FATAL ERROR: RepeatMasker giving up

[dmacguigan]

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
-rw-r--r-- 1 dmacguig grp-tkrabben   469749 Feb  8 22:44 batch-20.fa_batch-227.cat
-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
-rw-r--r-- 1 dmacguig grp-tkrabben   423177 Feb  8 22:48 batch-20.fa_batch-230.cat
-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
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-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
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-rw-r--r-- 1 dmacguig grp-tkrabben   479038 Feb  8 23:08 batch-20.fa_batch-241.cat
-rw-r--r-- 1 dmacguig grp-tkrabben   481014 Feb  8 23:04 batch-20.fa_batch-242.cat
-rw-r--r-- 1 dmacguig grp-tkrabben   483114 Feb  8 23:08 batch-20.fa_batch-243.cat
-rw-r--r-- 1 dmacguig grp-tkrabben   409816 Feb  8 23:08 batch-20.fa_batch-244.cat
-rw-r--r-- 1 dmacguig grp-tkrabben   387168 Feb  8 23:13 batch-20.fa_batch-245.cat
-rw-r--r-- 1 dmacguig grp-tkrabben   433624 Feb  8 23:14 batch-20.fa_batch-246.cat
-rw-r--r-- 1 dmacguig grp-tkrabben   434788 Feb  8 23:12 batch-20.fa_batch-247.cat
-rw-r--r-- 1 dmacguig grp-tkrabben   551526 Feb  8 23:15 batch-20.fa_batch-248.cat
-rw-r--r-- 1 dmacguig grp-tkrabben   494614 Feb  8 23:16 batch-20.fa_batch-249.cat
-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   769853 Feb  9 12:44 batch-20.fa_batch-679.cat
-rw-r--r-- 1 dmacguig grp-tkrabben    54784 Feb  9 12:31 batch-20.fa_batch-680.masked
-rw-r--r-- 1 dmacguig grp-tkrabben    36987 Feb  9 12:31 batch-20.fa_batch-680.tmp.simple1
-rw-r--r-- 1 dmacguig grp-tkrabben    56822 Feb  9 12:45 batch-20.fa_batch-681.masked
-rw-r--r-- 1 dmacguig grp-tkrabben    25797 Feb  9 12:45 batch-20.fa_batch-681.tmp.simple1
-rw-r--r-- 1 dmacguig grp-tkrabben    60787 Feb  9 11:56 batch-20.fa_batch-76.masked
-rw-r--r-- 1 dmacguig grp-tkrabben     3040 Feb  9 11:56 batch-20.fa_batch-76.tmp.simple1
-rw-r--r-- 1 dmacguig grp-tkrabben    60651 Feb  9 04:23 batch-20.fa_batch-77.masked
-rw-r--r-- 1 dmacguig grp-tkrabben     4316 Feb  9 04:23 batch-20.fa_batch-77.tmp.simple1
-rw-r--r-- 1 dmacguig grp-tkrabben   646911 Feb  8 19:20 batch-20.fa_batch-78.cat
-rw-r--r-- 1 dmacguig grp-tkrabben   443740 Feb  8 19:11 batch-20.fa_batch-79.cat
-rw-r--r-- 1 dmacguig grp-tkrabben   552688 Feb  8 19:14 batch-20.fa_batch-80.cat
-rw-r--r-- 1 dmacguig grp-tkrabben   551116 Feb  8 19:19 batch-20.fa_batch-81.cat
-rw-r--r-- 1 dmacguig grp-tkrabben   535071 Feb  8 19:23 batch-20.fa_batch-82.cat
-rw-r--r-- 1 dmacguig grp-tkrabben   643365 Feb  8 19:24 batch-20.fa_batch-83.cat
-rw-r--r-- 1 dmacguig grp-tkrabben   488313 Feb  8 19:28 batch-20.fa_batch-84.cat
-rw-r--r-- 1 dmacguig grp-tkrabben   676338 Feb  8 19:28 batch-20.fa_batch-85.cat
-rw-r--r-- 1 dmacguig grp-tkrabben   604724 Feb  8 19:34 batch-20.fa_batch-86.cat
-rw-r--r-- 1 dmacguig grp-tkrabben   531673 Feb  8 19:32 batch-20.fa_batch-87.cat
-rw-r--r-- 1 dmacguig grp-tkrabben   685227 Feb  8 19:37 batch-20.fa_batch-88.cat
-rw-r--r-- 1 dmacguig grp-tkrabben   591552 Feb  8 19:39 batch-20.fa_batch-89.cat
-rw-r--r-- 1 dmacguig grp-tkrabben   621657 Feb  8 19:39 batch-20.fa_batch-90.cat
-rw-r--r-- 1 dmacguig grp-tkrabben   634223 Feb  8 19:41 batch-20.fa_batch-91.cat
-rw-r--r-- 1 dmacguig grp-tkrabben   560125 Feb  8 19:44 batch-20.fa_batch-92.cat
-rw-r--r-- 1 dmacguig grp-tkrabben   493765 Feb  8 19:42 batch-20.fa_batch-93.cat
-rw-r--r-- 1 dmacguig grp-tkrabben   540352 Feb  8 19:48 batch-20.fa_batch-94.cat
-rw-r--r-- 1 dmacguig grp-tkrabben   458071 Feb  8 19:46 batch-20.fa_batch-95.cat
-rw-r--r-- 1 dmacguig grp-tkrabben   532525 Feb  8 19:47 batch-20.fa_batch-96.cat
-rw-r--r-- 1 dmacguig grp-tkrabben   553404 Feb  8 19:51 batch-20.fa_batch-97.cat
-rw-r--r-- 1 dmacguig grp-tkrabben   567714 Feb  8 19:52 batch-20.fa_batch-98.cat
-rw-r--r-- 1 dmacguig grp-tkrabben   456426 Feb  8 19:52 batch-20.fa_batch-99.cat
-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.

[rmhubley]

Looks like it died will in the alignment phase. Unfortunately there was no error details captured in those *.err files. My guess is you ran out of memory on the machine. You might want to check memory usage while rerunning it.