[2024-01-24 15:02:45,727] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:45,729] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:45,729] [INFO] DQC Reference Directory: /var/lib/cwl/stg426da40b-626e-4aff-874b-e23d63147576/dqc_reference
[2024-01-24 15:02:46,930] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:46,930] [INFO] Task started: Prodigal
[2024-01-24 15:02:46,931] [INFO] Running command: gunzip -c /var/lib/cwl/stg3ab35b6e-cd02-476c-9f93-957356e01924/GCF_001403795.1_J.donghaensisCECT7802_Velvet_Prokka_genomic.fna.gz | prodigal -d GCF_001403795.1_J.donghaensisCECT7802_Velvet_Prokka_genomic.fna/cds.fna -a GCF_001403795.1_J.donghaensisCECT7802_Velvet_Prokka_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:58,346] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:58,346] [INFO] Task started: HMMsearch
[2024-01-24 15:02:58,346] [INFO] Running command: hmmsearch --tblout GCF_001403795.1_J.donghaensisCECT7802_Velvet_Prokka_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg426da40b-626e-4aff-874b-e23d63147576/dqc_reference/reference_markers.hmm GCF_001403795.1_J.donghaensisCECT7802_Velvet_Prokka_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:02:58,629] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:02:58,632] [INFO] Found 6/6 markers.
[2024-01-24 15:02:58,677] [INFO] Query marker FASTA was written to GCF_001403795.1_J.donghaensisCECT7802_Velvet_Prokka_genomic.fna/markers.fasta
[2024-01-24 15:02:58,678] [INFO] Task started: Blastn
[2024-01-24 15:02:58,678] [INFO] Running command: blastn -query GCF_001403795.1_J.donghaensisCECT7802_Velvet_Prokka_genomic.fna/markers.fasta -db /var/lib/cwl/stg426da40b-626e-4aff-874b-e23d63147576/dqc_reference/reference_markers.fasta -out GCF_001403795.1_J.donghaensisCECT7802_Velvet_Prokka_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:59,643] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:59,647] [INFO] Selected 16 target genomes.
[2024-01-24 15:02:59,647] [INFO] Target genome list was writen to GCF_001403795.1_J.donghaensisCECT7802_Velvet_Prokka_genomic.fna/target_genomes.txt
[2024-01-24 15:02:59,656] [INFO] Task started: fastANI
[2024-01-24 15:02:59,657] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ab35b6e-cd02-476c-9f93-957356e01924/GCF_001403795.1_J.donghaensisCECT7802_Velvet_Prokka_genomic.fna.gz --refList GCF_001403795.1_J.donghaensisCECT7802_Velvet_Prokka_genomic.fna/target_genomes.txt --output GCF_001403795.1_J.donghaensisCECT7802_Velvet_Prokka_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:03:11,836] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:11,837] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg426da40b-626e-4aff-874b-e23d63147576/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:03:11,837] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg426da40b-626e-4aff-874b-e23d63147576/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:03:11,857] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:03:11,858] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:03:11,858] [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
Jannaschia marina	strain=SHC163	GCA_013404595.1	2741674	2741674	type	True	80.1222	750	1157	95	below_threshold
Jannaschia faecimaris	strain=DSM 100420	GCA_900107415.1	1244108	1244108	type	True	80.0591	703	1157	95	below_threshold
Jannaschia pohangensis	strain=DSM 19073	GCA_900113875.1	390807	390807	type	True	79.9341	691	1157	95	below_threshold
Jannaschia rubra	strain=CECT 5088	GCA_001403735.1	282197	282197	type	True	79.5227	570	1157	95	below_threshold
Jannaschia rubra	strain=DSM 16279	GCA_900113265.1	282197	282197	type	True	79.5037	575	1157	95	below_threshold
Jannaschia helgolandensis	strain=DSM 14858	GCA_900109285.1	188906	188906	type	True	79.3893	635	1157	95	below_threshold
Jannaschia formosa	strain=12N15	GCA_003340555.1	2259592	2259592	type	True	78.88	550	1157	95	below_threshold
Pseudooceanicola nanhaiensis	strain=CGMCC 1.6293	GCA_014645095.1	375761	375761	type	True	77.3316	303	1157	95	below_threshold
Pseudooceanicola nanhaiensis	strain=DSM 18065	GCA_000688295.1	375761	375761	type	True	77.331	300	1157	95	below_threshold
Loktanella atrilutea	strain=DSM 29326	GCA_900128995.1	366533	366533	type	True	77.2599	330	1157	95	below_threshold
Palleronia rufa	strain=MOLA 401	GCA_000743715.1	1530186	1530186	type	True	77.2031	275	1157	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	77.0243	281	1157	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	77.0236	281	1157	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	76.8644	300	1157	95	below_threshold
Mameliella sediminis	strain=DP3N28-2	GCA_019218285.1	2836866	2836866	type	True	76.8426	257	1157	95	below_threshold
Rhabdonatronobacter sediminivivens	strain=IM2376	GCA_013415485.1	2743469	2743469	type	True	76.6943	211	1157	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:03:11,860] [INFO] DFAST Taxonomy check result was written to GCF_001403795.1_J.donghaensisCECT7802_Velvet_Prokka_genomic.fna/tc_result.tsv
[2024-01-24 15:03:11,861] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:03:11,862] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:03:11,862] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg426da40b-626e-4aff-874b-e23d63147576/dqc_reference/checkm_data
[2024-01-24 15:03:11,864] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:03:11,904] [INFO] Task started: CheckM
[2024-01-24 15:03:11,904] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001403795.1_J.donghaensisCECT7802_Velvet_Prokka_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001403795.1_J.donghaensisCECT7802_Velvet_Prokka_genomic.fna/checkm_input GCF_001403795.1_J.donghaensisCECT7802_Velvet_Prokka_genomic.fna/checkm_result
[2024-01-24 15:03:49,347] [INFO] Task succeeded: CheckM
[2024-01-24 15:03:49,348] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:03:49,401] [INFO] ===== Completeness check finished =====
[2024-01-24 15:03:49,401] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:03:49,402] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001403795.1_J.donghaensisCECT7802_Velvet_Prokka_genomic.fna/markers.fasta)
[2024-01-24 15:03:49,402] [INFO] Task started: Blastn
[2024-01-24 15:03:49,402] [INFO] Running command: blastn -query GCF_001403795.1_J.donghaensisCECT7802_Velvet_Prokka_genomic.fna/markers.fasta -db /var/lib/cwl/stg426da40b-626e-4aff-874b-e23d63147576/dqc_reference/reference_markers_gtdb.fasta -out GCF_001403795.1_J.donghaensisCECT7802_Velvet_Prokka_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:51,149] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:51,154] [INFO] Selected 11 target genomes.
[2024-01-24 15:03:51,154] [INFO] Target genome list was writen to GCF_001403795.1_J.donghaensisCECT7802_Velvet_Prokka_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:03:51,162] [INFO] Task started: fastANI
[2024-01-24 15:03:51,162] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ab35b6e-cd02-476c-9f93-957356e01924/GCF_001403795.1_J.donghaensisCECT7802_Velvet_Prokka_genomic.fna.gz --refList GCF_001403795.1_J.donghaensisCECT7802_Velvet_Prokka_genomic.fna/target_genomes_gtdb.txt --output GCF_001403795.1_J.donghaensisCECT7802_Velvet_Prokka_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:04:00,629] [INFO] Task succeeded: fastANI
[2024-01-24 15:04:00,639] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:04:00,639] [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_001403795.1	s__Jannaschia donghaensis	100.0	1157	1157	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013404595.1	s__Jannaschia marina	80.1151	751	1157	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107415.1	s__Jannaschia faecimaris	80.0384	706	1157	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113875.1	s__Jannaschia pohangensis	79.948	688	1157	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001403735.1	s__Jannaschia rubra	79.5316	569	1157	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	99.99	99.99	0.99	0.99	2	-
GCF_900109285.1	s__Jannaschia helgolandensis	79.3893	635	1157	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003340555.1	s__Jannaschia formosa	78.8476	554	1157	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012395815.1	s__Roseicyclus sp012395815	77.7017	374	1157	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000688295.1	s__Pseudooceanicola nanhaiensis	77.3295	300	1157	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	100.00	100.00	1.00	1.00	2	-
GCA_006227805.1	s__Aestuariivita sp006227805	77.3155	229	1157	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariivita	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019218285.1	s__DP3N28-2 sp019218285	76.8338	258	1157	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__DP3N28-2	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:04:00,643] [INFO] GTDB search result was written to GCF_001403795.1_J.donghaensisCECT7802_Velvet_Prokka_genomic.fna/result_gtdb.tsv
[2024-01-24 15:04:00,644] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:04:00,650] [INFO] DFAST_QC result json was written to GCF_001403795.1_J.donghaensisCECT7802_Velvet_Prokka_genomic.fna/dqc_result.json
[2024-01-24 15:04:00,650] [INFO] DFAST_QC completed!
[2024-01-24 15:04:00,651] [INFO] Total running time: 0h1m15s