrabben 0 Feb 9 12:31 ncResults-1707499910-3449331-1221.90604380862.err
-rw-r--r-- 1 dmacguig grp-tkrabben 0 Feb 9 12:45 ncResults-1707500701-3449427-572.861815323762.err
Any suggestions for how to troubleshoot this would be greatly appreciated.
