[2024-01-24 14:38:46,637] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:38:46,639] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:38:46,639] [INFO] DQC Reference Directory: /var/lib/cwl/stg90c545ec-fb96-45e7-9c3c-d1a1e8609410/dqc_reference
[2024-01-24 14:38:48,057] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:38:48,058] [INFO] Task started: Prodigal
[2024-01-24 14:38:48,058] [INFO] Running command: gunzip -c /var/lib/cwl/stg6b9e812a-9d64-4b0e-bbc9-88ad04efdc96/GCF_014641455.1_ASM1464145v1_genomic.fna.gz | prodigal -d GCF_014641455.1_ASM1464145v1_genomic.fna/cds.fna -a GCF_014641455.1_ASM1464145v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:39:18,993] [INFO] Task succeeded: Prodigal
[2024-01-24 14:39:18,994] [INFO] Task started: HMMsearch
[2024-01-24 14:39:18,994] [INFO] Running command: hmmsearch --tblout GCF_014641455.1_ASM1464145v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg90c545ec-fb96-45e7-9c3c-d1a1e8609410/dqc_reference/reference_markers.hmm GCF_014641455.1_ASM1464145v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:39:19,296] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:39:19,298] [INFO] Found 6/6 markers.
[2024-01-24 14:39:19,347] [INFO] Query marker FASTA was written to GCF_014641455.1_ASM1464145v1_genomic.fna/markers.fasta
[2024-01-24 14:39:19,348] [INFO] Task started: Blastn
[2024-01-24 14:39:19,348] [INFO] Running command: blastn -query GCF_014641455.1_ASM1464145v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg90c545ec-fb96-45e7-9c3c-d1a1e8609410/dqc_reference/reference_markers.fasta -out GCF_014641455.1_ASM1464145v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:19,975] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:19,978] [INFO] Selected 20 target genomes.
[2024-01-24 14:39:19,978] [INFO] Target genome list was writen to GCF_014641455.1_ASM1464145v1_genomic.fna/target_genomes.txt
[2024-01-24 14:39:20,001] [INFO] Task started: fastANI
[2024-01-24 14:39:20,002] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b9e812a-9d64-4b0e-bbc9-88ad04efdc96/GCF_014641455.1_ASM1464145v1_genomic.fna.gz --refList GCF_014641455.1_ASM1464145v1_genomic.fna/target_genomes.txt --output GCF_014641455.1_ASM1464145v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:39:42,639] [INFO] Task succeeded: fastANI
[2024-01-24 14:39:42,640] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg90c545ec-fb96-45e7-9c3c-d1a1e8609410/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:39:42,640] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg90c545ec-fb96-45e7-9c3c-d1a1e8609410/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:39:42,664] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:39:42,665] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:39:42,665] [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 cavernae	strain=CGMCC 1.15197	GCA_014641455.1	2044852	2044852	type	True	100.0	1863	1864	95	conclusive
Hymenobacter crusticola	strain=MIMBbqt21	GCA_002154225.1	1770526	1770526	type	True	82.4239	1237	1864	95	below_threshold
Hymenobacter aquaticus	strain=JCM 31653	GCA_004765605.1	1867101	1867101	type	True	79.0058	811	1864	95	below_threshold
Hymenobacter daecheongensis	strain=DSM 21074	GCA_900141805.1	496053	496053	type	True	78.9277	692	1864	95	below_threshold
Hymenobacter chitinivorans	strain=DSM 11115	GCA_002797555.1	89969	89969	type	True	78.7607	788	1864	95	below_threshold
Hymenobacter elongatus	strain=JCM 17223	GCA_004745955.1	877208	877208	type	True	78.7285	600	1864	95	below_threshold
Hymenobacter telluris	strain=BT186	GCA_017313265.1	2816474	2816474	type	True	78.5984	763	1864	95	below_threshold
Hymenobacter citatus	strain=BT507	GCA_014333615.1	2763506	2763506	type	True	78.5676	709	1864	95	below_threshold
Hymenobacter guriensis	strain=BT594	GCA_015773195.1	2793065	2793065	type	True	78.5271	619	1864	95	below_threshold
Hymenobacter jejuensis	strain=17J68-5	GCA_006337165.1	2502781	2502781	type	True	78.4668	692	1864	95	below_threshold
Hymenobacter perfusus	strain=LMG 26000	GCA_003944765.1	1236770	1236770	type	True	78.4628	635	1864	95	below_threshold
Hymenobacter metallicola	strain=9PBR-1	GCA_004745645.1	2563114	2563114	type	True	78.4527	722	1864	95	below_threshold
Hymenobacter gelipurpurascens	strain=DSM 11116	GCA_900187375.1	89968	89968	type	True	78.2223	626	1864	95	below_threshold
Hymenobacter qilianensis	strain=JCM 19763	GCA_014489555.1	1385715	1385715	type	True	78.2072	590	1864	95	below_threshold
Hymenobacter qilianensis	strain=CGMCC 1.12720	GCA_014638675.1	1385715	1385715	type	True	78.1979	581	1864	95	below_threshold
Hymenobacter armeniacus	strain=BT189	GCA_014699055.1	2771358	2771358	type	True	78.107	641	1864	95	below_threshold
Hymenobacter fodinae	strain=92R-1	GCA_004745825.1	2510796	2510796	type	True	78.0556	587	1864	95	below_threshold
Hymenobacter radiodurans	strain=17J36-26	GCA_004355185.1	2496028	2496028	type	True	77.862	554	1864	95	below_threshold
Hymenobacter wooponensis	strain=JCM 19491	GCA_004745865.1	1525360	1525360	type	True	77.8527	568	1864	95	below_threshold
Hymenobacter setariae	strain=Fur1	GCA_007713685.1	2594794	2594794	type	True	77.5228	452	1864	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:39:42,667] [INFO] DFAST Taxonomy check result was written to GCF_014641455.1_ASM1464145v1_genomic.fna/tc_result.tsv
[2024-01-24 14:39:42,667] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:39:42,667] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:39:42,668] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg90c545ec-fb96-45e7-9c3c-d1a1e8609410/dqc_reference/checkm_data
[2024-01-24 14:39:42,669] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:39:42,728] [INFO] Task started: CheckM
[2024-01-24 14:39:42,729] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014641455.1_ASM1464145v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014641455.1_ASM1464145v1_genomic.fna/checkm_input GCF_014641455.1_ASM1464145v1_genomic.fna/checkm_result
[2024-01-24 14:41:03,189] [INFO] Task succeeded: CheckM
[2024-01-24 14:41:03,191] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:41:03,214] [INFO] ===== Completeness check finished =====
[2024-01-24 14:41:03,214] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:41:03,214] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014641455.1_ASM1464145v1_genomic.fna/markers.fasta)
[2024-01-24 14:41:03,215] [INFO] Task started: Blastn
[2024-01-24 14:41:03,215] [INFO] Running command: blastn -query GCF_014641455.1_ASM1464145v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg90c545ec-fb96-45e7-9c3c-d1a1e8609410/dqc_reference/reference_markers_gtdb.fasta -out GCF_014641455.1_ASM1464145v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:41:04,131] [INFO] Task succeeded: Blastn
[2024-01-24 14:41:04,135] [INFO] Selected 19 target genomes.
[2024-01-24 14:41:04,135] [INFO] Target genome list was writen to GCF_014641455.1_ASM1464145v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:41:04,154] [INFO] Task started: fastANI
[2024-01-24 14:41:04,155] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b9e812a-9d64-4b0e-bbc9-88ad04efdc96/GCF_014641455.1_ASM1464145v1_genomic.fna.gz --refList GCF_014641455.1_ASM1464145v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014641455.1_ASM1464145v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:41:26,344] [INFO] Task succeeded: fastANI
[2024-01-24 14:41:26,359] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:41:26,360] [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_014641455.1	s__Hymenobacter cavernae	100.0	1863	1864	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_002154225.1	s__Hymenobacter crusticola	82.433	1235	1864	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004765605.1	s__Hymenobacter aquaticus	79.0176	808	1864	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141805.1	s__Hymenobacter daecheongensis	78.9162	695	1864	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000737515.1	s__Hymenobacter sp000737515	78.8394	693	1864	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797555.1	s__Hymenobacter chitinivorans	78.7551	789	1864	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004745955.1	s__Hymenobacter elongatus	78.7142	602	1864	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017313265.1	s__Hymenobacter sp017313265	78.6061	761	1864	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014333615.1	s__Hymenobacter citatus	78.5497	711	1864	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004745645.1	s__Hymenobacter sp004745645	78.4692	719	1864	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006337165.1	s__Hymenobacter jejuensis	78.465	693	1864	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	97.30	97.30	0.94	0.94	2	-
GCF_003944765.1	s__Hymenobacter perfusus	78.4569	636	1864	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017589435.1	s__Hymenobacter defluvii	78.2763	638	1864	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	96.38	96.38	0.86	0.86	2	-
GCF_014489555.1	s__Hymenobacter qilianensis	78.2072	590	1864	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	99.95	99.95	1.00	1.00	2	-
GCF_002007105.1	s__Solirubrum sp002007105	78.1194	685	1864	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Solirubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013137895.1	s__Hymenobacter sp013137895	77.9268	543	1864	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004355185.1	s__Hymenobacter radiodurans	77.8742	552	1864	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	96.17	96.17	0.96	0.96	2	-
GCF_014333585.1	s__Hymenobacter sp014333585	77.8644	521	1864	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004745865.1	s__Hymenobacter wooponensis	77.8511	569	1864	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 14:41:26,361] [INFO] GTDB search result was written to GCF_014641455.1_ASM1464145v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:41:26,362] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:41:26,366] [INFO] DFAST_QC result json was written to GCF_014641455.1_ASM1464145v1_genomic.fna/dqc_result.json
[2024-01-24 14:41:26,366] [INFO] DFAST_QC completed!
[2024-01-24 14:41:26,366] [INFO] Total running time: 0h2m40s