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nigyta / dfast_core

DDBJ Fast Annotation and Submission Tool
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error pseudogene detection #41

Open aistBMRG opened 2 years ago

aistBMRG commented 2 years ago

Hi,

I am running dfast (version 1.2.14) on a large set of genomes. The vast majority completes without issue, and very fast, but for several genomes, annotation is aborted with the following type of error message in the application log file:

2022/03/01 15:16:15 10 CDS features were marked as possible pseudo due to internal stop codons. 2022/03/01 15:16:15 13 CDS features were marked as possible pseudo due to frameshift. 2022/03/01 15:16:15 Internal stop codons in the following 1 CDSs are translated to selenosysteine/pyrrolysine, which will be annotated with 'transl_except'. ['MGA_186'] 2022/03/01 15:16:15 Removed 1 CDSs. ['MGA_185'] 2022/03/01 15:16:28 Process aborted due to an error in PseudoGeneDetection. 2022/03/01 15:16:28 Error: mdb_env_open: No locks available

Would it be possible to let me know if you have any pointers as to what may cause this error?

Thanks in advance,

Dieter

nigyta commented 2 years ago

Dear Dieter @aistBMRG

Thank you for using DFAST. I saw this kind of error for the first time. Probably it was raised while running "makeblastdb" command. Please check it by invoking dfast again with "--debug" option and find a command like this: makeblastdb -dbtype prot -in OUT/PseudoGeneDetection/reference.faa -out OUT/PseudoGeneDetection/reference -hash_index -parse_seqids Please run the command manually to check whether the error can be reporoducible.

Or, if you can upload your genome to the DFAST web service (https://dfast.ddbj.nig.ac.jp/), I can look into it. If you wish, please email me at dfast@nig.ac.jp and let me know the job ID.