[2024-01-24 12:06:12,912] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:12,919] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:12,919] [INFO] DQC Reference Directory: /var/lib/cwl/stgd8355175-03c5-49ec-816b-bcd5c24e147d/dqc_reference
[2024-01-24 12:06:14,308] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:14,308] [INFO] Task started: Prodigal
[2024-01-24 12:06:14,309] [INFO] Running command: gunzip -c /var/lib/cwl/stg18ce7070-8b2b-4929-9d52-d4bad5ddf41b/GCF_016056375.1_ASM1605637v1_genomic.fna.gz | prodigal -d GCF_016056375.1_ASM1605637v1_genomic.fna/cds.fna -a GCF_016056375.1_ASM1605637v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:48,243] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:48,244] [INFO] Task started: HMMsearch
[2024-01-24 12:06:48,244] [INFO] Running command: hmmsearch --tblout GCF_016056375.1_ASM1605637v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd8355175-03c5-49ec-816b-bcd5c24e147d/dqc_reference/reference_markers.hmm GCF_016056375.1_ASM1605637v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:48,578] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:48,580] [INFO] Found 6/6 markers.
[2024-01-24 12:06:48,625] [INFO] Query marker FASTA was written to GCF_016056375.1_ASM1605637v1_genomic.fna/markers.fasta
[2024-01-24 12:06:48,625] [INFO] Task started: Blastn
[2024-01-24 12:06:48,626] [INFO] Running command: blastn -query GCF_016056375.1_ASM1605637v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd8355175-03c5-49ec-816b-bcd5c24e147d/dqc_reference/reference_markers.fasta -out GCF_016056375.1_ASM1605637v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:49,308] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:49,311] [INFO] Selected 14 target genomes.
[2024-01-24 12:06:49,311] [INFO] Target genome list was writen to GCF_016056375.1_ASM1605637v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:49,323] [INFO] Task started: fastANI
[2024-01-24 12:06:49,323] [INFO] Running command: fastANI --query /var/lib/cwl/stg18ce7070-8b2b-4929-9d52-d4bad5ddf41b/GCF_016056375.1_ASM1605637v1_genomic.fna.gz --refList GCF_016056375.1_ASM1605637v1_genomic.fna/target_genomes.txt --output GCF_016056375.1_ASM1605637v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:07:10,088] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:10,089] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd8355175-03c5-49ec-816b-bcd5c24e147d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:07:10,089] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd8355175-03c5-49ec-816b-bcd5c24e147d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:07:10,101] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:07:10,101] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:07:10,101] [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
Hymenobacter artigasi	strain=1B	GCA_012275535.1	2719616	2719616	type	True	87.5533	1322	1708	95	below_threshold
Hymenobacter rubidus	strain=DG7B	GCA_016734815.1	1441626	1441626	type	True	85.0374	1198	1708	95	below_threshold
Hymenobacter terricola	strain=3F2	GCA_017921975.2	2819236	2819236	type	True	84.898	1279	1708	95	below_threshold
Hymenobacter ruricola	strain=BT662	GCA_015694525.1	2791023	2791023	type	True	84.7866	1269	1708	95	below_threshold
Hymenobacter properus	strain=BT439	GCA_015694735.1	2791026	2791026	type	True	84.7299	1281	1708	95	below_threshold
Hymenobacter armeniacus	strain=BT189	GCA_014699055.1	2771358	2771358	type	True	84.7293	1262	1708	95	below_threshold
Hymenobacter frigidus	strain=CGMCC 1.14966	GCA_014640435.1	1524095	1524095	type	True	83.486	1045	1708	95	below_threshold
Hymenobacter sedentarius	strain=DG5B	GCA_001507645.1	1411621	1411621	type	True	83.0186	1092	1708	95	below_threshold
Hymenobacter lapidarius	strain=CCM 8643	GCA_001816145.1	1908237	1908237	type	True	82.7365	981	1708	95	below_threshold
Hymenobacter glacialis	strain=CCM 8648	GCA_001816165.1	1908236	1908236	type	True	82.5527	965	1708	95	below_threshold
Hymenobacter jeongseonensis	strain=BT683	GCA_015694725.1	2791027	2791027	type	True	82.3033	1030	1708	95	below_threshold
Hymenobacter montanus	strain=BT664	GCA_014699115.1	2771359	2771359	type	True	80.919	896	1708	95	below_threshold
Hymenobacter guriensis	strain=BT594	GCA_015773195.1	2793065	2793065	type	True	78.9152	682	1708	95	below_threshold
Hymenobacter metallicola	strain=9PBR-1	GCA_004745645.1	2563114	2563114	type	True	78.7247	679	1708	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:07:10,103] [INFO] DFAST Taxonomy check result was written to GCF_016056375.1_ASM1605637v1_genomic.fna/tc_result.tsv
[2024-01-24 12:07:10,103] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:07:10,103] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:07:10,103] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd8355175-03c5-49ec-816b-bcd5c24e147d/dqc_reference/checkm_data
[2024-01-24 12:07:10,104] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:07:10,160] [INFO] Task started: CheckM
[2024-01-24 12:07:10,160] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016056375.1_ASM1605637v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016056375.1_ASM1605637v1_genomic.fna/checkm_input GCF_016056375.1_ASM1605637v1_genomic.fna/checkm_result
[2024-01-24 12:08:32,078] [INFO] Task succeeded: CheckM
[2024-01-24 12:08:32,080] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:08:32,102] [INFO] ===== Completeness check finished =====
[2024-01-24 12:08:32,103] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:08:32,103] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016056375.1_ASM1605637v1_genomic.fna/markers.fasta)
[2024-01-24 12:08:32,104] [INFO] Task started: Blastn
[2024-01-24 12:08:32,104] [INFO] Running command: blastn -query GCF_016056375.1_ASM1605637v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd8355175-03c5-49ec-816b-bcd5c24e147d/dqc_reference/reference_markers_gtdb.fasta -out GCF_016056375.1_ASM1605637v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:08:33,040] [INFO] Task succeeded: Blastn
[2024-01-24 12:08:33,044] [INFO] Selected 12 target genomes.
[2024-01-24 12:08:33,044] [INFO] Target genome list was writen to GCF_016056375.1_ASM1605637v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:08:33,054] [INFO] Task started: fastANI
[2024-01-24 12:08:33,054] [INFO] Running command: fastANI --query /var/lib/cwl/stg18ce7070-8b2b-4929-9d52-d4bad5ddf41b/GCF_016056375.1_ASM1605637v1_genomic.fna.gz --refList GCF_016056375.1_ASM1605637v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016056375.1_ASM1605637v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:08:48,513] [INFO] Task succeeded: fastANI
[2024-01-24 12:08:48,526] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:08:48,526] [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_016056375.1	s__Hymenobacter negativus_A	100.0	1708	1708	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	97.78	97.78	0.95	0.95	3	conclusive
GCF_012275535.1	s__Hymenobacter artigasi	87.5537	1322	1708	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018967845.1	s__Hymenobacter sp018967845	87.1237	1239	1708	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	99.02	98.98	0.94	0.93	3	-
GCF_016734815.1	s__Hymenobacter rubidus	85.0472	1196	1708	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016427455.1	s__Hymenobacter sp016427455	84.7679	1233	1708	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	95.46	95.46	0.89	0.89	2	-
GCF_015694525.1	s__Hymenobacter ruricola	84.7594	1272	1708	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015694735.1	s__Hymenobacter properus	84.7032	1284	1708	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_017571495.1	s__Hymenobacter negativus	83.3066	1260	1708	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001507645.1	s__Hymenobacter sedentarius	83.0293	1091	1708	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001816145.1	s__Hymenobacter lapidarius	82.7618	978	1708	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015694725.1	s__Hymenobacter jeongseonensis	82.3178	1027	1708	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014699115.1	s__Hymenobacter sp014699115	80.9136	897	1708	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:08:48,528] [INFO] GTDB search result was written to GCF_016056375.1_ASM1605637v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:08:48,529] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:08:48,532] [INFO] DFAST_QC result json was written to GCF_016056375.1_ASM1605637v1_genomic.fna/dqc_result.json
[2024-01-24 12:08:48,533] [INFO] DFAST_QC completed!
[2024-01-24 12:08:48,533] [INFO] Total running time: 0h2m36s