[2024-01-24 11:34:55,211] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:55,215] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:55,215] [INFO] DQC Reference Directory: /var/lib/cwl/stg6bee09d7-5f7e-4d62-9933-ef5aa058de96/dqc_reference
[2024-01-24 11:34:56,742] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:56,743] [INFO] Task started: Prodigal
[2024-01-24 11:34:56,743] [INFO] Running command: gunzip -c /var/lib/cwl/stg218d8d08-89f2-4763-84f9-301fffc9e5bc/GCF_017571495.1_ASM1757149v1_genomic.fna.gz | prodigal -d GCF_017571495.1_ASM1757149v1_genomic.fna/cds.fna -a GCF_017571495.1_ASM1757149v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:40,052] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:40,052] [INFO] Task started: HMMsearch
[2024-01-24 11:35:40,053] [INFO] Running command: hmmsearch --tblout GCF_017571495.1_ASM1757149v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6bee09d7-5f7e-4d62-9933-ef5aa058de96/dqc_reference/reference_markers.hmm GCF_017571495.1_ASM1757149v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:40,385] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:40,386] [INFO] Found 6/6 markers.
[2024-01-24 11:35:40,445] [INFO] Query marker FASTA was written to GCF_017571495.1_ASM1757149v1_genomic.fna/markers.fasta
[2024-01-24 11:35:40,446] [INFO] Task started: Blastn
[2024-01-24 11:35:40,446] [INFO] Running command: blastn -query GCF_017571495.1_ASM1757149v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6bee09d7-5f7e-4d62-9933-ef5aa058de96/dqc_reference/reference_markers.fasta -out GCF_017571495.1_ASM1757149v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:41,090] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:41,095] [INFO] Selected 14 target genomes.
[2024-01-24 11:35:41,095] [INFO] Target genome list was writen to GCF_017571495.1_ASM1757149v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:41,102] [INFO] Task started: fastANI
[2024-01-24 11:35:41,102] [INFO] Running command: fastANI --query /var/lib/cwl/stg218d8d08-89f2-4763-84f9-301fffc9e5bc/GCF_017571495.1_ASM1757149v1_genomic.fna.gz --refList GCF_017571495.1_ASM1757149v1_genomic.fna/target_genomes.txt --output GCF_017571495.1_ASM1757149v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:58,770] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:58,770] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6bee09d7-5f7e-4d62-9933-ef5aa058de96/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:58,771] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6bee09d7-5f7e-4d62-9933-ef5aa058de96/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:58,782] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:35:58,782] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:35:58,783] [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 rubidus	strain=DG7B	GCA_016734815.1	1441626	1441626	type	True	83.4249	1271	2349	95	below_threshold
Hymenobacter armeniacus	strain=BT189	GCA_014699055.1	2771358	2771358	type	True	83.1127	1255	2349	95	below_threshold
Hymenobacter artigasi	strain=1B	GCA_012275535.1	2719616	2719616	type	True	83.0814	1252	2349	95	below_threshold
Hymenobacter terricola	strain=3F2	GCA_017921975.2	2819236	2819236	type	True	82.9951	1331	2349	95	below_threshold
Hymenobacter ruricola	strain=BT662	GCA_015694525.1	2791023	2791023	type	True	82.9593	1374	2349	95	below_threshold
Hymenobacter properus	strain=BT439	GCA_015694735.1	2791026	2791026	type	True	82.9152	1304	2349	95	below_threshold
Hymenobacter frigidus	strain=CGMCC 1.14966	GCA_014640435.1	1524095	1524095	type	True	81.8239	1013	2349	95	below_threshold
Hymenobacter sedentarius	strain=DG5B	GCA_001507645.1	1411621	1411621	type	True	81.6045	1054	2349	95	below_threshold
Hymenobacter lapidarius	strain=CCM 8643	GCA_001816145.1	1908237	1908237	type	True	81.4885	930	2349	95	below_threshold
Hymenobacter glacialis	strain=CCM 8648	GCA_001816165.1	1908236	1908236	type	True	81.4578	892	2349	95	below_threshold
Hymenobacter jeongseonensis	strain=BT683	GCA_015694725.1	2791027	2791027	type	True	80.9906	1034	2349	95	below_threshold
Hymenobacter montanus	strain=BT664	GCA_014699115.1	2771359	2771359	type	True	80.1929	887	2349	95	below_threshold
Hymenobacter metallicola	strain=9PBR-1	GCA_004745645.1	2563114	2563114	type	True	78.3792	656	2349	95	below_threshold
Hymenobacter guriensis	strain=BT594	GCA_015773195.1	2793065	2793065	type	True	78.3036	620	2349	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:58,784] [INFO] DFAST Taxonomy check result was written to GCF_017571495.1_ASM1757149v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:58,785] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:58,785] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:58,785] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6bee09d7-5f7e-4d62-9933-ef5aa058de96/dqc_reference/checkm_data
[2024-01-24 11:35:58,786] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:58,857] [INFO] Task started: CheckM
[2024-01-24 11:35:58,857] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017571495.1_ASM1757149v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017571495.1_ASM1757149v1_genomic.fna/checkm_input GCF_017571495.1_ASM1757149v1_genomic.fna/checkm_result
[2024-01-24 11:37:46,022] [INFO] Task succeeded: CheckM
[2024-01-24 11:37:46,024] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:37:46,048] [INFO] ===== Completeness check finished =====
[2024-01-24 11:37:46,048] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:37:46,048] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017571495.1_ASM1757149v1_genomic.fna/markers.fasta)
[2024-01-24 11:37:46,049] [INFO] Task started: Blastn
[2024-01-24 11:37:46,049] [INFO] Running command: blastn -query GCF_017571495.1_ASM1757149v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6bee09d7-5f7e-4d62-9933-ef5aa058de96/dqc_reference/reference_markers_gtdb.fasta -out GCF_017571495.1_ASM1757149v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:37:46,856] [INFO] Task succeeded: Blastn
[2024-01-24 11:37:46,861] [INFO] Selected 14 target genomes.
[2024-01-24 11:37:46,861] [INFO] Target genome list was writen to GCF_017571495.1_ASM1757149v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:37:46,900] [INFO] Task started: fastANI
[2024-01-24 11:37:46,900] [INFO] Running command: fastANI --query /var/lib/cwl/stg218d8d08-89f2-4763-84f9-301fffc9e5bc/GCF_017571495.1_ASM1757149v1_genomic.fna.gz --refList GCF_017571495.1_ASM1757149v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017571495.1_ASM1757149v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:38:05,068] [INFO] Task succeeded: fastANI
[2024-01-24 11:38:05,084] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:38:05,084] [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_017571495.1	s__Hymenobacter negativus	100.0	2346	2349	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_016734815.1	s__Hymenobacter rubidus	83.4111	1273	2349	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	83.1823	1274	2349	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	83.0883	1251	2349	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	83.0437	1274	2349	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	82.9693	1372	2349	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	82.9152	1304	2349	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_018967845.1	s__Hymenobacter sp018967845	82.7466	1143	2349	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	99.02	98.98	0.94	0.93	3	-
GCF_014640435.1	s__Hymenobacter frigidus	81.829	1012	2349	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	81.6173	1052	2349	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	81.4857	930	2349	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	81.4839	889	2349	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	80.9845	1035	2349	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	80.9756	1087	2349	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 11:38:05,086] [INFO] GTDB search result was written to GCF_017571495.1_ASM1757149v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:38:05,087] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:38:05,090] [INFO] DFAST_QC result json was written to GCF_017571495.1_ASM1757149v1_genomic.fna/dqc_result.json
[2024-01-24 11:38:05,090] [INFO] DFAST_QC completed!
[2024-01-24 11:38:05,091] [INFO] Total running time: 0h3m10s