[2024-01-24 13:43:27,036] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:43:27,037] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:43:27,038] [INFO] DQC Reference Directory: /var/lib/cwl/stg82bc4350-a1eb-494a-819d-f1f50b6d3594/dqc_reference
[2024-01-24 13:43:28,237] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:43:28,238] [INFO] Task started: Prodigal
[2024-01-24 13:43:28,239] [INFO] Running command: gunzip -c /var/lib/cwl/stg25e7c260-d811-4941-a616-03c32167c959/GCF_015330125.1_ASM1533012v1_genomic.fna.gz | prodigal -d GCF_015330125.1_ASM1533012v1_genomic.fna/cds.fna -a GCF_015330125.1_ASM1533012v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:43:45,760] [INFO] Task succeeded: Prodigal
[2024-01-24 13:43:45,760] [INFO] Task started: HMMsearch
[2024-01-24 13:43:45,760] [INFO] Running command: hmmsearch --tblout GCF_015330125.1_ASM1533012v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg82bc4350-a1eb-494a-819d-f1f50b6d3594/dqc_reference/reference_markers.hmm GCF_015330125.1_ASM1533012v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:43:45,993] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:43:45,994] [INFO] Found 6/6 markers.
[2024-01-24 13:43:46,032] [INFO] Query marker FASTA was written to GCF_015330125.1_ASM1533012v1_genomic.fna/markers.fasta
[2024-01-24 13:43:46,033] [INFO] Task started: Blastn
[2024-01-24 13:43:46,033] [INFO] Running command: blastn -query GCF_015330125.1_ASM1533012v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg82bc4350-a1eb-494a-819d-f1f50b6d3594/dqc_reference/reference_markers.fasta -out GCF_015330125.1_ASM1533012v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:43:46,684] [INFO] Task succeeded: Blastn
[2024-01-24 13:43:46,687] [INFO] Selected 11 target genomes.
[2024-01-24 13:43:46,688] [INFO] Target genome list was writen to GCF_015330125.1_ASM1533012v1_genomic.fna/target_genomes.txt
[2024-01-24 13:43:46,691] [INFO] Task started: fastANI
[2024-01-24 13:43:46,691] [INFO] Running command: fastANI --query /var/lib/cwl/stg25e7c260-d811-4941-a616-03c32167c959/GCF_015330125.1_ASM1533012v1_genomic.fna.gz --refList GCF_015330125.1_ASM1533012v1_genomic.fna/target_genomes.txt --output GCF_015330125.1_ASM1533012v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:43:56,737] [INFO] Task succeeded: fastANI
[2024-01-24 13:43:56,737] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg82bc4350-a1eb-494a-819d-f1f50b6d3594/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:43:56,737] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg82bc4350-a1eb-494a-819d-f1f50b6d3594/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:43:56,746] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:43:56,746] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:43:56,746] [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
Zobellia nedashkovskayae	strain=Asnod2-B07-B	GCA_015330125.1	2779510	2779510	type	True	100.0	1645	1645	95	conclusive
Zobellia barbeyronii	strain=KMM 6746	GCA_018603515.1	2748009	2748009	type	True	90.4897	1392	1645	95	below_threshold
Zobellia laminariae	strain=KMM 3676	GCA_009725995.1	248906	248906	type	True	89.9943	1379	1645	95	below_threshold
Zobellia amurskyensis	strain=KMM 3526	GCA_009725985.1	248905	248905	type	True	83.6165	1097	1645	95	below_threshold
Zobellia roscoffensis	strain=Asnod1-F08	GCA_015330165.1	2779508	2779508	type	True	83.0292	1060	1645	95	below_threshold
Zobellia russellii	strain=KMM 3677	GCA_018728565.1	248907	248907	type	True	81.2397	945	1645	95	below_threshold
Flavobacterium davisii	strain=90-106	GCA_019565505.1	2906077	2906077	type	True	76.5163	50	1645	95	below_threshold
Muricauda aurantiaca	strain=HME9304	GCA_003269425.1	1383885	1383885	type	True	76.3466	105	1645	95	below_threshold
Salegentibacter lacus	strain=LM13S	GCA_020164555.1	2873599	2873599	type	True	76.0476	58	1645	95	below_threshold
Flavobacterium defluvii	strain=DSM 17963	GCA_900129555.1	370979	370979	type	True	75.9779	58	1645	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:43:56,748] [INFO] DFAST Taxonomy check result was written to GCF_015330125.1_ASM1533012v1_genomic.fna/tc_result.tsv
[2024-01-24 13:43:56,748] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:43:56,748] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:43:56,748] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg82bc4350-a1eb-494a-819d-f1f50b6d3594/dqc_reference/checkm_data
[2024-01-24 13:43:56,749] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:43:56,795] [INFO] Task started: CheckM
[2024-01-24 13:43:56,796] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015330125.1_ASM1533012v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015330125.1_ASM1533012v1_genomic.fna/checkm_input GCF_015330125.1_ASM1533012v1_genomic.fna/checkm_result
[2024-01-24 13:44:46,495] [INFO] Task succeeded: CheckM
[2024-01-24 13:44:46,496] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:44:46,511] [INFO] ===== Completeness check finished =====
[2024-01-24 13:44:46,512] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:44:46,512] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015330125.1_ASM1533012v1_genomic.fna/markers.fasta)
[2024-01-24 13:44:46,512] [INFO] Task started: Blastn
[2024-01-24 13:44:46,512] [INFO] Running command: blastn -query GCF_015330125.1_ASM1533012v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg82bc4350-a1eb-494a-819d-f1f50b6d3594/dqc_reference/reference_markers_gtdb.fasta -out GCF_015330125.1_ASM1533012v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:44:47,373] [INFO] Task succeeded: Blastn
[2024-01-24 13:44:47,380] [INFO] Selected 8 target genomes.
[2024-01-24 13:44:47,380] [INFO] Target genome list was writen to GCF_015330125.1_ASM1533012v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:44:47,389] [INFO] Task started: fastANI
[2024-01-24 13:44:47,389] [INFO] Running command: fastANI --query /var/lib/cwl/stg25e7c260-d811-4941-a616-03c32167c959/GCF_015330125.1_ASM1533012v1_genomic.fna.gz --refList GCF_015330125.1_ASM1533012v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015330125.1_ASM1533012v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:44:56,679] [INFO] Task succeeded: fastANI
[2024-01-24 13:44:56,686] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:44:56,686] [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_015330125.1	s__Zobellia sp015330125	100.0	1645	1645	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	98.14	98.14	0.92	0.92	2	conclusive
GCF_018603515.1	s__Zobellia sp018603515	90.4897	1392	1645	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009725995.1	s__Zobellia laminariae	89.9943	1379	1645	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860745.1	s__Zobellia uliginosa_B	84.9055	1180	1645	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009725985.1	s__Zobellia amurskyensis	83.6332	1095	1645	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	98.14	98.14	0.91	0.91	2	-
GCF_015330165.1	s__Zobellia sp015330165	83.0292	1060	1645	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	98.41	98.41	0.92	0.92	2	-
GCF_018728565.1	s__Zobellia russellii	81.2395	945	1645	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	97.51	97.51	0.91	0.91	2	-
GCF_003269425.1	s__Muricauda maritima	76.3466	105	1645	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:44:56,689] [INFO] GTDB search result was written to GCF_015330125.1_ASM1533012v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:44:56,690] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:44:56,693] [INFO] DFAST_QC result json was written to GCF_015330125.1_ASM1533012v1_genomic.fna/dqc_result.json
[2024-01-24 13:44:56,693] [INFO] DFAST_QC completed!
[2024-01-24 13:44:56,693] [INFO] Total running time: 0h1m30s