[2024-01-24 12:29:28,906] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:29:28,913] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:29:28,913] [INFO] DQC Reference Directory: /var/lib/cwl/stga96fad7f-b16f-410f-bd71-555a46de37a0/dqc_reference
[2024-01-24 12:29:30,320] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:29:30,321] [INFO] Task started: Prodigal
[2024-01-24 12:29:30,321] [INFO] Running command: gunzip -c /var/lib/cwl/stg63a53c3c-fcbe-4ff2-bcf3-7fd5c9a61e5f/GCF_014699055.1_ASM1469905v1_genomic.fna.gz | prodigal -d GCF_014699055.1_ASM1469905v1_genomic.fna/cds.fna -a GCF_014699055.1_ASM1469905v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:30:06,279] [INFO] Task succeeded: Prodigal
[2024-01-24 12:30:06,280] [INFO] Task started: HMMsearch
[2024-01-24 12:30:06,280] [INFO] Running command: hmmsearch --tblout GCF_014699055.1_ASM1469905v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga96fad7f-b16f-410f-bd71-555a46de37a0/dqc_reference/reference_markers.hmm GCF_014699055.1_ASM1469905v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:30:06,640] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:30:06,642] [INFO] Found 6/6 markers.
[2024-01-24 12:30:06,687] [INFO] Query marker FASTA was written to GCF_014699055.1_ASM1469905v1_genomic.fna/markers.fasta
[2024-01-24 12:30:06,688] [INFO] Task started: Blastn
[2024-01-24 12:30:06,688] [INFO] Running command: blastn -query GCF_014699055.1_ASM1469905v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga96fad7f-b16f-410f-bd71-555a46de37a0/dqc_reference/reference_markers.fasta -out GCF_014699055.1_ASM1469905v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:30:07,348] [INFO] Task succeeded: Blastn
[2024-01-24 12:30:07,351] [INFO] Selected 16 target genomes.
[2024-01-24 12:30:07,352] [INFO] Target genome list was writen to GCF_014699055.1_ASM1469905v1_genomic.fna/target_genomes.txt
[2024-01-24 12:30:07,361] [INFO] Task started: fastANI
[2024-01-24 12:30:07,361] [INFO] Running command: fastANI --query /var/lib/cwl/stg63a53c3c-fcbe-4ff2-bcf3-7fd5c9a61e5f/GCF_014699055.1_ASM1469905v1_genomic.fna.gz --refList GCF_014699055.1_ASM1469905v1_genomic.fna/target_genomes.txt --output GCF_014699055.1_ASM1469905v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:30:30,192] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:30,193] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga96fad7f-b16f-410f-bd71-555a46de37a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:30:30,193] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga96fad7f-b16f-410f-bd71-555a46de37a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:30:30,207] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:30:30,207] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:30:30,207] [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 armeniacus	strain=BT189	GCA_014699055.1	2771358	2771358	type	True	100.0	1756	1756	95	conclusive
Hymenobacter ruricola	strain=BT662	GCA_015694525.1	2791023	2791023	type	True	88.0469	1393	1756	95	below_threshold
Hymenobacter properus	strain=BT439	GCA_015694735.1	2791026	2791026	type	True	86.2071	1349	1756	95	below_threshold
Hymenobacter rubidus	strain=DG7B	GCA_016734815.1	1441626	1441626	type	True	85.1553	1235	1756	95	below_threshold
Hymenobacter terricola	strain=3F2	GCA_017921975.2	2819236	2819236	type	True	84.7713	1252	1756	95	below_threshold
Hymenobacter artigasi	strain=1B	GCA_012275535.1	2719616	2719616	type	True	84.6467	1250	1756	95	below_threshold
Hymenobacter sedentarius	strain=DG5B	GCA_001507645.1	1411621	1411621	type	True	84.2357	1143	1756	95	below_threshold
Hymenobacter lapidarius	strain=CCM 8643	GCA_001816145.1	1908237	1908237	type	True	83.7717	1050	1756	95	below_threshold
Hymenobacter glacialis	strain=CCM 8648	GCA_001816165.1	1908236	1908236	type	True	83.6498	1024	1756	95	below_threshold
Hymenobacter frigidus	strain=CGMCC 1.14966	GCA_014640435.1	1524095	1524095	type	True	83.4153	1090	1756	95	below_threshold
Hymenobacter jeongseonensis	strain=BT683	GCA_015694725.1	2791027	2791027	type	True	83.1104	1127	1756	95	below_threshold
Hymenobacter montanus	strain=BT664	GCA_014699115.1	2771359	2771359	type	True	81.7973	960	1756	95	below_threshold
Hymenobacter guriensis	strain=BT594	GCA_015773195.1	2793065	2793065	type	True	79.3682	766	1756	95	below_threshold
Hymenobacter metallicola	strain=9PBR-1	GCA_004745645.1	2563114	2563114	type	True	79.263	768	1756	95	below_threshold
Frankia canadensis		GCA_900197875.1	1836972	1836972	type	True	74.6751	107	1756	95	below_threshold
Frankia saprophytica	strain=CN3	GCA_000235425.3	298655	298655	type	True	74.6032	113	1756	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:30:30,209] [INFO] DFAST Taxonomy check result was written to GCF_014699055.1_ASM1469905v1_genomic.fna/tc_result.tsv
[2024-01-24 12:30:30,210] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:30:30,210] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:30:30,210] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga96fad7f-b16f-410f-bd71-555a46de37a0/dqc_reference/checkm_data
[2024-01-24 12:30:30,211] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:30:30,262] [INFO] Task started: CheckM
[2024-01-24 12:30:30,262] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014699055.1_ASM1469905v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014699055.1_ASM1469905v1_genomic.fna/checkm_input GCF_014699055.1_ASM1469905v1_genomic.fna/checkm_result
[2024-01-24 12:31:59,339] [INFO] Task succeeded: CheckM
[2024-01-24 12:31:59,340] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.61%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:31:59,368] [INFO] ===== Completeness check finished =====
[2024-01-24 12:31:59,369] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:31:59,369] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014699055.1_ASM1469905v1_genomic.fna/markers.fasta)
[2024-01-24 12:31:59,370] [INFO] Task started: Blastn
[2024-01-24 12:31:59,370] [INFO] Running command: blastn -query GCF_014699055.1_ASM1469905v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga96fad7f-b16f-410f-bd71-555a46de37a0/dqc_reference/reference_markers_gtdb.fasta -out GCF_014699055.1_ASM1469905v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:00,276] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:00,281] [INFO] Selected 17 target genomes.
[2024-01-24 12:32:00,281] [INFO] Target genome list was writen to GCF_014699055.1_ASM1469905v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:32:00,293] [INFO] Task started: fastANI
[2024-01-24 12:32:00,293] [INFO] Running command: fastANI --query /var/lib/cwl/stg63a53c3c-fcbe-4ff2-bcf3-7fd5c9a61e5f/GCF_014699055.1_ASM1469905v1_genomic.fna.gz --refList GCF_014699055.1_ASM1469905v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014699055.1_ASM1469905v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:32:21,670] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:21,689] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:32:21,690] [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_016427455.1	s__Hymenobacter sp016427455	95.4567	1568	1756	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	95.46	95.46	0.89	0.89	2	conclusive
GCF_015694525.1	s__Hymenobacter ruricola	88.044	1393	1756	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	86.2004	1350	1756	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016734815.1	s__Hymenobacter rubidus	85.1316	1238	1756	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	84.7998	1242	1756	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	97.78	97.78	0.95	0.95	3	-
GCF_012275535.1	s__Hymenobacter artigasi	84.6676	1247	1756	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	84.2566	1141	1756	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	83.7795	1048	1756	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	83.6528	1024	1756	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014640435.1	s__Hymenobacter frigidus	83.4225	1090	1756	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	83.1394	1263	1756	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	83.1107	1127	1756	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115775.1	s__Hymenobacter arizonensis	82.9889	1180	1756	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	81.9909	1030	1756	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	81.8098	958	1756	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	79.3941	763	1756	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018613725.1	s__Hymenobacter sp018613725	79.3202	672	1756	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 12:32:21,693] [INFO] GTDB search result was written to GCF_014699055.1_ASM1469905v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:32:21,694] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:32:21,698] [INFO] DFAST_QC result json was written to GCF_014699055.1_ASM1469905v1_genomic.fna/dqc_result.json
[2024-01-24 12:32:21,698] [INFO] DFAST_QC completed!
[2024-01-24 12:32:21,698] [INFO] Total running time: 0h2m53s