[2023-06-18 19:17:34,514] [INFO] DFAST_QC pipeline started.
[2023-06-18 19:17:34,517] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 19:17:34,517] [INFO] DQC Reference Directory: /var/lib/cwl/stg78c587c6-9468-45fc-96fe-ef7d60ff884d/dqc_reference
[2023-06-18 19:17:36,321] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 19:17:36,322] [INFO] Task started: Prodigal
[2023-06-18 19:17:36,322] [INFO] Running command: gunzip -c /var/lib/cwl/stgc787aa1a-c23b-4b9e-bef0-154f3f71af61/GCA_018267545.1_ASM1826754v1_genomic.fna.gz | prodigal -d GCA_018267545.1_ASM1826754v1_genomic.fna/cds.fna -a GCA_018267545.1_ASM1826754v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 19:18:10,274] [INFO] Task succeeded: Prodigal
[2023-06-18 19:18:10,275] [INFO] Task started: HMMsearch
[2023-06-18 19:18:10,275] [INFO] Running command: hmmsearch --tblout GCA_018267545.1_ASM1826754v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg78c587c6-9468-45fc-96fe-ef7d60ff884d/dqc_reference/reference_markers.hmm GCA_018267545.1_ASM1826754v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 19:18:10,627] [INFO] Task succeeded: HMMsearch
[2023-06-18 19:18:10,628] [INFO] Found 6/6 markers.
[2023-06-18 19:18:10,690] [INFO] Query marker FASTA was written to GCA_018267545.1_ASM1826754v1_genomic.fna/markers.fasta
[2023-06-18 19:18:10,691] [INFO] Task started: Blastn
[2023-06-18 19:18:10,691] [INFO] Running command: blastn -query GCA_018267545.1_ASM1826754v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg78c587c6-9468-45fc-96fe-ef7d60ff884d/dqc_reference/reference_markers.fasta -out GCA_018267545.1_ASM1826754v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 19:18:11,278] [INFO] Task succeeded: Blastn
[2023-06-18 19:18:11,282] [INFO] Selected 22 target genomes.
[2023-06-18 19:18:11,283] [INFO] Target genome list was writen to GCA_018267545.1_ASM1826754v1_genomic.fna/target_genomes.txt
[2023-06-18 19:18:11,290] [INFO] Task started: fastANI
[2023-06-18 19:18:11,290] [INFO] Running command: fastANI --query /var/lib/cwl/stgc787aa1a-c23b-4b9e-bef0-154f3f71af61/GCA_018267545.1_ASM1826754v1_genomic.fna.gz --refList GCA_018267545.1_ASM1826754v1_genomic.fna/target_genomes.txt --output GCA_018267545.1_ASM1826754v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 19:18:29,391] [INFO] Task succeeded: fastANI
[2023-06-18 19:18:29,392] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg78c587c6-9468-45fc-96fe-ef7d60ff884d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 19:18:29,392] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg78c587c6-9468-45fc-96fe-ef7d60ff884d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 19:18:29,405] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 19:18:29,405] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 19:18:29,405] [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
Puia dinghuensis	strain=CGMCC 1.15448	GCA_014642875.1	1792502	1792502	type	True	77.9585	448	2153	95	below_threshold
Flaviaesturariibacter flavus	strain=17J68-12	GCA_004337505.1	2502780	2502780	type	True	76.5223	77	2153	95	below_threshold
Pseudobacter ginsenosidimutans	strain=DSM 18116	GCA_004291315.1	661488	661488	type	True	76.2267	88	2153	95	below_threshold
Pseudobacter ginsenosidimutans	strain=Gsoil 221	GCA_007970185.1	661488	661488	type	True	76.2264	88	2153	95	below_threshold
Niastella koreensis	strain=DSM 17620	GCA_002077985.1	354356	354356	type	True	76.218	71	2153	95	below_threshold
Niastella koreensis	strain=GR20-10	GCA_000246855.1	354356	354356	type	True	76.2114	70	2153	95	below_threshold
Flaviaesturariibacter aridisoli	strain=17J68-15	GCA_004343705.1	2545761	2545761	type	True	76.145	87	2153	95	below_threshold
Flavihumibacter rivuli	strain=IMCC34838	GCA_018595685.2	2838156	2838156	type	True	75.8783	67	2153	95	below_threshold
Dinghuibacter silviterrae	strain=DSM 100059	GCA_004366355.1	1539049	1539049	type	True	75.8253	100	2153	95	below_threshold
Sediminibacterium soli	strain=WSJ-3	GCA_009939225.1	2698829	2698829	type	True	75.8096	55	2153	95	below_threshold
Chitinophaga barathri	strain=YLT18	GCA_003614855.1	1647451	1647451	type	True	75.3211	52	2153	95	below_threshold
Chitinophaga chungangae	strain=MAH-28	GCA_017742215.1	2821488	2821488	type	True	75.309	54	2153	95	below_threshold
Chitinophaga barathri	strain=YLT18	GCA_003807585.1	1647451	1647451	type	True	75.2962	51	2153	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 19:18:29,407] [INFO] DFAST Taxonomy check result was written to GCA_018267545.1_ASM1826754v1_genomic.fna/tc_result.tsv
[2023-06-18 19:18:29,408] [INFO] ===== Taxonomy check completed =====
[2023-06-18 19:18:29,408] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 19:18:29,408] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg78c587c6-9468-45fc-96fe-ef7d60ff884d/dqc_reference/checkm_data
[2023-06-18 19:18:29,410] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 19:18:29,477] [INFO] Task started: CheckM
[2023-06-18 19:18:29,477] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018267545.1_ASM1826754v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018267545.1_ASM1826754v1_genomic.fna/checkm_input GCA_018267545.1_ASM1826754v1_genomic.fna/checkm_result
[2023-06-18 19:19:59,595] [INFO] Task succeeded: CheckM
[2023-06-18 19:19:59,597] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 19:19:59,619] [INFO] ===== Completeness check finished =====
[2023-06-18 19:19:59,619] [INFO] ===== Start GTDB Search =====
[2023-06-18 19:19:59,620] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018267545.1_ASM1826754v1_genomic.fna/markers.fasta)
[2023-06-18 19:19:59,620] [INFO] Task started: Blastn
[2023-06-18 19:19:59,620] [INFO] Running command: blastn -query GCA_018267545.1_ASM1826754v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg78c587c6-9468-45fc-96fe-ef7d60ff884d/dqc_reference/reference_markers_gtdb.fasta -out GCA_018267545.1_ASM1826754v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 19:20:00,416] [INFO] Task succeeded: Blastn
[2023-06-18 19:20:00,421] [INFO] Selected 15 target genomes.
[2023-06-18 19:20:00,421] [INFO] Target genome list was writen to GCA_018267545.1_ASM1826754v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 19:20:00,433] [INFO] Task started: fastANI
[2023-06-18 19:20:00,434] [INFO] Running command: fastANI --query /var/lib/cwl/stgc787aa1a-c23b-4b9e-bef0-154f3f71af61/GCA_018267545.1_ASM1826754v1_genomic.fna.gz --refList GCA_018267545.1_ASM1826754v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018267545.1_ASM1826754v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 19:20:15,610] [INFO] Task succeeded: fastANI
[2023-06-18 19:20:15,627] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 19:20:15,627] [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_018267545.1	s__Puia sp018267545	100.0	2140	2153	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Puia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018267585.1	s__Puia sp018267585	78.7837	574	2153	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Puia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014642875.1	s__Puia dinghuensis	77.9762	445	2153	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Puia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015654595.1	s__Puia sp015654595	77.8947	335	2153	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Puia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003167015.1	s__Puia sp003167015	77.6003	280	2153	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Puia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898505.1	s__Puia sp001898505	77.3283	284	2153	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Puia	95.0	100.00	100.00	1.00	1.00	2	-
GCA_015655015.1	s__Puia sp015655015	76.881	267	2153	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Puia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744515.1	s__Paraflavitalea sp017744515	76.3032	82	2153	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Paraflavitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004343705.1	s__Flaviaesturariibacter aridisoli	76.1614	86	2153	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flaviaesturariibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110245.1	s__Niastella yeongjuensis	76.0404	67	2153	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niastella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_017744805.1	s__Pseudobacter sp017744805	75.9146	67	2153	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Pseudobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004366355.1	s__Dinghuibacter silviterrae	75.8253	100	2153	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Dinghuibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 19:20:15,631] [INFO] GTDB search result was written to GCA_018267545.1_ASM1826754v1_genomic.fna/result_gtdb.tsv
[2023-06-18 19:20:15,631] [INFO] ===== GTDB Search completed =====
[2023-06-18 19:20:15,637] [INFO] DFAST_QC result json was written to GCA_018267545.1_ASM1826754v1_genomic.fna/dqc_result.json
[2023-06-18 19:20:15,637] [INFO] DFAST_QC completed!
[2023-06-18 19:20:15,637] [INFO] Total running time: 0h2m41s