[2023-06-19 04:14:12,141] [INFO] DFAST_QC pipeline started.
[2023-06-19 04:14:12,143] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 04:14:12,143] [INFO] DQC Reference Directory: /var/lib/cwl/stg58df199e-9d83-4e3c-8721-003705358abf/dqc_reference
[2023-06-19 04:14:14,160] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 04:14:14,161] [INFO] Task started: Prodigal
[2023-06-19 04:14:14,161] [INFO] Running command: gunzip -c /var/lib/cwl/stgcbec390b-a749-45b6-81d7-db7d5ae47cd4/GCA_018006695.1_ASM1800669v1_genomic.fna.gz | prodigal -d GCA_018006695.1_ASM1800669v1_genomic.fna/cds.fna -a GCA_018006695.1_ASM1800669v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 04:14:20,024] [INFO] Task succeeded: Prodigal
[2023-06-19 04:14:20,024] [INFO] Task started: HMMsearch
[2023-06-19 04:14:20,024] [INFO] Running command: hmmsearch --tblout GCA_018006695.1_ASM1800669v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg58df199e-9d83-4e3c-8721-003705358abf/dqc_reference/reference_markers.hmm GCA_018006695.1_ASM1800669v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 04:14:20,255] [INFO] Task succeeded: HMMsearch
[2023-06-19 04:14:20,257] [WARNING] Found 1/6 markers. [/var/lib/cwl/stgcbec390b-a749-45b6-81d7-db7d5ae47cd4/GCA_018006695.1_ASM1800669v1_genomic.fna.gz]
[2023-06-19 04:14:20,285] [INFO] Query marker FASTA was written to GCA_018006695.1_ASM1800669v1_genomic.fna/markers.fasta
[2023-06-19 04:14:20,285] [INFO] Task started: Blastn
[2023-06-19 04:14:20,285] [INFO] Running command: blastn -query GCA_018006695.1_ASM1800669v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg58df199e-9d83-4e3c-8721-003705358abf/dqc_reference/reference_markers.fasta -out GCA_018006695.1_ASM1800669v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 04:14:20,791] [INFO] Task succeeded: Blastn
[2023-06-19 04:14:20,795] [INFO] Selected 5 target genomes.
[2023-06-19 04:14:20,796] [INFO] Target genome list was writen to GCA_018006695.1_ASM1800669v1_genomic.fna/target_genomes.txt
[2023-06-19 04:14:20,799] [INFO] Task started: fastANI
[2023-06-19 04:14:20,799] [INFO] Running command: fastANI --query /var/lib/cwl/stgcbec390b-a749-45b6-81d7-db7d5ae47cd4/GCA_018006695.1_ASM1800669v1_genomic.fna.gz --refList GCA_018006695.1_ASM1800669v1_genomic.fna/target_genomes.txt --output GCA_018006695.1_ASM1800669v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 04:14:25,160] [INFO] Task succeeded: fastANI
[2023-06-19 04:14:25,161] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg58df199e-9d83-4e3c-8721-003705358abf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 04:14:25,161] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg58df199e-9d83-4e3c-8721-003705358abf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 04:14:25,171] [INFO] Found 5 fastANI hits (5 hits with ANI > threshold)
[2023-06-19 04:14:25,172] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-19 04:14:25,172] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Aeromonas salmonicida subsp. pectinolytica	strain=34mel	GCA_000447435.2	96473	645	type	True	96.8117	464	544	95	conclusive
Aeromonas salmonicida subsp. salmonicida	strain=CIP 103209	GCA_000820065.1	29491	645	type	True	96.4463	465	544	95	conclusive
Aeromonas salmonicida	strain=NCTC12959	GCA_900445115.1	645	645	type	True	96.4118	468	544	95	conclusive
Aeromonas salmonicida subsp. masoucida	strain=NBRC 13784	GCA_000647955.1	197700	645	type	True	96.3482	456	544	95	conclusive
Aeromonas salmonicida subsp. salmonicida	strain=ATCC 33658	GCA_001643305.1	29491	645	type	True	96.3348	468	544	95	conclusive
--------------------------------------------------------------------------------
[2023-06-19 04:14:25,174] [INFO] DFAST Taxonomy check result was written to GCA_018006695.1_ASM1800669v1_genomic.fna/tc_result.tsv
[2023-06-19 04:14:25,175] [INFO] ===== Taxonomy check completed =====
[2023-06-19 04:14:25,175] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 04:14:25,175] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg58df199e-9d83-4e3c-8721-003705358abf/dqc_reference/checkm_data
[2023-06-19 04:14:25,177] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 04:14:25,205] [INFO] Task started: CheckM
[2023-06-19 04:14:25,206] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018006695.1_ASM1800669v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018006695.1_ASM1800669v1_genomic.fna/checkm_input GCA_018006695.1_ASM1800669v1_genomic.fna/checkm_result
[2023-06-19 04:14:49,010] [INFO] Task succeeded: CheckM
[2023-06-19 04:14:49,012] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 16.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 04:14:49,032] [INFO] ===== Completeness check finished =====
[2023-06-19 04:14:49,032] [INFO] ===== Start GTDB Search =====
[2023-06-19 04:14:49,033] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018006695.1_ASM1800669v1_genomic.fna/markers.fasta)
[2023-06-19 04:14:49,033] [INFO] Task started: Blastn
[2023-06-19 04:14:49,033] [INFO] Running command: blastn -query GCA_018006695.1_ASM1800669v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg58df199e-9d83-4e3c-8721-003705358abf/dqc_reference/reference_markers_gtdb.fasta -out GCA_018006695.1_ASM1800669v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 04:14:49,461] [INFO] Task succeeded: Blastn
[2023-06-19 04:14:49,466] [INFO] Selected 5 target genomes.
[2023-06-19 04:14:49,466] [INFO] Target genome list was writen to GCA_018006695.1_ASM1800669v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 04:14:49,471] [INFO] Task started: fastANI
[2023-06-19 04:14:49,471] [INFO] Running command: fastANI --query /var/lib/cwl/stgcbec390b-a749-45b6-81d7-db7d5ae47cd4/GCA_018006695.1_ASM1800669v1_genomic.fna.gz --refList GCA_018006695.1_ASM1800669v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018006695.1_ASM1800669v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 04:14:54,047] [INFO] Task succeeded: fastANI
[2023-06-19 04:14:54,058] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 04:14:54,058] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_001643305.1	s__Aeromonas salmonicida	96.3348	468	544	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	99.08	96.89	0.95	0.86	74	conclusive
GCF_000820005.1	s__Aeromonas piscicola	90.8915	453	544	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.5033	97.81	97.81	0.93	0.93	2	-
GCF_000819745.1	s__Aeromonas bestiarum	90.4581	461	544	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.5033	97.44	97.31	0.93	0.91	4	-
GCF_000820025.1	s__Aeromonas popoffii	89.1404	430	544	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	98.17	98.00	0.92	0.89	4	-
GCF_000764645.1	s__Aeromonas finlandensis	85.8062	387	544	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 04:14:54,060] [INFO] GTDB search result was written to GCA_018006695.1_ASM1800669v1_genomic.fna/result_gtdb.tsv
[2023-06-19 04:14:54,061] [INFO] ===== GTDB Search completed =====
[2023-06-19 04:14:54,065] [INFO] DFAST_QC result json was written to GCA_018006695.1_ASM1800669v1_genomic.fna/dqc_result.json
[2023-06-19 04:14:54,065] [INFO] DFAST_QC completed!
[2023-06-19 04:14:54,065] [INFO] Total running time: 0h0m42s