[maker-devel] short scaffolds finish, long scaffolds (almost always) fail

[Devon O'Rourke]

Hello,

I apologize for not posting directly to the archived forum but it appears
that the option to enter new posts is disabled. Perhaps this is by design
so emails go directly to this address. I hope this is what you are looking
for.

Thank you for your continued support of Maker and your responses to the
forum posts. I have been running Maker (V3.01.02-beta) to annotate a
mammalian genome that consists of 22 chromosome-length scaffolds (between
~200-20Mb) and about 10,000 smaller fragments from 1Mb to 10kb in length.
In my various tests in running Maker, the vast majority of the smaller
fragments are annotated successfully, but nearly all the large scaffolds
fail with the same error code when I look at the 'run.log.child.0' file:
```
DIED RANK 0:6:0:0
DIED COUNT 2
```
(the master 'run.log' file just shows "DIED COUNT 2")

I struggled to find this exact error code anywhere on the forum and was
hoping you might be able to help me determine where I should start
troubleshooting. I thought perhaps it was an error concerning memory
requirements, so I altered the chunk size from the default to a few larger
sequence lengths (I've tried 1e6, 1e7, and 999,999,999 - all produce the
same outcome). I've tried running the program with parallel support using
either openMPI or mpich. I've tried running on a single node using 24 cpus
and 120g of RAM. It always stalls at the same step.

Interestingly, one of the 22 large scaffolds always finishes and produces
the .maker.proteins.fasta, .maker.transcripts.fasta, and .gff files, but
the other 21 of 22 large scaffolds fail. This makes me think perhaps it's
not a memory issue?

In the case of both the completed and failed scaffolds, the
"theVoid.scaffoldX" subdirectory(ies) containing the .rb.cat.gz, .rb.out,
.specific.ori.out, .specific.cat.gz, .specific.out,
te_proteins*fasta.repeat runner, the est *fasta.blastn, the altest
*fasta.tblastx, and protein *fasta.blastx files are all present (and appear
finished from what I can tell).
However, the particular contents in the parent directory to the
"theVoid.scaffold" folder differ. For the failed scaffolds, the contents
generally always look something like this (that is, they stall with the
same kind of files produced):
```
0
evidence_0.gff
query.fasta
query.masked.fasta
query.masked.fasta.index
query.masked.gff
run.log.child.0
scaffold22.0.final.section
scaffold22.0.pred.raw.section
scaffold22.0.raw.section
scaffold22.gff.ann
scaffold22.gff.def
scaffold22.gff.seq
```

For the completed scaffold, there are many more files created:
```
0
10
100
20
30
40
50
60
70
80
90
evidence_0.gff
evidence_10.gff
evidence_1.gff
evidence_2.gff
evidence_3.gff
evidence_4.gff
evidence_5.gff
evidence_6.gff
evidence_7.gff
evidence_8.gff
evidence_9.gff
query.fasta
query.masked.fasta
query.masked.fasta.index
query.masked.gff
run.log.child.0
run.log.child.1
run.log.child.10
run.log.child.2
run.log.child.3
run.log.child.4
run.log.child.5
run.log.child.6
run.log.child.7
run.log.child.8
run.log.child.9
scaffold4.0-1.raw.section
scaffold4.0.final.section
scaffold4.0.pred.raw.section
scaffold4.0.raw.section
scaffold4.10.final.section
scaffold4.10.pred.raw.section
scaffold4.10.raw.section
scaffold4.1-2.raw.section
scaffold4.1.final.section
scaffold4.1.pred.raw.section
scaffold4.1.raw.section
scaffold4.2-3.raw.section
scaffold4.2.final.section
scaffold4.2.pred.raw.section
scaffold4.2.raw.section
scaffold4.3-4.raw.section
scaffold4.3.final.section
scaffold4.3.pred.raw.section
scaffold4.3.raw.section
scaffold4.4-5.raw.section
scaffold4.4.final.section
scaffold4.4.pred.raw.section
scaffold4.4.raw.section
scaffold4.5-6.raw.section
scaffold4.5.final.section
scaffold4.5.pred.raw.section
scaffold4.5.raw.section
scaffold4.6-7.raw.section
scaffold4.6.final.section
scaffold4.6.pred.raw.section
scaffold4.6.raw.section
scaffold4.7-8.raw.section
scaffold4.7.final.section
scaffold4.7.pred.raw.section
scaffold4.7.raw.section
scaffold4.8-9.raw.section
scaffold4.8.final.section
scaffold4.8.pred.raw.section
scaffold4.8.raw.section
scaffold4.9-10.raw.section
scaffold4.9.final.section
scaffold4.9.pred.raw.section
scaffold4.9.raw.section
```

Thanks for any troubleshooting tips you can offer.

Cheers,
Devon

-- 
Devon O'Rourke
Postdoctoral researcher, Northern Arizona University
Lab of Jeffrey T. Foster - https://fozlab.weebly.com/
twitter: @thesciencedork
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