-species Viridiplantae finds no repeats

[tallnuttrbgv]

Hi,

I am using a module install of RepeatMasker 4.2.0 on an HPC and I have no control over the install, so I apologise for my lack of knowledge about that. I am trying to run it on a plant genome with the following:

RepeatMasker -pa 12 -species Viridiplantae -uncurated -dir repeatmasker /g/data/dy44/r12.42_Elaeocarpus_repeat/purge/Elaeocarpus_purged_rpt.fasta

However, it looks like an empty DB is created and no repeats are found. See stdout and stderr below. I cannot find any information on why it asks, "is a Viridiplantae a primate?0" or why the DB is empty.

Thanks for any suggestions.

Theo.

stdout:

RepeatMasker version 4.2.0
Search Engine: HMMER [ 3.4 (Aug 2023) ]

Using Master RepeatMasker Database: /g/data/if89/apps/RepeatMasker/4.2.0/RepeatMasker/Libraries/famdb
Title : Dfam
Version : 3.9
Date : 2025-03-10
Families : 272,503

Species/Taxa Search:
Viridiplantae [NCBI Taxonomy ID: 33090]

Including only curated families:
0 families in ancestor taxa; 0 lineage-specific families

Building species libraries in: /home/554/ta0341/.RepeatMaskerCache/HMM-Dfam_3.9/viridiplantae

analyzing file /g/data/dy44/r12.42_Elaeocarpus_repeat/purge/Elaeocarpus_purged_rpt.fasta
identifying Simple Repeats in batch 1 of 5552
identifying Simple Repeats in batch 2 of 5552
identifying Simple Repeats in batch 4 of 5552
identifying Simple Repeats in batch 5 of 5552
identifying Simple Repeats in batch 7 of 5552
identifying Simple Repeats in batch 6 of 5552
identifying Simple Repeats in batch 10 of 5552
identifying Simple Repeats in batch 11 of 5552
identifying Simple Repeats in batch 12 of 5552
identifying Simple Repeats in batch 9 of 5552
identifying Simple Repeats in batch 8 of 5552
is a Viridiplantae a primate?0
identifying Simple Repeats in batch 5 of 5552
is a Viridiplantae a primate?0
... etc. 16k lines.
.....
ProcessRepeats: Masking sequences
ProcessRepeats: Generating table output

done

stderr:
Loading python3/3.12.1
Loading requirement: intel-mkl/2023.2.0
Loading RepeatMasker/4.2.0
Loading requirement: TRF/4.09.1 python3/3.9.2 hmmer/3.4 blast/2.14.1
perllib/v5.26.3 rmblast/2.14.0
Traceback (most recent call last):
File "/g/data/if89/apps/RepeatMasker/4.2.0/RepeatMasker/famdb.py", line 953, in main
args.func(args)
File "/g/data/if89/apps/RepeatMasker/4.2.0/RepeatMasker/famdb.py", line 330, in command_lineage
totals, present = get_lineage_totals(
File "/g/data/if89/apps/RepeatMasker/4.2.0/RepeatMasker/famdb.py", line 276, in get_lineage_totals
new_counts, new_present = get_lineage_totals(
File "/g/data/if89/apps/RepeatMasker/4.2.0/RepeatMasker/famdb.py", line 276, in get_lineage_totals
new_counts, new_present = get_lineage_totals(
File "/g/data/if89/apps/RepeatMasker/4.2.0/RepeatMasker/famdb.py", line 264, in get_lineage_totals
for acc in accessions:
TypeError: 'NoneType' object is not iterable
Traceback (most recent call last):
File "/g/data/if89/apps/RepeatMasker/4.2.0/RepeatMasker/famdb.py", line 953, in main
args.func(args)
File "/g/data/if89/apps/RepeatMasker/4.2.0/RepeatMasker/famdb.py", line 330, in command_lineage
totals, present = get_lineage_totals(
File "/g/data/if89/apps/RepeatMasker/4.2.0/RepeatMasker/famdb.py", line 276, in get_lineage_totals
new_counts, new_present = get_lineage_totals(
File "/g/data/if89/apps/RepeatMasker/4.2.0/RepeatMasker/famdb.py", line 276, in get_lineage_totals
new_counts, new_present = get_lineage_totals(
File "/g/data/if89/apps/RepeatMasker/4.2.0/RepeatMasker/famdb.py", line 264, in get_lineage_totals
for acc in accessions:
TypeError: 'NoneType' object is not iterable