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harta55 / EnTAP

EnTAP is moving to GitLab for future changes https://gitlab.com/PlantGenomicsLab/EnTAP
https://entap.readthedocs.io/en/latest/
GNU General Public License v3.0
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Error code (106) #28

Closed guyleonard closed 3 years ago

guyleonard commented 3 years ago

Hi, I am getting error code 106 during the TransDecoder parsing stage in EnTAP v0.10.7-beta.

Error in TransDecoder parsing of file at: /home/zoo/zool2474/guy/eli/transcriptomics/DAS/DAS_trinity_no_DSLs_zoo/entap_test/frame_selection//TransDecoder/Trinity_entap_input.fasta.transdecoder.pep
Error:
std::exception

Input is from Trinity v2.11.0 and looks like:

>TRINITY_DN104188_c0_g1_i1 len=214 path=[0:0-213]
TGTAAGCCTTTTTGAATCGGGCATTTTCATCTTCAACCACAACAAAGTAGTAGCCTGTGGCAAA....

and the file it says it has an issue with looks like:

>TRINITY_DN100000_c0_g1_i1.p3 TRINITY_DN100000_c0_g1~~TRINITY_DN100000_c0_g1_i1.p3  ORF type:internal len:75 (+),score=21.78 TRINITY_DN100000_c0_g1_i1:3-224(+)
VKRPLAWLKVEFFTVSAGVGTGVGSSVVGTDVGSSVGVSPSTGVATGVGIGMGSDVWALP

Otherwise TransDecoder seemed to run correctly. Any ideas?

guyleonard commented 3 years ago

Solved it as soon as I post - obviously.

It seems to work when you remove blank spaces from the fasta header of the input.

>TRINITY_DN104188_c0_g1_i1 len=214 path=[0:0-213]
TGTAAGCCTTTTTGAATCGGGCATTTTCATCTTCAACCACAACAAAGTAGTAGCCTGTGGCAAA....

becomes

>TRINITY_DN104188_c0_g1_i1_len=214_path=[0:0-213]
TGTAAGCCTTTTTGAATCGGGCATTTTCATCTTCAACCACAACAAAGTAGTAGCCTGTGGCAAA....

I used reformat.sh from BBTools reformat.sh in=reads.fasta out=fixed.fasta addunderscore