ValueError: max() arg is an empty sequence

[sandravelascoc]

Hi, everyone:

I am running docker/singularity version of MitoHiFi with apptainer as:

apptainer run -C -B /home -B /project -B /scratch -W ${SLURM_TMPDIR} mitohifi.sif python3 /opt/MitoHiFi/src/mitohifi.py -c /home/velascoc/projects/def-strelkov/velascoc/HiFi/pggb/S16_OS00FE2B_DA230375_bc2089.p_ctg_prefixed.fa -f /home/velascoc/scratch/HiFi/MitoHiFi/P_brassicae_Mitochondrion_LS992577_1.fasta -g /home/velascoc/scratch/HiFi/MitoHiFi/P_brassicae_Mitochondrion_LS992577_1.gb -t 4 -o 4

However, I get the following error:

/opt/MitoHiFi/src/parallel_annotation.py:69: UserWarning: Contig S16#1#ptg000007c does not have an annotation file, check MitoFinder's log
  warnings.warn("Contig "+ contig_id + " does not have an annotation file, check MitoFinder's log")
Traceback (most recent call last):
  File "/opt/MitoHiFi/src/mitohifi.py", line 566, in <module>
    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
Program finished with exit code 1 at: Wed Oct  2 14:03:41 PDT 2024

The weird thing is that the command works perfectly with some .gb files and does not work with other .gb files. For example, using NC_034004 as a reference, I get the expected output files, while when I use LS992577, I get the error.

I know that the error is caused by mitofinder and is associated with the genome I am using as a reference. However, I don't know how to fix it. Does anyone have any idea?

I created the container as:
apptainer build mitohifi.sif docker://ghcr.io/marcelauliano/mitohifi:master

and the version is:

 apptainer shell mitohifi.sif
 Apptainer>  python3 /opt/MitoHiFi/src/mitohifi.py --version
 MitoHiFi 3.2.1

Thanks
Sandra

[bioinfoMMS]

Any luck on this? I am having the same issue with two different reference mitochondria genbank files and the singularity container. I have gotten MitoHifi to work in the past with the same command on a different organism so not sure what is going on here.

[bbrunet]

I just encountered the same issue too. I'm using the conda installation, with everything installed today and the genbank file fetched today.

[foreignsand]

I'm having the same issue using MitoHiFi as a docker image on my local machine running MacOs Sequoia 15.1.

[dgpinheiro]

I'm having the same issue using MitoHiF-3.2.2.

Traceback (most recent call last):
File "/usr/local/bioinfo/MitoHiFi-3.2.2/src/mitohifi.py", line 567, in
main()
File "/usr/local/bioinfo/MitoHiFi-3.2.2/src/mitohifi.py", line 304, in main
tRNA_ref = fetch.get_ref_tRNA()
File "/srv/bioinfo/MitoHiFi-3.2.2/src/fetch.py", line 48, in get_ref_tRNA
reference_tRNA = max(tRNAs, key=tRNAs.get)
ValueError: max() arg is an empty sequence

The issue was solved by fixing the MitoFinder installation, the "python-xml" package was missing.

[bbrunet]

I ended up figuring out that mitohifi was getting tripped up on the fact that none of the putative mitochondrial contigs were circularized and as a result mitofinder would not proceed with annotation. After mapping the reads to the reference and assembling them into contigs using Flye, I was able to get mitohifi to run to completion using the contigs as input. I ended up using the docker image via singularity in the end, and it all works fine now so long as the input contigs are circular.