[2024-01-24 15:18:32,525] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:32,527] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:32,527] [INFO] DQC Reference Directory: /var/lib/cwl/stg43ffa356-2807-43eb-9e1f-200ae8ecc3f8/dqc_reference
[2024-01-24 15:18:34,812] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:34,814] [INFO] Task started: Prodigal
[2024-01-24 15:18:34,814] [INFO] Running command: gunzip -c /var/lib/cwl/stgc2ff5285-1534-4b52-8b9a-271c090a2f50/GCF_002934445.1_ASM293444v1_genomic.fna.gz | prodigal -d GCF_002934445.1_ASM293444v1_genomic.fna/cds.fna -a GCF_002934445.1_ASM293444v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:44,227] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:44,227] [INFO] Task started: HMMsearch
[2024-01-24 15:18:44,227] [INFO] Running command: hmmsearch --tblout GCF_002934445.1_ASM293444v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg43ffa356-2807-43eb-9e1f-200ae8ecc3f8/dqc_reference/reference_markers.hmm GCF_002934445.1_ASM293444v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:44,450] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:44,451] [INFO] Found 6/6 markers.
[2024-01-24 15:18:44,478] [INFO] Query marker FASTA was written to GCF_002934445.1_ASM293444v1_genomic.fna/markers.fasta
[2024-01-24 15:18:44,478] [INFO] Task started: Blastn
[2024-01-24 15:18:44,478] [INFO] Running command: blastn -query GCF_002934445.1_ASM293444v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg43ffa356-2807-43eb-9e1f-200ae8ecc3f8/dqc_reference/reference_markers.fasta -out GCF_002934445.1_ASM293444v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:45,088] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:45,091] [INFO] Selected 14 target genomes.
[2024-01-24 15:18:45,091] [INFO] Target genome list was writen to GCF_002934445.1_ASM293444v1_genomic.fna/target_genomes.txt
[2024-01-24 15:18:45,139] [INFO] Task started: fastANI
[2024-01-24 15:18:45,140] [INFO] Running command: fastANI --query /var/lib/cwl/stgc2ff5285-1534-4b52-8b9a-271c090a2f50/GCF_002934445.1_ASM293444v1_genomic.fna.gz --refList GCF_002934445.1_ASM293444v1_genomic.fna/target_genomes.txt --output GCF_002934445.1_ASM293444v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:18:54,093] [INFO] Task succeeded: fastANI
[2024-01-24 15:18:54,093] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg43ffa356-2807-43eb-9e1f-200ae8ecc3f8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:18:54,093] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg43ffa356-2807-43eb-9e1f-200ae8ecc3f8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:18:54,104] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:18:54,104] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:18:54,104] [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
Nonlabens xylanidelens	strain=DSM 16809	GCA_002934445.1	191564	191564	type	True	100.0	1080	1081	95	conclusive
Nonlabens xylanidelens	strain=DSM 16809	GCA_002954345.1	191564	191564	type	True	99.9923	1080	1081	95	conclusive
Nonlabens ulvanivorans	strain=DSM 22727	GCA_003001855.1	906888	906888	type	True	79.5423	400	1081	95	below_threshold
Nonlabens dokdonensis	strain=DSM 17205	GCA_003254015.1	328515	328515	type	True	79.4314	555	1081	95	below_threshold
Nonlabens dokdonensis	strain=DSW-6	GCA_000332115.1	328515	328515	type	True	79.4298	563	1081	95	below_threshold
Nonlabens ulvanivorans	strain=PLR	GCA_000732625.1	906888	906888	type	True	79.4167	404	1081	95	below_threshold
Nonlabens arenilitoris	strain=KCTC 32109	GCA_002954765.1	1217969	1217969	type	True	79.0316	395	1081	95	below_threshold
Nonlabens spongiae	strain=JCM 13191	GCA_002117125.1	331648	331648	type	True	76.74	130	1081	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	76.4519	68	1081	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	76.4268	67	1081	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	76.3768	61	1081	95	below_threshold
Aureibaculum flavum	strain=A20	GCA_016406085.1	2795986	2795986	type	True	75.9619	57	1081	95	below_threshold
Aureibaculum luteum	strain=SM1352	GCA_003449015.1	1548456	1548456	type	True	75.8959	56	1081	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:18:54,106] [INFO] DFAST Taxonomy check result was written to GCF_002934445.1_ASM293444v1_genomic.fna/tc_result.tsv
[2024-01-24 15:18:54,107] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:18:54,107] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:18:54,107] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg43ffa356-2807-43eb-9e1f-200ae8ecc3f8/dqc_reference/checkm_data
[2024-01-24 15:18:54,108] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:18:54,140] [INFO] Task started: CheckM
[2024-01-24 15:18:54,141] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002934445.1_ASM293444v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002934445.1_ASM293444v1_genomic.fna/checkm_input GCF_002934445.1_ASM293444v1_genomic.fna/checkm_result
[2024-01-24 15:19:25,335] [INFO] Task succeeded: CheckM
[2024-01-24 15:19:25,336] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:19:25,357] [INFO] ===== Completeness check finished =====
[2024-01-24 15:19:25,357] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:19:25,358] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002934445.1_ASM293444v1_genomic.fna/markers.fasta)
[2024-01-24 15:19:25,358] [INFO] Task started: Blastn
[2024-01-24 15:19:25,358] [INFO] Running command: blastn -query GCF_002934445.1_ASM293444v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg43ffa356-2807-43eb-9e1f-200ae8ecc3f8/dqc_reference/reference_markers_gtdb.fasta -out GCF_002934445.1_ASM293444v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:26,158] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:26,161] [INFO] Selected 8 target genomes.
[2024-01-24 15:19:26,161] [INFO] Target genome list was writen to GCF_002934445.1_ASM293444v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:19:26,183] [INFO] Task started: fastANI
[2024-01-24 15:19:26,183] [INFO] Running command: fastANI --query /var/lib/cwl/stgc2ff5285-1534-4b52-8b9a-271c090a2f50/GCF_002934445.1_ASM293444v1_genomic.fna.gz --refList GCF_002934445.1_ASM293444v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002934445.1_ASM293444v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:19:32,084] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:32,092] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:19:32,092] [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_002934445.1	s__Nonlabens xylanidelens	100.0	1080	1081	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCA_002162835.1	s__Nonlabens dokdonensis_B	79.6597	473	1081	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002831625.1	s__Nonlabens sp002831625	79.58	533	1081	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012974865.1	s__Nonlabens sp012974865	79.5462	552	1081	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000332115.1	s__Nonlabens dokdonensis	79.4472	561	1081	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002954765.1	s__Nonlabens arenilitoris	79.0316	395	1081	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018401815.1	s__Nonlabens sp018401815	78.9539	459	1081	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	99.14	99.12	0.97	0.97	3	-
GCF_002117125.1	s__Nonlabens spongiae	76.7575	129	1081	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:19:32,094] [INFO] GTDB search result was written to GCF_002934445.1_ASM293444v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:19:32,094] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:19:32,098] [INFO] DFAST_QC result json was written to GCF_002934445.1_ASM293444v1_genomic.fna/dqc_result.json
[2024-01-24 15:19:32,098] [INFO] DFAST_QC completed!
[2024-01-24 15:19:32,098] [INFO] Total running time: 0h0m60s