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marcelauliano / MitoHiFi

Find, circularise and annotate mitogenome from PacBio assemblies
MIT License
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mitohifi error #97

Closed ghost closed 4 months ago

ghost commented 5 months ago

Hi i am getting this error while running the latest version of the Mitohifi, i read the previous ones but they seems to be not-working. 

  File "mitohifi.py", line 302, in main
    tRNA_ref = fetch.get_ref_tRNA()
  File "/work/sablok/organelle/mitochondrial/MitoHiFi-master/src/fetch.py", line 48, in get_ref_tRNA
    reference_tRNA = max(tRNAs, key=tRNAs.get)
ValueError: max() arg is an empty sequence

can you help with the same. Thank you, Gaurav

zajacn commented 5 months ago

I am getting the same issue. Following the previous issues reported I ran the mitohifi through conda installation but then also through singularity.

For singularity I ran: singularity build mitohifi.sif docker://ghcr.io/marcelauliano/mitohifi:master singularity exec -B $PWD mitohifi.sif mitohifi.py -c contigs.fasta -f reference.fasta -g reference.gbk -t 1 -a animal --circular-size 14000

Error I get: Traceback (most recent call last): File "/opt/MitoHiFi/src/mitohifi.py", line 566, in main() File "/opt/MitoHiFi/src/mitohifi.py", line 303, in main tRNA_ref = fetch.get_ref_tRNA() File "/opt/MitoHiFi/src/fetch.py", line 48, in get_ref_tRNA reference_tRNA = max(tRNAs, key=tRNAs.get) ValueError: max() arg is an empty sequence

ghost commented 4 months ago

Hi any possible solution or alternative for the same. Did you @zajacn figured out another version. Thank you for the information.