-run_mode 3 command syntax

[linzhi2013]

-run_mode 3 command syntax

[linzhi2013]

Hello,

I would like to use -run_mode 3, but i'm not clear about which files to use. You provide this as your example:

python3 MitoZ.py all2 --genetic_code 5 --clade Arthropoda --outprefix test
--thread_number 12 --fastq1 clean.1.fq.gz --fastq2 clean.2.fq.gz
--fastq_read_length 150 --insert_size 250
--run_mode 3
--filter_taxa_method 1
--requiring_taxa 'Arthropoda'
--quick_mode_seq_file quickMode.fa
--quick_mode_fa_genes_file quick_mode_fa_genes.txt
--missing_PCGs ND4L ND6 ND2
--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

But I don't know how to write the command with these output files:

IC11_AAH1795_Hymenoptera_Ichneumonidae_Campodorus_ultimus.cds
IC11_AAH1795_Hymenoptera_Ichneumonidae_Campodorus_ultimus.fasta
IC11_AAH1795_Hymenoptera_Ichneumonidae_Campodorus_ultimus.misc_feature
IC11_AAH1795_Hymenoptera_Ichneumonidae_Campodorus_ultimus.rrna
IC11_AAH1795_Hymenoptera_Ichneumonidae_Campodorus_ultimus.trna
IC11_AAH1795_Hymenoptera_Ichneumonidae_Campodorus_ultimus_mitoscaf.fa.gbf
IC11_AAH1795_Hymenoptera_Ichneumonidae_Campodorus_ultimus_mitoscaf.fa.sqn
IC11_AAH1795_Hymenoptera_Ichneumonidae_Campodorus_ultimus_mitoscaf.fa.tbl
IC11_AAH1795_Hymenoptera_Ichneumonidae_Campodorus_ultimus_mitoscaf.fa.val
README.txt
circos.png
circos.svg
errorsummary.val
summary.txt
work71.hmmtblout.besthit.sim.filtered.high_abundance_10.0X.reformat.sorted.Not-picked
work71.hmmtblout.besthit.sim.filtered.high_abundance_10.0X.reformat.sorted.Not-picked.fa
work71.hmmtblout.besthit.sim.filtered.low_abundance
work71.hmmtblout.besthit.sim.filtered.low_abundance.fasta
work71.mitogenome.fa
work71.most_related_species.txt

• which mitogenome fasta file to use?
• which work71.hmmtblout.besthit.sim.filtered files to use?
• there are no clean.{1,2}.fq.gz files. Should I use python3 MitoZ.py all instead?

This is my attempt:

python3 MitoZ.py all2 --genetic_code 5 --clade Arthropoda --outprefix test
--thread_number 12 --fastq1 clean.1.fq.gz --fastq2 clean.2.fq.gz
--fastq_read_length 150 --insert_size 250
--run_mode 3
--filter_taxa_method 1
--requiring_taxa 'Arthropoda'
--quick_mode_seq_file work71.mitogenome.fa
--quick_mode_fa_genes_file work71.mitogenome_genes.txt
--missing_PCGs ATP6 ATP8 COX3 ND2 ND3 ND4 ND4L ND5
--quick_mode_score_file work71.hmmtblout.besthit.sim.filtered.high_abundance_10.0X.reformat.sorted.Not-picked
--quick_mode_prior_seq_file work71.hmmtblout.besthit.sim.filtered.high_abundance_10.0X.reformat.sorted.Not-picked.fa

Where work71.mitogenome_genes.txt contains the following text:

scaffold41 ND1 CYTB ND6
C5251 COX2 COX1

This is from the summary.txt

#Seq_id Length(bp) Circularity Closely_related_species
scaffold41 2499 no Diadegma semiclausum
C5251 2608 no Diadegma semiclausum

#Seq_id Start End Length(bp) Direction Type Gene_name Gene_prodcut Total_freq_occurred

scaffold41 21 930 910 + CDS ND1 NADH dehydrogenase subunit 1 1
scaffold41 933 1000 68 - tRNA trnS(uga) tRNA-Ser 1
scaffold41 1032 2191 1160 - CDS CYTB cytochrome b 1
scaffold41 2183 2486 304 - CDS ND6 NADH dehydrogenase subunit 6 1
C5251 92 156 65 - tRNA trnD(guc) tRNA-Asp 1
C5251 155 227 73 - tRNA trnK(cuu) tRNA-Lys 1
C5251 227 903 677 - CDS COX2 cytochrome c oxidase subunit II 1
C5251 962 2501 1540 - CDS COX1 cytochrome c oxidase subunit I 1

Protein coding genes totally found: 5

tRNA genes totally found: 3
rRNA genes totally found: 0
Genes totally found: 8

Potential missing genes:

#Gene total_missing_number
ATP6 1
ATP8 1
COX3 1
ND2 1
ND3 1
ND4 1
ND4L 1
ND5 1
l-rRNA 1
s-rRNA 1
tRNA-Ala 1
tRNA-Arg 1
tRNA-Asn 1
tRNA-Cys 1
tRNA-Gln 1
tRNA-Glu 1
tRNA-Gly 1
tRNA-His 1
tRNA-Ile 1
tRNA-Leu 2
tRNA-Met 1
tRNA-Phe 1
tRNA-Pro 1
tRNA-Ser 1
tRNA-Thr 1
tRNA-Trp 1
tRNA-Tyr 1
tRNA-Val 1
The missing genes might be foud from the
'.high_abundance' and '.low_abundance' files!

Hi Doug,

Sorry for the confusion.
In short, you can look for the files required by -run_mode 3 in your quick-mode-run tmp directory.

which mitogenome fasta file to use?

you can use the the file work71.mitogenome.fa. this is a file that should only contain correct mitochondrial sequences.

This file is also in tmp/ZZZ.assembly

which work71.hmmtblout.besthit.sim.filtered files to use?

In the tmp/ZZZ.assembly directory.

there are no clean.{1,2}.fq.gz files. Should I use python3 MitoZ.py all instead?

Generally, before NGS assembly, we have to filter our raw reads (provided by sequencing companies) and then use the clean reads to perform assembly.

1. Suppose now you have the raw reads, then you can run MitoZ with the all subcommand and with quick mode. In this case, MitoZ has output the clean reads and assembly under the tmp/ZZZ.cleandata directory,

2. If you already have your own 'clean' fastq files, you can just provide them to MitoZ for any run mode.

When you finish, you may also found some good results in work31.mitogenome.fa and work91.mitogenome.fa (in the result directory and/or tmp/ZZZ.assembly2 ) if you are lucky.

Please just ask if you still get into troubles.

guanliang