[2024-01-24 12:39:42,117] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:39:42,127] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:39:42,127] [INFO] DQC Reference Directory: /var/lib/cwl/stga5762f58-3b74-4b0b-8736-18e12233ec77/dqc_reference
[2024-01-24 12:39:43,405] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:39:43,406] [INFO] Task started: Prodigal
[2024-01-24 12:39:43,406] [INFO] Running command: gunzip -c /var/lib/cwl/stgb60a1a80-2eed-4fa6-8974-a9c560fdd3b8/GCF_004363805.1_ASM436380v1_genomic.fna.gz | prodigal -d GCF_004363805.1_ASM436380v1_genomic.fna/cds.fna -a GCF_004363805.1_ASM436380v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:39:57,204] [INFO] Task succeeded: Prodigal
[2024-01-24 12:39:57,205] [INFO] Task started: HMMsearch
[2024-01-24 12:39:57,205] [INFO] Running command: hmmsearch --tblout GCF_004363805.1_ASM436380v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga5762f58-3b74-4b0b-8736-18e12233ec77/dqc_reference/reference_markers.hmm GCF_004363805.1_ASM436380v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:39:57,485] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:39:57,486] [INFO] Found 6/6 markers.
[2024-01-24 12:39:57,536] [INFO] Query marker FASTA was written to GCF_004363805.1_ASM436380v1_genomic.fna/markers.fasta
[2024-01-24 12:39:57,536] [INFO] Task started: Blastn
[2024-01-24 12:39:57,537] [INFO] Running command: blastn -query GCF_004363805.1_ASM436380v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga5762f58-3b74-4b0b-8736-18e12233ec77/dqc_reference/reference_markers.fasta -out GCF_004363805.1_ASM436380v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:39:58,481] [INFO] Task succeeded: Blastn
[2024-01-24 12:39:58,484] [INFO] Selected 23 target genomes.
[2024-01-24 12:39:58,485] [INFO] Target genome list was writen to GCF_004363805.1_ASM436380v1_genomic.fna/target_genomes.txt
[2024-01-24 12:39:58,490] [INFO] Task started: fastANI
[2024-01-24 12:39:58,490] [INFO] Running command: fastANI --query /var/lib/cwl/stgb60a1a80-2eed-4fa6-8974-a9c560fdd3b8/GCF_004363805.1_ASM436380v1_genomic.fna.gz --refList GCF_004363805.1_ASM436380v1_genomic.fna/target_genomes.txt --output GCF_004363805.1_ASM436380v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:40:20,684] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:20,685] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga5762f58-3b74-4b0b-8736-18e12233ec77/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:40:20,685] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga5762f58-3b74-4b0b-8736-18e12233ec77/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:40:20,704] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:40:20,704] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:40:20,705] [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
Paludibacterium purpuratum	strain=CECT 8976	GCA_004363805.1	1144873	1144873	type	True	100.0	1326	1328	95	conclusive
Chromobacterium violaceum	strain=NCTC9757	GCA_900446805.1	536	536	type	True	78.95	476	1328	95	below_threshold
Chromobacterium violaceum	strain=ATCC 12472	GCA_000007705.1	536	536	type	True	78.9422	469	1328	95	below_threshold
Paludibacterium paludis	strain=BCRC 80514	GCA_018802605.1	1225769	1225769	type	True	78.902	359	1328	95	below_threshold
Chromobacterium piscinae	strain=DSM 23278	GCA_021129175.1	686831	686831	type	True	78.8998	431	1328	95	below_threshold
Chromobacterium phragmitis	strain=IIBBL 112-1	GCA_003325475.1	2202141	2202141	type	True	78.8928	446	1328	95	below_threshold
Chromobacterium amazonense	strain=DSM 26508	GCA_001855565.1	1382803	1382803	type	True	78.8876	424	1328	95	below_threshold
Crenobacter luteus	strain=DSM 27258	GCA_004345725.1	1452487	1452487	type	True	78.854	358	1328	95	below_threshold
Chromobacterium paludis	strain=IIBBL 257-1	GCA_008275125.1	2605945	2605945	type	True	78.8317	457	1328	95	below_threshold
Chromobacterium aquaticum	strain=DSM 19852	GCA_021129195.1	467180	467180	type	True	78.8297	424	1328	95	below_threshold
Paludibacterium paludis	strain=KCTC 32182	GCA_014652495.1	1225769	1225769	type	True	78.8037	354	1328	95	below_threshold
Chromobacterium sinusclupearum	strain=MWU13-2610	GCA_002902845.1	2077146	2077146	type	True	78.789	445	1328	95	below_threshold
Chromobacterium alticapitis	strain=MWU14-2602	GCA_002924365.1	2073169	2073169	type	True	78.7519	438	1328	95	below_threshold
Chromobacterium sphagni	strain=IIBBL 14B-1	GCA_001855555.1	1903179	1903179	type	True	78.7459	434	1328	95	below_threshold
Vogesella fluminis	strain=KCTC 23713	GCA_014652335.1	1069161	1069161	type	True	78.5074	342	1328	95	below_threshold
Crenobacter cavernae	strain=K1W11S-77	GCA_003355495.1	2290923	2290923	type	True	78.3639	350	1328	95	below_threshold
Paludibacterium yongneupense	strain=DSM 18731	GCA_000422925.1	400061	400061	type	True	78.3036	364	1328	95	below_threshold
Chitiniphilus shinanonensis	strain=DSM 23277	GCA_000374805.1	553088	553088	type	True	77.5132	254	1328	95	below_threshold
Massilia solisilvae	strain=JCM 31607	GCA_024753215.1	1811225	1811225	type	True	76.6231	179	1328	95	below_threshold
Paraburkholderia lycopersici	strain=TNe-862	GCA_900096975.1	416944	416944	type	True	76.4068	123	1328	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	76.2359	135	1328	95	below_threshold
Caballeronia terrestris		GCA_001544515.2	1226301	1226301	type	True	75.9592	115	1328	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:40:20,706] [INFO] DFAST Taxonomy check result was written to GCF_004363805.1_ASM436380v1_genomic.fna/tc_result.tsv
[2024-01-24 12:40:20,707] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:40:20,707] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:40:20,707] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga5762f58-3b74-4b0b-8736-18e12233ec77/dqc_reference/checkm_data
[2024-01-24 12:40:20,708] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:40:20,749] [INFO] Task started: CheckM
[2024-01-24 12:40:20,750] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004363805.1_ASM436380v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004363805.1_ASM436380v1_genomic.fna/checkm_input GCF_004363805.1_ASM436380v1_genomic.fna/checkm_result
[2024-01-24 12:41:00,474] [INFO] Task succeeded: CheckM
[2024-01-24 12:41:00,476] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:41:00,499] [INFO] ===== Completeness check finished =====
[2024-01-24 12:41:00,500] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:41:00,500] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004363805.1_ASM436380v1_genomic.fna/markers.fasta)
[2024-01-24 12:41:00,500] [INFO] Task started: Blastn
[2024-01-24 12:41:00,501] [INFO] Running command: blastn -query GCF_004363805.1_ASM436380v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga5762f58-3b74-4b0b-8736-18e12233ec77/dqc_reference/reference_markers_gtdb.fasta -out GCF_004363805.1_ASM436380v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:41:02,242] [INFO] Task succeeded: Blastn
[2024-01-24 12:41:02,245] [INFO] Selected 16 target genomes.
[2024-01-24 12:41:02,245] [INFO] Target genome list was writen to GCF_004363805.1_ASM436380v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:41:02,253] [INFO] Task started: fastANI
[2024-01-24 12:41:02,254] [INFO] Running command: fastANI --query /var/lib/cwl/stgb60a1a80-2eed-4fa6-8974-a9c560fdd3b8/GCF_004363805.1_ASM436380v1_genomic.fna.gz --refList GCF_004363805.1_ASM436380v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004363805.1_ASM436380v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:41:15,404] [INFO] Task succeeded: fastANI
[2024-01-24 12:41:15,419] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:41:15,419] [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_004363805.1	s__Paludibacterium purpuratum	100.0	1326	1328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Paludibacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_019232825.1	s__Paludibacterium sp019232825	82.5655	825	1328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Paludibacterium	95.0	99.73	99.73	0.94	0.94	2	-
GCF_018802765.1	s__Paludibacterium sp018802765	81.8205	707	1328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Paludibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177275.1	s__Pseudogulbenkiania subflava	79.1733	408	1328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Pseudogulbenkiania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000527175.1	s__Pseudogulbenkiania sp000527175	79.1521	438	1328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Pseudogulbenkiania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016192025.1	s__Pseudogulbenkiania sp016192025	79.0592	297	1328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Pseudogulbenkiania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018802605.1	s__Paludibacterium paludis	78.891	363	1328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Paludibacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016428945.1	s__Chromobacterium sp016428945	78.8644	435	1328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	97.99	97.99	0.89	0.89	2	-
GCF_002848345.1	s__Chromobacterium sp002848345	78.8481	462	1328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004345725.1	s__Crenobacter luteus	78.8429	359	1328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Crenobacter	95.0	98.88	98.88	0.93	0.93	2	-
GCF_001043555.1	s__Chromobacterium sp001043555	78.7535	442	1328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003355495.1	s__Crenobacter cavernae	78.3857	348	1328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Crenobacter	95.0	96.17	96.17	0.93	0.93	2	-
GCF_000422925.1	s__Paludibacterium yongneupense	78.3038	366	1328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Paludibacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000374805.1	s__Chitiniphilus shinanonensis	77.503	256	1328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Chitiniphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002840765.1	s__Azonexus sp002840765	76.6471	121	1328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001544515.1	s__Caballeronia terrestris	75.946	116	1328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:41:15,421] [INFO] GTDB search result was written to GCF_004363805.1_ASM436380v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:41:15,422] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:41:15,426] [INFO] DFAST_QC result json was written to GCF_004363805.1_ASM436380v1_genomic.fna/dqc_result.json
[2024-01-24 12:41:15,426] [INFO] DFAST_QC completed!
[2024-01-24 12:41:15,426] [INFO] Total running time: 0h1m33s