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Old 05-12-2017, 11:28 AM   #1
ohakoh
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Location: Canada

Join Date: May 2017
Posts: 1
Default RepeatModeler error: fail at round 5

Hi everyone,

I am running RepeatModeler on a reference genome with no previous database of repeats.

I was able to perform BuildDatabase fine.
When I run RepeatModeler, it goes through the first 5 rounds then I received this error:

Not an ARRAY reference at /data/apps/RepeatModeler/TRFMask line 185.
BLAST Database error: No alias or index file found for nucleotide database [/data/user/mySpecies/Reference2/RM_5142.FriMay121121512017/round-4/sampleDB-4.fa] in search path [/data/user/mySpecies/Reference2::]

Not an ARRAY reference at /data/apps/RepeatModeler/TRFMask line 185.
BLAST Database error: No alias or index file found for nucleotide database [/data/user/mySpecies/Reference2/RM_5142.FriMay121121512017/round-5/sampleDB-5.fa] in search path [/data/user/mySpecies/Reference2::]

Not an ARRAY reference at /data/apps/RepeatModeler/TRFMask line 185.
BLAST Database error: No alias or index file found for nucleotide database [/data/user/mySpecies/Reference2/RM_5142.FriMay121121512017/round-2/sampleDB-2.fa] in search path [/data/user/mySpecies/Reference2::]

Not an ARRAY reference at /data/apps/RepeatModeler/TRFMask line 185.
BLAST Database error: No alias or index file found for nucleotide database [/data/user/mySpecies/Reference2/RM_5142.FriMay121121512017/round-3/sampleDB-3.fa] in search path [/data/user/mySpecies/Reference2::]

Not an ARRAY reference at /data/apps/RepeatModeler/TRFMask line 185.
BLAST Database error: No alias or index file found for nucleotide database [/data/user/mySpecies/Reference2/RM_5142.FriMay121121512017/round-4/sampleDB-4.fa] in search path [/data/user/mySpecies/Reference2::]

Not an ARRAY reference at /data/apps/RepeatModeler/TRFMask line 185.
BLAST Database error: No alias or index file found for nucleotide database [/data/user/mySpecies/Reference2/RM_5142.FriMay121121512017/round-5/sampleDB-5.fa] in search path [/data/user/mySpecies/Reference2::]nine the output directories


I am uncertain as to what database it is trying to search for.

Furthermore, examining the output I got within the directory (RM_5142.FriMay121121512017/), files such as sampleDB-2.fa, sampleDB-3.fa, sampleDB-4.fa, sampleDB-5.fa are all basically empty. I am pretty sure they are suppose to hold some information.

Thank you for all your help!
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