Error in annotating PCGs

[microbpro-cat]

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)

source code

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

yes

How much data (roughly) did you use for mitogenome assembly? e.g. 5Gbp?

5GB

The command you used?

mitoz annotate
--fastafiles /mnt/HDD5/project/Echino_RefMitogenomes/E_miyagawai_hunan.fasta
--outprefix annotated_mt
--species_name "Echinostoma mekongi"
--clade Nematoda
--workdir /mnt/HDD5/project/mitoz/trial/14th

Problem description

I had the same issue with issue#212 and did the same as the guideline. The empty summary.txt was fixed, but unfortunately PCG annotation doesn't work. I can't find the error. I'll upload the log file. Thank you.

Log messages from MitoZ (stdout and stderr, e.g., both m.log and m.err files)

mitoz.log

[linzhi2013]

the error came from

2025-04-15 16:55:57,550 - mitoz.utility.utility - ERROR - 
Error occured when running command:
export WISECONFIGDIR=/mnt/HDD5/project/mitoz/soft/mitoz3.6/share/wise2/wisecfg
perl /mnt/HDD5/project/mitoz/soft/mitoz3.6/lib/python3.8/site-packages/mitoz/annotate/script/MT_annotation_BGI_V1.32/MT_annotation_BGI.pl -i /mnt/HDD5/project/mitoz/trial/15th/tmp_annotated_mt_E_miyagawai_hunan.fasta_mitoscaf.fa/annotated_mt_E_miyagawai_hunan.fasta_mitoscaf.fa -d /mnt/HDD5/project/mitoz/flatwrom_custom_profiles/MT_database/Nematoda_CDS_protein.fa -o ./ -g 5 -cpu 8

since the stderr output was not provided, I can't figure out what was wrong with it.

Best

[microbpro-cat]

mitoz.log

summary.txt

I didn't know what upload, so I uploaded as much as I can.

[linzhi2013]

In *nix system, when you run a command, for example, mitoz 1>m.log 2>m.err , the standard output goes to the file m.log, and the standard error goes to the file m.err.

In your case, you should do something like:

mitoz annotate \
--fastafiles /mnt/HDD5/project/Echino_RefMitogenomes/E_miyagawai_hunan.fasta \
--outprefix annotated_mt \
--species_name "Echinostoma mekongi" \
--clade Nematoda \
--workdir /mnt/HDD5/project/mitoz/trial/14th  1>m.log 2>m.err

and then upload both m.log and m.err.

[microbpro-cat]

m.log

m.err.zip
m.err file is not allowed to upload, so I compressed the file. Thank you.

[linzhi2013]

2025-04-17 14:33:02,553 - mitoz.utility.utility - INFO - 
export WISECONFIGDIR=/mnt/HDD5/project/mitoz/soft/mitoz3.6/share/wise2/wisecfg
perl /mnt/HDD5/project/mitoz/soft/mitoz3.6/lib/python3.8/site-packages/mitoz/annotate/script/MT_annotation_BGI_V1.32/MT_annotation_BGI.pl -i /mnt/HDD5/project/mitoz/trial/14th/tmp_annotated_mt_E_miyagawai_hunan.fasta_mitoscaf.fa/annotated_mt_E_miyagawai_hunan.fasta_mitoscaf.fa -d /mnt/HDD5/project/mitoz/soft/mitoz3.6/lib/python3.8/site-packages/mitoz/profiles/MT_database/Nematoda_CDS_protein.fa -o ./ -g 5 -cpu 8


makeblastdb -in /mnt/HDD5/project/mitoz/trial/14th/tmp_annotated_mt_E_miyagawai_hunan.fasta_mitoscaf.fa/annotated_mt_E_miyagawai_hunan.fasta_mitoscaf.fa -dbtype nucl
Error: NCBI C++ Exception:
    T0 "/opt/conda/conda-bld/blast_1658184301332/work/blast/c++/src/objtools/blast/seqdb_writer/build_db.cpp", line 1069: Error: (CMultisourceException::eInvalid) BLASTDB::ncbi::CBuildDatabase::CreateDirectories() - You do not have write permissions on 'tmp_annotated_mt_E_miyagawai_hunan.fasta_mitoscaf.fa'

run the tblastn shell file
BLAST Database error: No alias or index file found for nucleotide database [/mnt/HDD5/project/mitoz/trial/14th/tmp_annotated_mt_E_miyagawai_hunan.fasta_mitoscaf.fa/annotated_mt_E_miyagawai_hunan.fasta_mitoscaf.fa] in search path [/mnt/HDD5/project/mitoz/trial/14th/tmp_annotated_mt_E_miyagawai_hunan.fasta_mitoscaf.fa::]

[microbpro-cat]

What does the error mean? I don't get the error.

[linzhi2013]

I don't know why you got You do not have write permissions on 'tmp_annotated_mt_E_miyagawai_hunan.fasta_mitoscaf.fa'

[microbpro-cat]

Because of the log 'You do not have write permissions' I tried at a different tower. But still PCGs were not annotated. I'll upload my log and other files.

mitoz.log
m.log

m.err.zip

annotated_mt_get127.fasta_mitoscaf.fa.most_related_species.txt

summary.txt

[linzhi2013]

In the m.err file,

regular match fails: >YP_009519769.1_cytb_NC_039532_Ref1:368aa	[mRNA]	locus=GetO_127:761:1867:+

regular match fails: >YP_009519770.1_nd4l_NC_039532_Ref4:90aa	[mRNA]	locus=GetO_127:1871:2140:+

regular match fails: >YP_009519771.1_nd4_NC_039532_Ref2:420aa	[mRNA]	locus=GetO_127:2104:3384:+

regular match fails: >YP_009519772.1_atp6_NC_039532_Ref1:172aa	[mRNA]	locus=GetO_127:3625:4140:+

regular match fails: >YP_009519773.1_nd2_NC_039532_Ref12:289aa	[mRNA]	locus=GetO_127:4153:5019:+

regular match fails: >YP_009519774.1_nd1_NC_039532_Ref1:289aa	[mRNA]	locus=GetO_127:5256:6155:+

regular match fails: >YP_009519776.1_cox1_NC_039532_Ref2:512aa	[mRNA]	locus=GetO_127:6957:8492:+

regular match fails: >YP_009519777.1_cox2_NC_039532_Ref1:202aa	[mRNA]	locus=GetO_127:10404:11009:+

regular match fails: >YP_009519778.1_nd6_NC_039532_Ref1:150aa	[mRNA]	locus=GetO_127:11024:11473:+

regular match fails: >YP_009519779.1_nd5_NC_039532_Ref14:509aa	[mRNA]	locus=GetO_127:11819:13381:+

regular match fails: >YP_009734327.1_cox3_NC_046395_Ref1:214aa	[mRNA]	locus=GetO_127:42:683:+

regular match fails: >YP_009734334.1_nad3_NC_046395_Ref1:118aa	[mRNA]	locus=GetO_127:6461:6814:+

Did you create a custom database? these sequence IDs do not follow the required format (https://github.com/linzhi2013/MitoZ/wiki/Extending-MitoZ-s-database)

gi_NC_XXX_YYY_Cerapanorpa_obtusa_319_aa

please use the standard gene names, e.g., COX1 instead of cox1.

[microbpro-cat]

m.err.zip

m.log
mitoz.log

summary.txt

I used the standard gene names, e.g., COX1 instead of cox1.
but still have the same issue. would you check this problem again? Thank you.