[2024-01-24 14:21:50,279] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:21:50,284] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:21:50,284] [INFO] DQC Reference Directory: /var/lib/cwl/stg4ea0188f-0700-49f4-a0fb-8a5e866a65a5/dqc_reference
[2024-01-24 14:21:51,710] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:21:51,711] [INFO] Task started: Prodigal
[2024-01-24 14:21:51,711] [INFO] Running command: gunzip -c /var/lib/cwl/stgabbb0e83-6474-4b03-b5cf-6a1de56b0da1/GCF_025628885.1_ASM2562888v1_genomic.fna.gz | prodigal -d GCF_025628885.1_ASM2562888v1_genomic.fna/cds.fna -a GCF_025628885.1_ASM2562888v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:25,102] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:25,103] [INFO] Task started: HMMsearch
[2024-01-24 14:22:25,103] [INFO] Running command: hmmsearch --tblout GCF_025628885.1_ASM2562888v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4ea0188f-0700-49f4-a0fb-8a5e866a65a5/dqc_reference/reference_markers.hmm GCF_025628885.1_ASM2562888v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:25,466] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:25,467] [INFO] Found 6/6 markers.
[2024-01-24 14:22:25,537] [INFO] Query marker FASTA was written to GCF_025628885.1_ASM2562888v1_genomic.fna/markers.fasta
[2024-01-24 14:22:25,537] [INFO] Task started: Blastn
[2024-01-24 14:22:25,537] [INFO] Running command: blastn -query GCF_025628885.1_ASM2562888v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4ea0188f-0700-49f4-a0fb-8a5e866a65a5/dqc_reference/reference_markers.fasta -out GCF_025628885.1_ASM2562888v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:26,141] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:26,146] [INFO] Selected 25 target genomes.
[2024-01-24 14:22:26,147] [INFO] Target genome list was writen to GCF_025628885.1_ASM2562888v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:26,181] [INFO] Task started: fastANI
[2024-01-24 14:22:26,182] [INFO] Running command: fastANI --query /var/lib/cwl/stgabbb0e83-6474-4b03-b5cf-6a1de56b0da1/GCF_025628885.1_ASM2562888v1_genomic.fna.gz --refList GCF_025628885.1_ASM2562888v1_genomic.fna/target_genomes.txt --output GCF_025628885.1_ASM2562888v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:22:49,403] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:49,403] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4ea0188f-0700-49f4-a0fb-8a5e866a65a5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:22:49,404] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4ea0188f-0700-49f4-a0fb-8a5e866a65a5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:22:49,416] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:22:49,416] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:22:49,416] [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
Flavisolibacter tropicus	strain=LCS9	GCA_001644645.1	1492898	1492898	type	True	77.0819	146	2299	95	below_threshold
Niastella vici	strain=DJ57	GCA_002077945.1	1703345	1703345	type	True	76.6595	137	2299	95	below_threshold
Niastella populi	strain=CCTCC AB 208238	GCA_002078015.1	550983	550983	type	True	76.4931	78	2299	95	below_threshold
Lacibacter luteus	strain=TTM-7	GCA_004118265.1	2508719	2508719	type	True	76.3991	75	2299	95	below_threshold
Flavisolibacter ginsengisoli	strain=DSM 18119	GCA_900129295.1	462367	462367	type	True	76.3965	120	2299	95	below_threshold
Flavisolibacter ginsenosidimutans	strain=Gsoil 636	GCA_007970805.1	661481	661481	type	True	76.3811	73	2299	95	below_threshold
Niastella koreensis	strain=GR20-10	GCA_000246855.1	354356	354356	type	True	76.3236	101	2299	95	below_threshold
Niastella koreensis	strain=DSM 17620	GCA_002077985.1	354356	354356	type	True	76.2847	98	2299	95	below_threshold
Cnuella takakiae	strain=DSM 26897	GCA_900129015.1	1302690	1302690	type	True	76.2124	117	2299	95	below_threshold
Lacibacter cauensis	strain=CGMCC 1.7271	GCA_007830055.1	510947	510947	type	True	76.2004	63	2299	95	below_threshold
Niabella hibiscisoli	strain=THG-DN5.5	GCA_022512515.1	1825928	1825928	type	True	76.1958	59	2299	95	below_threshold
Deminuibacter soli	strain=K23C18032701	GCA_003412455.1	2291815	2291815	type	True	76.1735	63	2299	95	below_threshold
Paraflavitalea soli	strain=5GH32-13	GCA_003555545.1	2315862	2315862	type	True	76.0302	90	2299	95	below_threshold
Chitinophaga tropicalis	strain=ysch24	GCA_009758205.1	2683588	2683588	type	True	75.9994	65	2299	95	below_threshold
Chitinophaga pinensis	strain=DSM 2588	GCA_000024005.1	79329	79329	type	True	75.9512	59	2299	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:22:49,418] [INFO] DFAST Taxonomy check result was written to GCF_025628885.1_ASM2562888v1_genomic.fna/tc_result.tsv
[2024-01-24 14:22:49,418] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:22:49,419] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:22:49,419] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4ea0188f-0700-49f4-a0fb-8a5e866a65a5/dqc_reference/checkm_data
[2024-01-24 14:22:49,420] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:22:49,491] [INFO] Task started: CheckM
[2024-01-24 14:22:49,492] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025628885.1_ASM2562888v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025628885.1_ASM2562888v1_genomic.fna/checkm_input GCF_025628885.1_ASM2562888v1_genomic.fna/checkm_result
[2024-01-24 14:24:19,326] [INFO] Task succeeded: CheckM
[2024-01-24 14:24:19,327] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:24:19,360] [INFO] ===== Completeness check finished =====
[2024-01-24 14:24:19,360] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:24:19,361] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025628885.1_ASM2562888v1_genomic.fna/markers.fasta)
[2024-01-24 14:24:19,361] [INFO] Task started: Blastn
[2024-01-24 14:24:19,361] [INFO] Running command: blastn -query GCF_025628885.1_ASM2562888v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4ea0188f-0700-49f4-a0fb-8a5e866a65a5/dqc_reference/reference_markers_gtdb.fasta -out GCF_025628885.1_ASM2562888v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:24:20,200] [INFO] Task succeeded: Blastn
[2024-01-24 14:24:20,204] [INFO] Selected 31 target genomes.
[2024-01-24 14:24:20,204] [INFO] Target genome list was writen to GCF_025628885.1_ASM2562888v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:24:20,246] [INFO] Task started: fastANI
[2024-01-24 14:24:20,247] [INFO] Running command: fastANI --query /var/lib/cwl/stgabbb0e83-6474-4b03-b5cf-6a1de56b0da1/GCF_025628885.1_ASM2562888v1_genomic.fna.gz --refList GCF_025628885.1_ASM2562888v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025628885.1_ASM2562888v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:24:47,381] [INFO] Task succeeded: fastANI
[2024-01-24 14:24:47,406] [INFO] Found 23 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:24:47,406] [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_001644645.1	s__Flavisolibacter_B tropicus	77.0819	146	2299	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavisolibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002077945.1	s__Niastella vici	76.6745	136	2299	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niastella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002078015.1	s__Niastella populi	76.4931	78	2299	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niastella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004118265.1	s__Lacibacter luteus	76.4231	74	2299	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Lacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003332885.2	s__Paracnuella aquatica	76.4143	126	2299	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Paracnuella	95.0	95.63	95.63	0.92	0.92	2	-
GCA_014163555.1	s__Flavisolibacter sp014163555	76.4017	108	2299	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129295.1	s__Flavisolibacter ginsengisoli	76.3798	121	2299	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000246855.1	s__Niastella koreensis	76.3236	101	2299	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niastella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_001898485.1	s__46-32 sp001898485	76.2826	70	2299	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__46-32	95.0	99.14	98.30	0.96	0.92	3	-
GCF_007830055.1	s__Lacibacter cauensis	76.1854	62	2299	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Lacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013327885.1	s__Flavisolibacter sp013327885	76.15	97	2299	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002399735.1	s__Terrimonas sp002399735	76.149	58	2299	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Terrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017745135.1	s__Flavisolibacter sp017745135	76.1428	89	2299	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012927185.1	s__Pseudobacter sp012927185	76.1371	62	2299	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Pseudobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001302245.1	s__PMP191F sp001302245	76.0815	106	2299	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__PMP191F	95.0	99.37	99.37	0.95	0.95	2	-
GCF_000374045.1	s__Segetibacter koreensis	76.0303	60	2299	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Segetibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003555545.1	s__Paraflavitalea soli	76.0302	90	2299	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Paraflavitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003243445.1	s__46-32 sp003243445	75.9353	82	2299	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__46-32	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013695175.1	s__JACDAZ01 sp013695175	75.8215	76	2299	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JACDAZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002050435.1	s__Flavisolibacter sp002050435	75.7639	71	2299	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001601815.1	s__Flavihumibacter sp001601815	75.6723	62	2299	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavihumibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015069695.1	s__JADCRZ01 sp015069695	75.6401	63	2299	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JADCRZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016786805.1	s__JJ008 sp016786805	75.4988	57	2299	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:24:47,409] [INFO] GTDB search result was written to GCF_025628885.1_ASM2562888v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:24:47,410] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:24:47,420] [INFO] DFAST_QC result json was written to GCF_025628885.1_ASM2562888v1_genomic.fna/dqc_result.json
[2024-01-24 14:24:47,420] [INFO] DFAST_QC completed!
[2024-01-24 14:24:47,420] [INFO] Total running time: 0h2m57s