[2024-01-24 10:57:50,265] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:50,266] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:50,267] [INFO] DQC Reference Directory: /var/lib/cwl/stge1545c9d-2174-4572-af6b-bde0aacb42f5/dqc_reference
[2024-01-24 10:57:52,640] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:52,641] [INFO] Task started: Prodigal
[2024-01-24 10:57:52,641] [INFO] Running command: gunzip -c /var/lib/cwl/stg695adc08-306d-4616-946f-50f843528009/GCF_017921975.2_ASM1792197v2_genomic.fna.gz | prodigal -d GCF_017921975.2_ASM1792197v2_genomic.fna/cds.fna -a GCF_017921975.2_ASM1792197v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:58:32,665] [INFO] Task succeeded: Prodigal
[2024-01-24 10:58:32,665] [INFO] Task started: HMMsearch
[2024-01-24 10:58:32,666] [INFO] Running command: hmmsearch --tblout GCF_017921975.2_ASM1792197v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge1545c9d-2174-4572-af6b-bde0aacb42f5/dqc_reference/reference_markers.hmm GCF_017921975.2_ASM1792197v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:58:32,984] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:58:32,986] [INFO] Found 6/6 markers.
[2024-01-24 10:58:33,038] [INFO] Query marker FASTA was written to GCF_017921975.2_ASM1792197v2_genomic.fna/markers.fasta
[2024-01-24 10:58:33,038] [INFO] Task started: Blastn
[2024-01-24 10:58:33,038] [INFO] Running command: blastn -query GCF_017921975.2_ASM1792197v2_genomic.fna/markers.fasta -db /var/lib/cwl/stge1545c9d-2174-4572-af6b-bde0aacb42f5/dqc_reference/reference_markers.fasta -out GCF_017921975.2_ASM1792197v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:33,671] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:33,675] [INFO] Selected 17 target genomes.
[2024-01-24 10:58:33,676] [INFO] Target genome list was writen to GCF_017921975.2_ASM1792197v2_genomic.fna/target_genomes.txt
[2024-01-24 10:58:33,684] [INFO] Task started: fastANI
[2024-01-24 10:58:33,684] [INFO] Running command: fastANI --query /var/lib/cwl/stg695adc08-306d-4616-946f-50f843528009/GCF_017921975.2_ASM1792197v2_genomic.fna.gz --refList GCF_017921975.2_ASM1792197v2_genomic.fna/target_genomes.txt --output GCF_017921975.2_ASM1792197v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:55,038] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:55,038] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge1545c9d-2174-4572-af6b-bde0aacb42f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:55,039] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge1545c9d-2174-4572-af6b-bde0aacb42f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:55,057] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:58:55,058] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:58:55,058] [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 terricola	strain=3F2	GCA_017921975.2	2819236	2819236	type	True	100.0	2080	2089	95	conclusive
Hymenobacter artigasi	strain=1B	GCA_012275535.1	2719616	2719616	type	True	85.2225	1295	2089	95	below_threshold
Hymenobacter rubidus	strain=DG7B	GCA_016734815.1	1441626	1441626	type	True	84.777	1225	2089	95	below_threshold
Hymenobacter ruricola	strain=BT662	GCA_015694525.1	2791023	2791023	type	True	84.6825	1278	2089	95	below_threshold
Hymenobacter armeniacus	strain=BT189	GCA_014699055.1	2771358	2771358	type	True	84.551	1246	2089	95	below_threshold
Hymenobacter frigidus	strain=CGMCC 1.14966	GCA_014640435.1	1524095	1524095	type	True	84.0684	1105	2089	95	below_threshold
Hymenobacter properus	strain=BT439	GCA_015694735.1	2791026	2791026	type	True	83.8805	1237	2089	95	below_threshold
Hymenobacter sedentarius	strain=DG5B	GCA_001507645.1	1411621	1411621	type	True	83.8197	1153	2089	95	below_threshold
Hymenobacter glacialis	strain=CCM 8648	GCA_001816165.1	1908236	1908236	type	True	83.3756	995	2089	95	below_threshold
Hymenobacter lapidarius	strain=CCM 8643	GCA_001816145.1	1908237	1908237	type	True	83.3218	1063	2089	95	below_threshold
Hymenobacter jeongseonensis	strain=BT683	GCA_015694725.1	2791027	2791027	type	True	82.9485	1135	2089	95	below_threshold
Hymenobacter terrenus	strain=MIMtkLc17	GCA_000972495.1	1629124	1629124	type	True	82.1685	1112	2089	95	below_threshold
Hymenobacter montanus	strain=BT664	GCA_014699115.1	2771359	2771359	type	True	81.7855	972	2089	95	below_threshold
Hymenobacter guriensis	strain=BT594	GCA_015773195.1	2793065	2793065	type	True	78.9767	733	2089	95	below_threshold
Hymenobacter metallicola	strain=9PBR-1	GCA_004745645.1	2563114	2563114	type	True	78.6946	755	2089	95	below_threshold
Frankia canadensis		GCA_900197875.1	1836972	1836972	type	True	74.6588	94	2089	95	below_threshold
Lujinxingia vulgaris	strain=TMQ4	GCA_007997015.1	2600176	2600176	type	True	74.6322	64	2089	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:55,060] [INFO] DFAST Taxonomy check result was written to GCF_017921975.2_ASM1792197v2_genomic.fna/tc_result.tsv
[2024-01-24 10:58:55,060] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:55,060] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:55,060] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge1545c9d-2174-4572-af6b-bde0aacb42f5/dqc_reference/checkm_data
[2024-01-24 10:58:55,061] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:55,121] [INFO] Task started: CheckM
[2024-01-24 10:58:55,122] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017921975.2_ASM1792197v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017921975.2_ASM1792197v2_genomic.fna/checkm_input GCF_017921975.2_ASM1792197v2_genomic.fna/checkm_result
[2024-01-24 11:00:33,993] [INFO] Task succeeded: CheckM
[2024-01-24 11:00:33,994] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:00:34,018] [INFO] ===== Completeness check finished =====
[2024-01-24 11:00:34,018] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:00:34,019] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017921975.2_ASM1792197v2_genomic.fna/markers.fasta)
[2024-01-24 11:00:34,019] [INFO] Task started: Blastn
[2024-01-24 11:00:34,019] [INFO] Running command: blastn -query GCF_017921975.2_ASM1792197v2_genomic.fna/markers.fasta -db /var/lib/cwl/stge1545c9d-2174-4572-af6b-bde0aacb42f5/dqc_reference/reference_markers_gtdb.fasta -out GCF_017921975.2_ASM1792197v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:00:34,917] [INFO] Task succeeded: Blastn
[2024-01-24 11:00:34,923] [INFO] Selected 17 target genomes.
[2024-01-24 11:00:34,923] [INFO] Target genome list was writen to GCF_017921975.2_ASM1792197v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:00:34,945] [INFO] Task started: fastANI
[2024-01-24 11:00:34,946] [INFO] Running command: fastANI --query /var/lib/cwl/stg695adc08-306d-4616-946f-50f843528009/GCF_017921975.2_ASM1792197v2_genomic.fna.gz --refList GCF_017921975.2_ASM1792197v2_genomic.fna/target_genomes_gtdb.txt --output GCF_017921975.2_ASM1792197v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:00:57,013] [INFO] Task succeeded: fastANI
[2024-01-24 11:00:57,032] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:00:57,033] [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_012275535.1	s__Hymenobacter artigasi	85.2228	1295	2089	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	84.8006	1230	2089	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	84.7794	1224	2089	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016056375.1	s__Hymenobacter negativus_A	84.7261	1288	2089	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	97.78	97.78	0.95	0.95	3	-
GCF_015694525.1	s__Hymenobacter ruricola	84.6829	1278	2089	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	84.4798	1275	2089	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	95.46	95.46	0.89	0.89	2	-
GCF_014640435.1	s__Hymenobacter frigidus	84.0819	1104	2089	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	83.871	1238	2089	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001507645.1	s__Hymenobacter sedentarius	83.8198	1153	2089	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	83.3597	1058	2089	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001816165.1	s__Hymenobacter glacialis	83.3512	998	2089	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000715495.1	s__Hymenobacter sp000715495	83.2561	1109	2089	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017571495.1	s__Hymenobacter negativus	83.0476	1304	2089	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	82.9171	1140	2089	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000972495.1	s__Hymenobacter terrenus	82.172	1112	2089	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	81.7664	975	2089	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003583925.1	s__Hymenobacter rubripertinctus	79.3899	753	2089	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 11:00:57,035] [INFO] GTDB search result was written to GCF_017921975.2_ASM1792197v2_genomic.fna/result_gtdb.tsv
[2024-01-24 11:00:57,035] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:00:57,040] [INFO] DFAST_QC result json was written to GCF_017921975.2_ASM1792197v2_genomic.fna/dqc_result.json
[2024-01-24 11:00:57,040] [INFO] DFAST_QC completed!
[2024-01-24 11:00:57,040] [INFO] Total running time: 0h3m7s