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linzhi2013 / MitoZ

MitoZ: A toolkit for assembly, annotation, and visualization of animal mitochondrial genomes
https://doi.org/10.1093/nar/gkz173
GNU General Public License v3.0
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Error encountered in mt_assembly using mitoz all command #165

Open timz0605 opened 2 years ago

timz0605 commented 2 years ago

MitoZ version?

3.4

How did you install MitoZ? (e.g. Docker, Udocker, Singularity, Conda-Pack, Conda, or source code)

Conda-Pack

Did you run a test after your installation, and was the test run okay?

Yes

The command you used?

Problem description

Hello. I am using mitoz for batch processing of samples, but am encountering the same issue for all samples. I have checked the loop and input (exact same files) and they run fine on others' computers. However, I have been getting the same issue every time I try to run the program. The log file all have similar lengths and they all terminate by saying:

mitoz.utility.utility - WARNING - filter_by_abundance(): All sequences are low abundance (<10X)

I have tried running the program on a single sample, and it can successfully output the final mitochondrial genome. I am kind of stuck in the situation and could not come up with a good explanation. I would really appreciate your help!

Log messages from MitoZ (stdout and stderr)

Below is part of the log file where it starts to show errors

2022-10-11 17:26:18,606 - mitoz.utility.utility - INFO - /home/zhangm2/miniconda3/envs/mitoz3.4/bin/python3.8 /home/zhangm2/miniconda3/envs/mitoz3.4/lib/python3.8/site-packages/mitoz/findmitoscaf/script/filter_taxonomy_by_CDS_annotation.py -fa S317.megahit.hmmtblout.besthit.sim.fa -MTsoft /home/zhangm2/miniconda3/envs/mitoz3.4/lib/python3.8/site-packages/mitoz/annotate/script/MT_annotation_BGI_V1.32/MT_annotation_BGI.pl -db /home/zhangm2/miniconda3/envs/mitoz3.4/lib/python3.8/site-packages/mitoz/profiles/MT_database/Animal_CDS_protein.fa -thread 12 -genetic_code 4 -requiring_taxa 'Porifera-sponges' -relax 0 -WISECONFIGDIR /home/zhangm2/miniconda3/envs/mitoz3.4/lib/python3.8/site-packages/mitoz/annotate/script/wisecfg -outf S317.megahit.hmmtblout.besthit.sim.filtered-by-taxa.fa

2022-10-11 17:46:43,359 - mitoz.utility.utility - ERROR - Error occured when running command: /home/zhangm2/miniconda3/envs/mitoz3.4/bin/python3.8 /home/zhangm2/miniconda3/envs/mitoz3.4/lib/python3.8/site-packages/mitoz/findmitoscaf/script/filter_taxonomy_by_CDS_annotation.py -fa S317.megahit.hmmtblout.besthit.sim.fa -MTsoft /home/zhangm2/miniconda3/envs/mitoz3.4/lib/python3.8/site-packages/mitoz/annotate/script/MT_annotation_BGI_V1.32/MT_annotation_BGI.pl -db /home/zhangm2/miniconda3/envs/mitoz3.4/lib/python3.8/site-packages/mitoz/profiles/MT_database/Animal_CDS_protein.fa -thread 12 -genetic_code 4 -requiring_taxa 'Porifera-sponges' -relax 0 -WISECONFIGDIR /home/zhangm2/miniconda3/envs/mitoz3.4/lib/python3.8/site-packages/mitoz/annotate/script/wisecfg -outf S317.megahit.hmmtblout.besthit.sim.filtered-by-taxa.fa

2022-10-11 17:46:43,360 - mitoz.utility.utility - INFO - /home/zhangm2/miniconda3/envs/mitoz3.4/bin/python3.8 /home/zhangm2/miniconda3/envs/mitoz3.4/lib/python3.8/site-packages/mitoz/findmitoscaf/script/filter_hmm-besthit-sim.py S317.megahit.hmmtblout.besthit.sim.filtered-by-taxa.fa S317.megahit.hmmtblout.besthit.sim S317.megahit.hmmtblout.besthit.sim.filtered-by-taxa

2022-10-11 17:46:43,440 - mitoz.utility.utility - ERROR - Error occured when running command: /home/zhangm2/miniconda3/envs/mitoz3.4/bin/python3.8 /home/zhangm2/miniconda3/envs/mitoz3.4/lib/python3.8/site-packages/mitoz/findmitoscaf/script/filter_hmm-besthit-sim.py S317.megahit.hmmtblout.besthit.sim.filtered-by-taxa.fa S317.megahit.hmmtblout.besthit.sim S317.megahit.hmmtblout.besthit.sim.filtered-by-taxa

timz0605 commented 2 years ago

I think I might have found out how the error was encountered... For the option Clade and requiring_taxa, the option Porifera-sponges always give me an error during the mt_assembly step (since I am working with sponges and cnidarians). However, when I use Arthropoda as the clade, everything now works fine. I am wondering if this is a bug that needs to be fixed since I have tried updating the ete toolkit.

linzhi2013 commented 2 years ago

Hi Timz0605,

Thanks for reporting the issue.

I will check the program later, I don't know if there are bugs.

And yes, you can also try Arthropoda or Chordata for the -clade option (but you should also set the correct genetic code for your sample)

You can have a look the DM01.megahit.hmmtblout.besthit.sim.filtered-by-taxa.high_abundance_10.0X and DM01.megahit.hmmtblout.besthit.sim.filtered-by-taxa.low_abundance.fasta to learn if the below message is true or not:

mitoz.utility.utility - WARNING - filter_by_abundance(): All sequences are low abundance (<10X)

(See https://github.com/linzhi2013/MitoZ/wiki/Tutorial#2-the-mitogenome-assembly-step)