Errors occurs when findmitoscaf mode runs #228
Description
on which platform/server? (Windows? Windows Sublinux? MacOS? Ubuntu? etc.) Ubuntu
MitoZ version? 3.6
How did you install MitoZ? (e.g. Docker, Udocker, Singularity, Conda-Pack, Conda, or source code) Conda
Did you run a test after your installation, and was the test run okay?
I forgot, but it can run on the other data sets
How much data (roughly) did you use for mitogenome assembly? e.g. 5Gbp?
1 Gbp
The command you used?
mitoz findmitoscaf --fastafile ../00_annotation_start/Tilapia_TFS_strain_genome_v1.fasta --outprefix marine_tilapia_MTW02 --workdir . --thread_number 128 --requiring_taxa Chordata --clade Chordata --min_abundance 0
Problem description
I want to exclude any potential mitochondrial sequence from my nuclear genome. I have removed one of the candidates. I wonder if mitoz can report no candidate if there is no one, or it just complain ERROR.
Log messages from MitoZ (stdout and stderr, e.g., both m.log and m.err files)
2025-05-05 11:21:34,996 - mitoz.utility.utility - INFO -
Found: /home/abieskawa/miniconda3/envs/mitoz3.6/bin/spades.py
2025-05-05 11:21:34,996 - mitoz.utility.utility - INFO -
Found: /home/abieskawa/miniconda3/envs/mitoz3.6/bin/megahit
2025-05-05 11:21:34,996 - mitoz.utility.utility - INFO -
findmitoscaf.main() got args:
Namespace(abundance_pattern='abun\=([0-9]+\.[0-9])', clade='Chordata', debug=False, fastafile='../00_annotation_start/Tilapia_TFS_strain_genome_v1.fasta', filter_by_taxa=True, fq1='', fq2='', func=<function main at 0x7d775e25adc0>, genetic_code='auto', logger=<Logger mitoz.utility.utility (DEBUG)>, min_abundance=10, outprefix='marine_tilapia_MTW02', profiles_dir='/home/abieskawa/miniconda3/envs/mitoz3.6/lib/python3.8/site-packages/mitoz/profiles', requiring_relax='0', requiring_taxa='Chordata', skip_read_mapping=False, slow_search=False, thread_number='128', workdir='.')
2025-05-05 11:21:34,996 - mitoz.utility.utility - INFO -
findmitoscaf.main() got updated args:
Namespace(abundance_pattern='abun\=([0-9]+\.[0-9])', clade='Chordata', debug=False, fastafile='../00_annotation_start/Tilapia_TFS_strain_genome_v1.fasta', filter_by_taxa=True, fq1='', fq2='', func=<function main at 0x7d775e25adc0>, genetic_code='2', logger=<Logger mitoz.utility.utility (DEBUG)>, min_abundance=10, outprefix='marine_tilapia_MTW02', profiles_dir='/home/abieskawa/miniconda3/envs/mitoz3.6/lib/python3.8/site-packages/mitoz/profiles', requiring_relax='0', requiring_taxa='Chordata', skip_read_mapping=False, slow_search=False, thread_number='128', workdir='.')
2025-05-05 11:21:34,996 - mitoz.utility.utility - INFO -
findmitoscaf.main() nhmmer_profile:
/home/abieskawa/miniconda3/envs/mitoz3.6/lib/python3.8/site-packages/mitoz/profiles/CDS_HMM/Chordata_CDS.hmm
2025-05-05 11:21:34,996 - mitoz.utility.utility - INFO -
findmitoscaf.main() defined_gene_length_f:
/home/abieskawa/miniconda3/envs/mitoz3.6/lib/python3.8/site-packages/mitoz/profiles/CDS_HMM/Chordata_CDS_length_list
2025-05-05 11:21:34,996 - mitoz.utility.utility - INFO -
findmitoscaf.main() MT_annotation_BGI_pro_db:
/home/abieskawa/miniconda3/envs/mitoz3.6/lib/python3.8/site-packages/mitoz/profiles/MT_database/Animal_CDS_protein.fa
2025-05-05 11:21:34,996 - mitoz.utility.utility - INFO -
findmitoscaf.main() workdir:
/home/abieskawa/output/marine_tilapia_MTW02/00_check_mitochondria_mitoz
2025-05-05 11:21:34,996 - mitoz.utility.utility - INFO -
findmitoscaf.main() result_wdir:
/home/abieskawa/output/marine_tilapia_MTW02/00_check_mitochondria_mitoz/marine_tilapia_MTW02.result
2025-05-05 11:21:34,996 - mitoz.utility.utility - INFO -
findmitoscaf.main() got assembly_file:
/home/abieskawa/output/marine_tilapia_MTW02/00_annotation_start/Tilapia_TFS_strain_genome_v1.fasta
2025-05-05 11:21:34,996 - mitoz.utility.utility - INFO -
findmitoscaf.main() got
fq1:
fq2:
2025-05-05 11:21:34,996 - mitoz.utility.utility - ERROR -
Failed to extract the abundance information from the seqid!
abundance_pattern: abun\=([0-9]+\.*[0-9]*)
The seqid of your input assembly file is like: >scaffold45
You may need to adapt the regular expression using the '--abundance_pattern' option,
Or set '--min_abundance 0' if you do NOT want to filter sequences by abundance!
2025-05-05 11:22:07,292 - mitoz.utility.utility - INFO -
Found: /home/abieskawa/miniconda3/envs/mitoz3.6/bin/spades.py
2025-05-05 11:22:07,293 - mitoz.utility.utility - INFO -
Found: /home/abieskawa/miniconda3/envs/mitoz3.6/bin/megahit
2025-05-05 11:22:07,293 - mitoz.utility.utility - INFO -
findmitoscaf.main() got args:
Namespace(abundance_pattern='abun\=([0-9]+\.[0-9])', clade='Chordata', debug=False, fastafile='../00_annotation_start/Tilapia_TFS_strain_genome_v1.fasta', filter_by_taxa=True, fq1='', fq2='', func=<function main at 0x78516f73cdc0>, genetic_code='auto', logger=<Logger mitoz.utility.utility (DEBUG)>, min_abundance=0.0, outprefix='marine_tilapia_MTW02', profiles_dir='/home/abieskawa/miniconda3/envs/mitoz3.6/lib/python3.8/site-packages/mitoz/profiles', requiring_relax='0', requiring_taxa='Chordata', skip_read_mapping=False, slow_search=False, thread_number='128', workdir='.')
2025-05-05 11:22:07,293 - mitoz.utility.utility - INFO -
findmitoscaf.main() got updated args:
Namespace(abundance_pattern='abun\=([0-9]+\.[0-9])', clade='Chordata', debug=False, fastafile='../00_annotation_start/Tilapia_TFS_strain_genome_v1.fasta', filter_by_taxa=True, fq1='', fq2='', func=<function main at 0x78516f73cdc0>, genetic_code='2', logger=<Logger mitoz.utility.utility (DEBUG)>, min_abundance=0.0, outprefix='marine_tilapia_MTW02', profiles_dir='/home/abieskawa/miniconda3/envs/mitoz3.6/lib/python3.8/site-packages/mitoz/profiles', requiring_relax='0', requiring_taxa='Chordata', skip_read_mapping=False, slow_search=False, thread_number='128', workdir='.')
2025-05-05 11:22:07,293 - mitoz.utility.utility - INFO -
findmitoscaf.main() nhmmer_profile:
/home/abieskawa/miniconda3/envs/mitoz3.6/lib/python3.8/site-packages/mitoz/profiles/CDS_HMM/Chordata_CDS.hmm
2025-05-05 11:22:07,293 - mitoz.utility.utility - INFO -
findmitoscaf.main() defined_gene_length_f:
/home/abieskawa/miniconda3/envs/mitoz3.6/lib/python3.8/site-packages/mitoz/profiles/CDS_HMM/Chordata_CDS_length_list
2025-05-05 11:22:07,293 - mitoz.utility.utility - INFO -
findmitoscaf.main() MT_annotation_BGI_pro_db:
/home/abieskawa/miniconda3/envs/mitoz3.6/lib/python3.8/site-packages/mitoz/profiles/MT_database/Animal_CDS_protein.fa
2025-05-05 11:22:07,293 - mitoz.utility.utility - INFO -
findmitoscaf.main() workdir:
/home/abieskawa/output/marine_tilapia_MTW02/00_check_mitochondria_mitoz
2025-05-05 11:22:07,293 - mitoz.utility.utility - INFO -
findmitoscaf.main() result_wdir:
/home/abieskawa/output/marine_tilapia_MTW02/00_check_mitochondria_mitoz/marine_tilapia_MTW02.result
2025-05-05 11:22:07,293 - mitoz.utility.utility - INFO -
findmitoscaf.main() got assembly_file:
/home/abieskawa/output/marine_tilapia_MTW02/00_annotation_start/Tilapia_TFS_strain_genome_v1.fasta
2025-05-05 11:22:07,293 - mitoz.utility.utility - INFO -
findmitoscaf.main() got
fq1:
fq2:
2025-05-05 11:22:07,293 - mitoz.utility.utility - INFO -
We will skip read-mapping during findmitoscaf().
2025-05-05 11:22:07,293 - mitoz.utility.utility - INFO -
tiara mt_expected_result_file: mitochondrion_Tilapia_TFS_strain_genome_v1.fasta
2025-05-05 11:22:07,293 - mitoz.utility.utility - INFO -
tiara --input /home/abieskawa/output/marine_tilapia_MTW02/00_annotation_start/Tilapia_TFS_strain_genome_v1.fasta --output marine_tilapia_MTW02.tiara.out.txt --to_fasta mit pla pro --threads 128 --prob_cutoff 0.65 0.60 --probabilities --min_len 1000
2025-05-05 11:25:30,215 - mitoz.utility.utility - INFO -
nhmmer -o marine_tilapia_MTW02.hmmout --tblout marine_tilapia_MTW02.hmmtblout --cpu 128 /home/abieskawa/miniconda3/envs/mitoz3.6/lib/python3.8/site-packages/mitoz/profiles/CDS_HMM/Chordata_CDS.hmm mitochondrion_Tilapia_TFS_strain_genome_v1.fasta
2025-05-05 11:25:31,031 - mitoz.utility.utility - INFO -
/home/abieskawa/miniconda3/envs/mitoz3.6/bin/python3.8 /home/abieskawa/miniconda3/envs/mitoz3.6/lib/python3.8/site-packages/mitoz/findmitoscaf/script/get_besthit_of_each_CDS_from_nhmmer.py marine_tilapia_MTW02.hmmtblout marine_tilapia_MTW02.hmmtblout.besthit
2025-05-05 11:25:31,069 - mitoz.utility.utility - INFO -
/home/abieskawa/miniconda3/envs/mitoz3.6/bin/python3.8 /home/abieskawa/miniconda3/envs/mitoz3.6/lib/python3.8/site-packages/mitoz/findmitoscaf/script/simlify_nhmmer_tbl_besthit.py marine_tilapia_MTW02.hmmtblout.besthit marine_tilapia_MTW02.hmmtblout.besthit.sim
2025-05-05 11:25:31,104 - mitoz.utility.utility - INFO -
/home/abieskawa/miniconda3/envs/mitoz3.6/bin/python3.8 /home/abieskawa/miniconda3/envs/mitoz3.6/lib/python3.8/site-packages/mitoz/findmitoscaf/script/extract_fasta.py -i mitochondrion_Tilapia_TFS_strain_genome_v1.fasta -q marine_tilapia_MTW02.hmmtblout.besthit.sim -o marine_tilapia_MTW02.hmmtblout.besthit.sim.fa
2025-05-05 11:25:31,153 - mitoz.utility.utility - INFO -
filter_by_nhmmer() return:
mitochondrion_Tilapia_TFS_strain_genome_v1.fasta, marine_tilapia_MTW02.hmmtblout.besthit.sim, marine_tilapia_MTW02.hmmtblout.besthit.sim.fa
2025-05-05 11:25:31,167 - mitoz.utility.utility - INFO -
/home/abieskawa/miniconda3/envs/mitoz3.6/bin/python3.8 /home/abieskawa/miniconda3/envs/mitoz3.6/lib/python3.8/site-packages/mitoz/findmitoscaf/script/filter_taxonomy_by_CDS_annotation.py -fa marine_tilapia_MTW02.hmmtblout.besthit.sim.fa -MTsoft /home/abieskawa/miniconda3/envs/mitoz3.6/lib/python3.8/site-packages/mitoz/annotate/script/MT_annotation_BGI_V1.32/MT_annotation_BGI.pl -db /home/abieskawa/miniconda3/envs/mitoz3.6/lib/python3.8/site-packages/mitoz/profiles/MT_database/Animal_CDS_protein.fa -thread 128 -genetic_code 2 -requiring_taxa 'Chordata' -relax 0 -WISECONFIGDIR /home/abieskawa/miniconda3/envs/mitoz3.6/share/wise2/wisecfg -outf marine_tilapia_MTW02.hmmtblout.besthit.sim.filtered-by-taxa.fa
2025-05-05 11:25:42,717 - mitoz.utility.utility - ERROR -
Error occured when running command:
/home/abieskawa/miniconda3/envs/mitoz3.6/bin/python3.8 /home/abieskawa/miniconda3/envs/mitoz3.6/lib/python3.8/site-packages/mitoz/findmitoscaf/script/filter_taxonomy_by_CDS_annotation.py -fa marine_tilapia_MTW02.hmmtblout.besthit.sim.fa -MTsoft /home/abieskawa/miniconda3/envs/mitoz3.6/lib/python3.8/site-packages/mitoz/annotate/script/MT_annotation_BGI_V1.32/MT_annotation_BGI.pl -db /home/abieskawa/miniconda3/envs/mitoz3.6/lib/python3.8/site-packages/mitoz/profiles/MT_database/Animal_CDS_protein.fa -thread 128 -genetic_code 2 -requiring_taxa 'Chordata' -relax 0 -WISECONFIGDIR /home/abieskawa/miniconda3/envs/mitoz3.6/share/wise2/wisecfg -outf marine_tilapia_MTW02.hmmtblout.besthit.sim.filtered-by-taxa.fa
2025-05-05 11:25:42,718 - mitoz.utility.utility - INFO -
/home/abieskawa/miniconda3/envs/mitoz3.6/bin/python3.8 /home/abieskawa/miniconda3/envs/mitoz3.6/lib/python3.8/site-packages/mitoz/findmitoscaf/script/filter_hmm-besthit-sim.py marine_tilapia_MTW02.hmmtblout.besthit.sim.filtered-by-taxa.fa marine_tilapia_MTW02.hmmtblout.besthit.sim marine_tilapia_MTW02.hmmtblout.besthit.sim.filtered-by-taxa
2025-05-05 11:25:42,752 - mitoz.utility.utility - ERROR -
Error occured when running command:
/home/abieskawa/miniconda3/envs/mitoz3.6/bin/python3.8 /home/abieskawa/miniconda3/envs/mitoz3.6/lib/python3.8/site-packages/mitoz/findmitoscaf/script/filter_hmm-besthit-sim.py marine_tilapia_MTW02.hmmtblout.besthit.sim.filtered-by-taxa.fa marine_tilapia_MTW02.hmmtblout.besthit.sim marine_tilapia_MTW02.hmmtblout.besthit.sim.filtered-by-taxa
2025-05-05 11:25:42,753 - mitoz.utility.utility - INFO -
do_filter_by_taxa() return:
hmm_outf_tbl_besthit_sim_filtered_by_taxa:marine_tilapia_MTW02.hmmtblout.besthit.sim.filtered-by-taxa
hmm_besthit_filtered_by_taxa_fa: marine_tilapia_MTW02.hmmtblout.besthit.sim.filtered-by-taxa.fa
2025-05-05 11:25:42,753 - mitoz.utility.utility - INFO -
/home/abieskawa/miniconda3/envs/mitoz3.6/bin/python3.8 /home/abieskawa/miniconda3/envs/mitoz3.6/lib/python3.8/site-packages/mitoz/findmitoscaf/script/circle_check.py marine_tilapia_MTW02.hmmtblout.besthit.sim.filtered-by-taxa.fa marine_tilapia_MTW02 3
2025-05-05 11:25:42,941 - mitoz.utility.utility - ERROR -
Error occured when running command:
/home/abieskawa/miniconda3/envs/mitoz3.6/bin/python3.8 /home/abieskawa/miniconda3/envs/mitoz3.6/lib/python3.8/site-packages/mitoz/findmitoscaf/script/circle_check.py marine_tilapia_MTW02.hmmtblout.besthit.sim.filtered-by-taxa.fa marine_tilapia_MTW02 3
2025-05-05 11:25:42,942 - mitoz.utility.utility - INFO -
quick_circle_check() return:
/home/abieskawa/output/marine_tilapia_MTW02/00_check_mitochondria_mitoz/marine_tilapia_MTW02.mitogenome.fa
2025-05-05 11:25:42,942 - mitoz.utility.utility - INFO -
gather_result() creating: /home/abieskawa/output/marine_tilapia_MTW02/00_check_mitochondria_mitoz/marine_tilapia_MTW02.result
2025-05-05 11:25:42,943 - mitoz.utility.utility - INFO -
cp -r marine_tilapia_MTW02.hmmtblout.besthit.sim.filtered-by-taxa.fa /home/abieskawa/output/marine_tilapia_MTW02/00_check_mitochondria_mitoz/marine_tilapia_MTW02.mitogenome.fa /home/abieskawa/output/marine_tilapia_MTW02/00_check_mitochondria_mitoz/marine_tilapia_MTW02.overlap_information /home/abieskawa/output/marine_tilapia_MTW02/00_check_mitochondria_mitoz/marine_tilapia_MTW02.result
2025-05-05 11:25:42,959 - mitoz.utility.utility - ERROR -
Error occured when running command:
cp -r marine_tilapia_MTW02.hmmtblout.besthit.sim.filtered-by-taxa.fa /home/abieskawa/output/marine_tilapia_MTW02/00_check_mitochondria_mitoz/marine_tilapia_MTW02.mitogenome.fa /home/abieskawa/output/marine_tilapia_MTW02/00_check_mitochondria_mitoz/marine_tilapia_MTW02.overlap_information /home/abieskawa/output/marine_tilapia_MTW02/00_check_mitochondria_mitoz/marine_tilapia_MTW02.result