Comments (8)
Error in mmseqs
, new version input options. Updated as (removed --dont-split-seq-by-len)
https://github.com/KristinaGagalova/pante2/blob/0d9667a91134151c709e1339185e38c5c034ad8a/main.nf#L1433
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Error in tRNAscan
tRNAscan-SE -E -o "A_fumigatus_A1163_chr1_chr2_trnascan.txt" -f "A_fumigatus_A1163_chr1_chr2_trnascan_ss.txt" -s "A_fumigatus_A1163_chr1_chr2_trnascan_iso.txt" -m "A_fumigatus_A1163_chr1_chr2_trnascan_stats.txt" -b "A_fumigatus_A1163_chr1_chr2_trnascan.bed" -a "A_fumigatus_A1163_chr1_chr2_trnascan.fasta" --forceow --log trna.log --thread "1" "A_fumigatus_A1163_chr1_chr2.fasta"
Command exit status:
2
Command output:
(empty)
Command error:
Unable to open /tmp/.tmpdir.51260915//tscan206255.fpass for writing. Aborting program.
tmp directory has to be changed from the config file.
UPDATE:
THIS ONLY HAPPENS ON DUG - missing /tmp
directory on the HPC system
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Will address #10 even if won't fix it with the old versions
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Updates on RepeatModeler (-pa option is not available anymore)
https://github.com/KristinaGagalova/pante2/blob/cef5f787e91e5464752b6524eaffabaf154eb724/main.nf#L1329
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Bio.Alphabet change - update of the script needed or roll back to another version. More details here
ImportError: Bio.Alphabet has been removed from Biopython. In many cases, the alphabet can simply be ignored and removed from scripts. In a few cases, you may need to specify the ``molecule_type`` as an annotation on a SeqRecord for your script to work correctly. Please see https://biopython.org/wiki/Alphabet for more information.
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Missing library to DECIPHER
Error in library("optparse") : there is no package called ‘optparse’
Calls: suppressPackageStartupMessages -> withCallingHandlers -> library
Error in library("optparse") : there is no package called ‘optparse’
Calls: suppressPackageStartupMessages -> withCallingHandlers -> library
...
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Bio.Alphabet depreciated (see before)
ImportError: Bio.Alphabet has been removed from Biopython. In many cases, the alphabet can simply be ignored and removed from scripts. In a few cases, you may need to specify the ``molecule_type`` as an annotation on a SeqRecord for your script to work correctly. Please see https://biopython.org/wiki/Alphabet for more information.
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RepeatModeller 2.x.x does not have engine
. The command needs to be updated
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Related Issues (17)
- Missing GyDB database HOT 1
- Missing Rfam database
- Pfam database has changed to Interpro
- Issue with containers
- Databases download restart doesn't work as expected
- Error in creating repeatmasker lib HOT 2
- Cannot run from GitHub
- Check run with rnammer HOT 1
- Compile monolith pante container doesn't work HOT 2
- Decrease disk usage with h5 file format HOT 4
- RepeatMasker 4.1.5 uses a different database type - h5 HOT 1
- Add OcculterCut from mamba
- Test nimbus config better
- Rnammer docker image does not work as expected
- Pipeline failing at searchProfilesVsGenomes stage on assemblies HOT 8
- Include annotated NCBI hits
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