Comments (7)
jebrosen
commented on August 11, 2024
Can you post the output of ls -l /Volumes/userdata/staff_users/josephguhlin/.RepeatMaskerCache/CONS-Dfam_3.1/general/? It looks like there could be a problem with the cached library files.
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jguhlin
commented on August 11, 2024
total 240
-rw-r--r-- 1 josephguhlin deardenlab 16320 Jan 31 01:29 is.lib
-rw-r--r-- 1 josephguhlin deardenlab 20480 Jan 31 01:29 is.lib.ndb
-rw-r--r-- 1 josephguhlin deardenlab 684 Jan 31 01:29 is.lib.nhr
-rw-r--r-- 1 josephguhlin deardenlab 288 Jan 31 01:29 is.lib.nin
-rw-r--r-- 1 josephguhlin deardenlab 116 Jan 31 01:29 is.lib.not
-rw-r--r-- 1 josephguhlin deardenlab 3972 Jan 31 01:29 is.lib.nsq
-rw-r--r-- 1 josephguhlin deardenlab 16384 Jan 31 01:29 is.lib.ntf
-rw-r--r-- 1 josephguhlin deardenlab 40 Jan 31 01:29 is.lib.nto
-rw-r--r-- 1 josephguhlin deardenlab 85970 Jan 31 01:29 l1.lib
-rw-r--r-- 1 josephguhlin deardenlab 20480 Jan 31 01:29 l1.lib.ndb
-rw-r--r-- 1 josephguhlin deardenlab 3632 Jan 31 01:29 l1.lib.nhr
-rw-r--r-- 1 josephguhlin deardenlab 720 Jan 31 01:29 l1.lib.nin
-rw-r--r-- 1 josephguhlin deardenlab 548 Jan 31 01:29 l1.lib.not
-rw-r--r-- 1 josephguhlin deardenlab 24246 Jan 31 01:29 l1.lib.nsq
-rw-r--r-- 1 josephguhlin deardenlab 16384 Jan 31 01:29 l1.lib.ntf
-rw-r--r-- 1 josephguhlin deardenlab 184 Jan 31 01:29 l1.lib.nto
-rw-r--r-- 1 josephguhlin deardenlab 131 Jan 31 01:29 refineableHash.dat
-rw-r--r-- 1 josephguhlin deardenlab 410 Jan 31 01:29 rmblastdb.logfrom tetools.
jguhlin
commented on August 11, 2024
I think it's something with the system I'm running it on, running it on my desktop linux system works just fine.
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jebrosen
commented on August 11, 2024
Those files look about as expected, and I have never had a similar problem to yours. I would try deleting the .RepeatMaskerCache directory just in case; it will be re-generated as needed. Hopefully it was a fluke and future runs will succeed - if it fails again, we will look into it.
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jebrosen
commented on August 11, 2024
Were you able to run RepeatMasker successfully on that system, or to reproduce an unsuccessful run?
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jguhlin
commented on August 11, 2024
I was, but was unable to use the singularity container to do so.
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jebrosen
commented on August 11, 2024
A new version of the container including a new version of RepeatMasker has been released, and I have not heard of this problem from anyone else. Closing this for now, but if this issue comes up again anyone please feel free to comment or reopen!
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