[maker-devel] tblastx of alt-ESTs failing on single scaffold

[Daren Card]

Hello,

I am having an issue running MAKER and am hoping to get some
troubleshooting guidance. I am running MAKER v. 2.31.10 on a Unix cluster
using a Singularity image with BLAST v. 2.9.0+ and Exonerate v. 3.3.2. I am
running MAKER with the following command options: "-fix_nucleotides
-nodatastore -RM_off". I am providing assembled transcripts from the target
species (est) and a close relative (alt-est) and proteins from several
species within the same general clade (Squamata). Gene models are being
derived from Augustus with est2genome and protein2genome turned off. I have
largely successfully run MAKER on a couple of genomes from the same
vertebrate genus, but have this lingering problem with a single scaffold
from one of the genomes. If it were pretty short, I'd just ignore it, but
it is 2 Mb, so I do not want to miss out on annotating it.

When I ran MAKER on the entire genome, it finished properly except for this
problematic scaffold. So I separated that scaffold out and tried running it
alone with otherwise the same settings. Each time, it appears I get the
same error during the 1st try when MAKER runs.

ERROR: TBLASTX does not appear to be finished in Widget::tblastx::keepers
--> rank=23, hostname=holy7c18405.rc.fas.harvard.edu
--> rank=23, hostname=holy7c18405.rc.fas.harvard.edu
--> rank=23, hostname=holy7c18405.rc.fas.harvard.edu
--> rank=23, hostname=holy7c18405.rc.fas.harvard.edu
ERROR: Failed while doing tblastx of alt-ESTs
ERROR: Chunk failed at level:4, tier_type:3
FAILED CONTIG:scaffold_77

ERROR: Chunk failed at level:4, tier_type:0
FAILED CONTIG:scaffold_77

Then MAKER keeps retrying and apparently hitting the same problem. I
checked the logs the best I can and see the following issue within
run.log.child.0 for that scaffold.

STARTED lerBou1_maker_rnd2.maker.output/lerBou1_maker_rnd2_datastore/scaffold_77/theVoid.scaffold_77/0/scaffold_77.0.lerEdw1_Trinity_combined_denovo_refguided%2Ecdhit%2Efasta.tblastx
DIED    RANK    17:4:0:0
DIED    COUNT   7

This output file noted there is not present to check, which must stem from
whatever issue there is.

I'm not sure what to do next about this issue and see no obvious
information about what the problem is besides failure of tblastx to run.
Any help that anyone can provide is greatly appreciated.

Kind regards,
Daren Card

NSF Postdoctoral Fellow
Harvard University
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20201029/c9d878b2/attachment-0002.html>