[2024-01-24 10:56:34,717] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:56:34,722] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:56:34,722] [INFO] DQC Reference Directory: /var/lib/cwl/stg2ae690d5-640b-4424-9221-73ef72d23ffa/dqc_reference
[2024-01-24 10:56:36,714] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:56:36,715] [INFO] Task started: Prodigal
[2024-01-24 10:56:36,715] [INFO] Running command: gunzip -c /var/lib/cwl/stg298237ce-890d-43cc-ae01-559d7e56ce35/GCF_007713685.1_ASM771368v1_genomic.fna.gz | prodigal -d GCF_007713685.1_ASM771368v1_genomic.fna/cds.fna -a GCF_007713685.1_ASM771368v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:09,344] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:09,344] [INFO] Task started: HMMsearch
[2024-01-24 10:57:09,344] [INFO] Running command: hmmsearch --tblout GCF_007713685.1_ASM771368v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2ae690d5-640b-4424-9221-73ef72d23ffa/dqc_reference/reference_markers.hmm GCF_007713685.1_ASM771368v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:09,651] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:09,653] [INFO] Found 6/6 markers.
[2024-01-24 10:57:09,704] [INFO] Query marker FASTA was written to GCF_007713685.1_ASM771368v1_genomic.fna/markers.fasta
[2024-01-24 10:57:09,704] [INFO] Task started: Blastn
[2024-01-24 10:57:09,705] [INFO] Running command: blastn -query GCF_007713685.1_ASM771368v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2ae690d5-640b-4424-9221-73ef72d23ffa/dqc_reference/reference_markers.fasta -out GCF_007713685.1_ASM771368v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:10,330] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:10,334] [INFO] Selected 16 target genomes.
[2024-01-24 10:57:10,334] [INFO] Target genome list was writen to GCF_007713685.1_ASM771368v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:10,348] [INFO] Task started: fastANI
[2024-01-24 10:57:10,349] [INFO] Running command: fastANI --query /var/lib/cwl/stg298237ce-890d-43cc-ae01-559d7e56ce35/GCF_007713685.1_ASM771368v1_genomic.fna.gz --refList GCF_007713685.1_ASM771368v1_genomic.fna/target_genomes.txt --output GCF_007713685.1_ASM771368v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:57:27,366] [INFO] Task succeeded: fastANI
[2024-01-24 10:57:27,366] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2ae690d5-640b-4424-9221-73ef72d23ffa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:57:27,367] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2ae690d5-640b-4424-9221-73ef72d23ffa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:57:27,379] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:57:27,379] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:57:27,379] [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 setariae	strain=Fur1	GCA_007713685.1	2594794	2594794	type	True	100.0	2025	2025	95	conclusive
Hymenobacter ginkgonis	strain=HMF4947	GCA_009755225.1	2682976	2682976	type	True	80.8231	1058	2025	95	below_threshold
Hymenobacter polaris	strain=RP-2-7	GCA_012927305.1	2682546	2682546	type	True	80.6075	1063	2025	95	below_threshold
Hymenobacter baengnokdamensis	strain=BRD72	GCA_008728635.1	2615203	2615203	type	True	80.2264	837	2025	95	below_threshold
Hymenobacter caeli	strain=9A	GCA_013294115.1	2735894	2735894	type	True	79.1211	759	2025	95	below_threshold
Hymenobacter armeniacus	strain=BT189	GCA_014699055.1	2771358	2771358	type	True	79.0041	743	2025	95	below_threshold
Hymenobacter properus	strain=BT439	GCA_015694735.1	2791026	2791026	type	True	78.8719	747	2025	95	below_threshold
Hymenobacter nivis	strain=NBRC 111535	GCA_003149515.1	1850093	1850093	type	True	78.741	741	2025	95	below_threshold
Hymenobacter lapidarius	strain=CCM 8643	GCA_001816145.1	1908237	1908237	type	True	78.4953	545	2025	95	below_threshold
Hymenobacter jeongseonensis	strain=BT683	GCA_015694725.1	2791027	2791027	type	True	78.3549	560	2025	95	below_threshold
Hymenobacter frigidus	strain=CGMCC 1.14966	GCA_014640435.1	1524095	1524095	type	True	78.3531	584	2025	95	below_threshold
Hymenobacter aerophilus	strain=DSM 13606	GCA_000382225.1	119644	119644	type	True	78.1436	486	2025	95	below_threshold
Hymenobacter telluris	strain=BT186	GCA_017313265.1	2816474	2816474	type	True	78.133	541	2025	95	below_threshold
Hymenobacter actinosclerus	strain=DSM 15310	GCA_900111515.1	82805	82805	type	True	77.9912	470	2025	95	below_threshold
Hymenobacter guriensis	strain=BT594	GCA_015773195.1	2793065	2793065	type	True	77.6912	466	2025	95	below_threshold
Hymenobacter lapidiphilus	strain=P5342	GCA_013377885.1	2608003	2608003	type	True	77.5802	435	2025	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:57:27,381] [INFO] DFAST Taxonomy check result was written to GCF_007713685.1_ASM771368v1_genomic.fna/tc_result.tsv
[2024-01-24 10:57:27,381] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:57:27,381] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:57:27,382] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2ae690d5-640b-4424-9221-73ef72d23ffa/dqc_reference/checkm_data
[2024-01-24 10:57:27,383] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:57:27,438] [INFO] Task started: CheckM
[2024-01-24 10:57:27,438] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007713685.1_ASM771368v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007713685.1_ASM771368v1_genomic.fna/checkm_input GCF_007713685.1_ASM771368v1_genomic.fna/checkm_result
[2024-01-24 10:58:49,642] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:49,644] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:49,667] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:49,668] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:49,668] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007713685.1_ASM771368v1_genomic.fna/markers.fasta)
[2024-01-24 10:58:49,669] [INFO] Task started: Blastn
[2024-01-24 10:58:49,669] [INFO] Running command: blastn -query GCF_007713685.1_ASM771368v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2ae690d5-640b-4424-9221-73ef72d23ffa/dqc_reference/reference_markers_gtdb.fasta -out GCF_007713685.1_ASM771368v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:50,497] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:50,501] [INFO] Selected 12 target genomes.
[2024-01-24 10:58:50,501] [INFO] Target genome list was writen to GCF_007713685.1_ASM771368v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:50,510] [INFO] Task started: fastANI
[2024-01-24 10:58:50,510] [INFO] Running command: fastANI --query /var/lib/cwl/stg298237ce-890d-43cc-ae01-559d7e56ce35/GCF_007713685.1_ASM771368v1_genomic.fna.gz --refList GCF_007713685.1_ASM771368v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007713685.1_ASM771368v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:59:04,475] [INFO] Task succeeded: fastANI
[2024-01-24 10:59:04,489] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:59:04,489] [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
GCA_007713685.1	s__Hymenobacter sp007713685	100.0	2025	2025	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_016427535.1	s__Hymenobacter sp016427535	88.0625	1601	2025	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013256625.1	s__Hymenobacter sp013256625	81.2497	1006	2025	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017571525.1	s__Hymenobacter sp017571525	81.1994	1050	2025	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004684095.1	s__Hymenobacter sp004684095	81.0093	1119	2025	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009755225.1	s__Hymenobacter sp009755225	80.8143	1059	2025	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012927305.1	s__Hymenobacter polaris	80.579	1068	2025	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001596155.1	s__Hymenobacter sp001596155	80.3327	975	2025	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013256425.1	s__Hymenobacter sp013256425	80.2408	862	2025	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008728635.1	s__Hymenobacter baengnokdamensis	80.2387	834	2025	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111515.1	s__Hymenobacter actinosclerus	78.0009	470	2025	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013377885.1	s__Hymenobacter lapidiphilus	77.5874	434	2025	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 10:59:04,491] [INFO] GTDB search result was written to GCF_007713685.1_ASM771368v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:59:04,491] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:59:04,494] [INFO] DFAST_QC result json was written to GCF_007713685.1_ASM771368v1_genomic.fna/dqc_result.json
[2024-01-24 10:59:04,495] [INFO] DFAST_QC completed!
[2024-01-24 10:59:04,495] [INFO] Total running time: 0h2m30s