Issue with seeding

[miramastoras]

Hello! I'm encountering an error running sedef on the prairie vole reference (MicOch1.0), and I'm unsure of what may be causing it. It seems to be having a problem with the seeding step. From looking at the code in sedef.sh, I think it may be having trouble parsing the chromosomes, in line 126

numchrs= `sedef translate ${input} 2>/dev/null`

But I'm having trouble debugging much further than this. Please see below for the error message:

Start: Mon Aug 17 16:30:55 PDT 2020
SEDEF: FASTA=/share/dennislab/databases/assemblies/MichOch1.0/soft_masked/Microtus_ochrogaster.MicOch1.0.dna_sm.fa; output=/share/dennislab/projects/vole/sedef; jobs=5; force=y
Output file name /share/dennislab/projects/vole/sedef exists! Removing it.

************************************************************************
Running SD seeding...
0% 0:0=0s
Seeding time: 0:00.88
SD seeding done: done running 0 jobs!
grep: /share/dennislab/projects/vole/sedef/log/seeds/*.log: No such file or directory
grep: /share/dennislab/projects/vole/sedef/log/seeds/*.log: No such file or directory
(standard_in) 1: syntax error
Single-core running time:  hours ( seconds)
grep: /share/dennislab/projects/vole/sedef/log/seeds/*.log: No such file or directory
(standard_in) 1: syntax error
Memory used:  MB
************************************************************************
Running SD alignment...
************************************************************************
Running SD alignment...
100% 1000:0=0s /usr/bin/time -f'TIMING: %e %M' sedef align generate -k 11 "/share/dennislab/databases/assemblies/MichOch1.0/soft_masked/Microtus_ochrogaster.MicOch1.0.dna_sm.fa" /share/dennislab/projects/vole/sedef/align/bucket_0999 >/share/den
Aligning time: 0:28.42
SD alignment done: finished 1000 jobs!
Single-core running time: 0 hours (51.5 seconds)
Memory used: 5 MB
************************************************************************
Running SD reporting...
cat: '/share/dennislab/projects/vole/sedef/seeds/*.bed': No such file or directory
Processed hit 0 out of 0... done!
Report time: 0:00.03 (5816 MB, user 0.03)
Line counts:
 0 /share/dennislab/projects/vole/sedef/aligned.bed
 1 /share/dennislab/projects/vole/sedef/final.bed
 0 /share/dennislab/projects/vole/sedef/potentials.bed
 0 /share/dennislab/projects/vole/sedef/seeds.bed
 1 total
End: Mon Aug 17 16:31:36 PDT 2020
************************************************************************
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Any ideas or suggestions would be helpful. I have attached a file with instructions to download the reference I am using (unfortunately I don't have a way to easily share it online). Please let me know if you need me to provide additional files.

Best, Mira Mastoras

[inumanag]

Hi @miramastoras

Thanks for the report. I will check it out ASAP.

[miramastoras]

@inumanag Hello, have you had a chance to take a look yet? Thank you very much for the help!

[inumanag]

Hi @miramastoras

Just pushed the fix. Let me know if you still have issues. Thanks for the bug report!