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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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[tbl2asn] This copy of tbl2asn is more than a year old. Please download the current version #113

Closed QindongTang closed 2 years ago

QindongTang commented 3 years ago

Hi I was trying to run multi-Kmer mode after all2 but had error as following: `[tbl2asn] This copy of tbl2asn is more than a year old. Please download the current version. [tbl2asn] SeqID lcl|work71_C368266 is present on multiple Bioseqs in record 2021-03-05 16:53:56 /storage/home/tang/software/Miniconda3/ENTER/envs/mitozEnv/bin/python3 /storage/projects/Riparia/softwares/mitoz/release_MitoZ_v2.3/bin/common/genbank_gene_stat_v2.py kmer_mitoscaf.fa.gbf kmer.most_related_species.txt all2 > summary.txt

Traceback (most recent call last): File "/storage/projects/Riparia/softwares/mitoz/release_MitoZ_v2.3/bin/common/genbank_gene_stat_v2.py", line 238, in main() File "/storage/projects/Riparia/softwares/mitoz/release_MitoZ_v2.3/bin/common/genbank_gene_stat_v2.py", line 202, in main seqid_len_topology_relatedSP = get_seq_topology_and_related_sp(gbfile=gbfile, closely_related_sp_file=closely_related_sp_file) File "/storage/projects/Riparia/softwares/mitoz/release_MitoZ_v2.3/bin/common/genbank_gene_stat_v2.py", line 173, in get_seq_topology_and_related_sp for rec in SeqIO.parse(gbfile, 'gb'): File "/storage/home/tang/software/Miniconda3/ENTER/envs/mitozEnv/lib/python3.6/site-packages/Bio/SeqIO/init.py", line 607, in parse return iterator_generator(handle) File "/storage/home/tang/software/Miniconda3/ENTER/envs/mitozEnv/lib/python3.6/site-packages/Bio/SeqIO/InsdcIO.py", line 93, in init super().init(source, mode="t", fmt="GenBank") File "/storage/home/tang/software/Miniconda3/ENTER/envs/mitozEnv/lib/python3.6/site-packages/Bio/SeqIO/Interfaces.py", line 47, in init self.stream = open(source, "r" + mode) FileNotFoundError: [Errno 2] No such file or directory: 'kmer_mitoscaf.fa.gbf' Error occured when running command: /storage/home/tang/software/Miniconda3/ENTER/envs/mitozEnv/bin/python3 /storage/projects/Riparia/softwares/mitoz/release_MitoZ_v2.3/bin/common/genbank_gene_stat_v2.py kmer_mitoscaf.fa.gbf kmer.most_related_species.txt all2 > summary.txt`

my code as following:

python3 /storage/projects/Riparia/softwares/mitoz/release_MitoZ_v2.3/MitoZ.py all2 --genetic_code 2 --clade Chordata --outprefix kmer \ --thread_number 12 \ --fastq1 /storage/projects/Riparia/mt_genome_assembly/Rdfyb6_zebra/Rdfyb6_zebra_unmapped_fq_clean.cleandata/clean.Rdfyb6_zebra_unmapped.R1.gz \ --fastq2 /storage/projects/Riparia/mt_genome_assembly/Rdfyb6_zebra/Rdfyb6_zebra_unmapped_fq_clean.cleandata/clean.Rdfyb6_zebra_unmapped.R2.gz \ --fastq_read_length 137 --insert_size 250 \ --run_mode 3 \ --filter_taxa_method 1 \ --requiring_taxa 'Chordata' \ --quick_mode_seq_file work71.hmmout.fa \ --quick_mode_fa_genes_file quick_mode_fa_genes.txt \ --missing_PCGs ND4L ND5 ND6 tRNA-His tRNA-Leu tRNA-Ser \ --quick_mode_score_file work71.hmmtblout.besthit.sim.filtered.high_abundance_10.0X.reformat.sorted \ --quick_mode_prior_seq_file work71.hmmtblout.besthit.sim.filtered.fa

I couldn't find what caused the problem and which step generate the gbf file in the log file. Thanks for reply!

linzhi2013 commented 3 years ago

Probably it was because [tbl2asn] This copy of tbl2asn is more than a year old. Please download the current version.. This program is from NCBI, and I knew that if this message is printed out, then the program will NOT run and just exit. Therefore, here it failed to generate the kmer_mitoscaf.fa.gbf file.

You can enter the mitozEnv environment first, for example

$ source activate mitozEnv

then update the tbl2asn program by:

$ conda update tbl2asn