[2024-01-24 13:31:34,698] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:34,701] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:34,701] [INFO] DQC Reference Directory: /var/lib/cwl/stg77f52283-c105-4827-9b22-0162838310b5/dqc_reference
[2024-01-24 13:31:36,172] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:36,175] [INFO] Task started: Prodigal
[2024-01-24 13:31:36,176] [INFO] Running command: gunzip -c /var/lib/cwl/stga836b726-9c39-44fe-870e-d9c382e32cdf/GCF_001507645.1_ASM150764v1_genomic.fna.gz | prodigal -d GCF_001507645.1_ASM150764v1_genomic.fna/cds.fna -a GCF_001507645.1_ASM150764v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:09,320] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:09,321] [INFO] Task started: HMMsearch
[2024-01-24 13:32:09,321] [INFO] Running command: hmmsearch --tblout GCF_001507645.1_ASM150764v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg77f52283-c105-4827-9b22-0162838310b5/dqc_reference/reference_markers.hmm GCF_001507645.1_ASM150764v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:09,681] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:09,682] [INFO] Found 6/6 markers.
[2024-01-24 13:32:09,724] [INFO] Query marker FASTA was written to GCF_001507645.1_ASM150764v1_genomic.fna/markers.fasta
[2024-01-24 13:32:09,725] [INFO] Task started: Blastn
[2024-01-24 13:32:09,725] [INFO] Running command: blastn -query GCF_001507645.1_ASM150764v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg77f52283-c105-4827-9b22-0162838310b5/dqc_reference/reference_markers.fasta -out GCF_001507645.1_ASM150764v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:10,391] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:10,394] [INFO] Selected 13 target genomes.
[2024-01-24 13:32:10,395] [INFO] Target genome list was writen to GCF_001507645.1_ASM150764v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:10,405] [INFO] Task started: fastANI
[2024-01-24 13:32:10,405] [INFO] Running command: fastANI --query /var/lib/cwl/stga836b726-9c39-44fe-870e-d9c382e32cdf/GCF_001507645.1_ASM150764v1_genomic.fna.gz --refList GCF_001507645.1_ASM150764v1_genomic.fna/target_genomes.txt --output GCF_001507645.1_ASM150764v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:27,392] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:27,393] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg77f52283-c105-4827-9b22-0162838310b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:27,393] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg77f52283-c105-4827-9b22-0162838310b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:27,404] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:32:27,404] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:27,404] [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 sedentarius	strain=DG5B	GCA_001507645.1	1411621	1411621	type	True	100.0	1622	1622	95	conclusive
Hymenobacter armeniacus	strain=BT189	GCA_014699055.1	2771358	2771358	type	True	84.2763	1144	1622	95	below_threshold
Hymenobacter lapidarius	strain=CCM 8643	GCA_001816145.1	1908237	1908237	type	True	84.0387	1031	1622	95	below_threshold
Hymenobacter jeongseonensis	strain=BT683	GCA_015694725.1	2791027	2791027	type	True	83.9938	1120	1622	95	below_threshold
Hymenobacter glacialis	strain=CCM 8648	GCA_001816165.1	1908236	1908236	type	True	83.912	1026	1622	95	below_threshold
Hymenobacter terricola	strain=3F2	GCA_017921975.2	2819236	2819236	type	True	83.8182	1142	1622	95	below_threshold
Hymenobacter rubidus	strain=DG7B	GCA_016734815.1	1441626	1441626	type	True	83.4416	1075	1622	95	below_threshold
Hymenobacter artigasi	strain=1B	GCA_012275535.1	2719616	2719616	type	True	83.2084	1133	1622	95	below_threshold
Hymenobacter frigidus	strain=CGMCC 1.14966	GCA_014640435.1	1524095	1524095	type	True	83.0536	1034	1622	95	below_threshold
Hymenobacter montanus	strain=BT664	GCA_014699115.1	2771359	2771359	type	True	81.9833	942	1622	95	below_threshold
Hymenobacter terrenus	strain=MIMtkLc17	GCA_000972495.1	1629124	1629124	type	True	81.9474	988	1622	95	below_threshold
Hymenobacter metallicola	strain=9PBR-1	GCA_004745645.1	2563114	2563114	type	True	79.4534	653	1622	95	below_threshold
Hymenobacter guriensis	strain=BT594	GCA_015773195.1	2793065	2793065	type	True	79.2974	682	1622	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:27,406] [INFO] DFAST Taxonomy check result was written to GCF_001507645.1_ASM150764v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:27,406] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:27,406] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:27,407] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg77f52283-c105-4827-9b22-0162838310b5/dqc_reference/checkm_data
[2024-01-24 13:32:27,408] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:27,455] [INFO] Task started: CheckM
[2024-01-24 13:32:27,455] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001507645.1_ASM150764v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001507645.1_ASM150764v1_genomic.fna/checkm_input GCF_001507645.1_ASM150764v1_genomic.fna/checkm_result
[2024-01-24 13:33:47,984] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:47,985] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:48,007] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:48,008] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:48,008] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001507645.1_ASM150764v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:48,009] [INFO] Task started: Blastn
[2024-01-24 13:33:48,009] [INFO] Running command: blastn -query GCF_001507645.1_ASM150764v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg77f52283-c105-4827-9b22-0162838310b5/dqc_reference/reference_markers_gtdb.fasta -out GCF_001507645.1_ASM150764v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:48,915] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:48,920] [INFO] Selected 14 target genomes.
[2024-01-24 13:33:48,920] [INFO] Target genome list was writen to GCF_001507645.1_ASM150764v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:48,949] [INFO] Task started: fastANI
[2024-01-24 13:33:48,950] [INFO] Running command: fastANI --query /var/lib/cwl/stga836b726-9c39-44fe-870e-d9c382e32cdf/GCF_001507645.1_ASM150764v1_genomic.fna.gz --refList GCF_001507645.1_ASM150764v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001507645.1_ASM150764v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:34:07,009] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:07,024] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:34:07,025] [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_001507645.1	s__Hymenobacter sedentarius	100.0	1622	1622	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016427455.1	s__Hymenobacter sp016427455	84.2477	1148	1622	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	95.46	95.46	0.89	0.89	2	-
GCF_001816145.1	s__Hymenobacter lapidarius	84.0054	1035	1622	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	83.9962	1120	1622	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	83.9199	1026	1622	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	83.6966	1142	1622	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016734815.1	s__Hymenobacter rubidus	83.464	1074	1622	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012275535.1	s__Hymenobacter artigasi	83.2383	1129	1622	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	83.2297	1026	1622	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	83.0761	1031	1622	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	82.988	1077	1622	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	99.02	98.98	0.94	0.93	3	-
GCF_016056375.1	s__Hymenobacter negativus_A	82.9729	1113	1622	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	97.78	97.78	0.95	0.95	3	-
GCF_014699115.1	s__Hymenobacter sp014699115	82.0019	940	1622	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	81.9511	986	1622	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 13:34:07,026] [INFO] GTDB search result was written to GCF_001507645.1_ASM150764v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:34:07,027] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:34:07,030] [INFO] DFAST_QC result json was written to GCF_001507645.1_ASM150764v1_genomic.fna/dqc_result.json
[2024-01-24 13:34:07,031] [INFO] DFAST_QC completed!
[2024-01-24 13:34:07,031] [INFO] Total running time: 0h2m32s