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!
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!