[2024-01-24 12:14:09,747] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:09,750] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:09,751] [INFO] DQC Reference Directory: /var/lib/cwl/stg8b2158db-50b8-44ce-9410-d04a8933413b/dqc_reference
[2024-01-24 12:14:11,179] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:11,180] [INFO] Task started: Prodigal
[2024-01-24 12:14:11,180] [INFO] Running command: gunzip -c /var/lib/cwl/stgc92e75cf-91ae-47d8-a51b-423f376eba86/GCF_001418035.1_ASM141803v1_genomic.fna.gz | prodigal -d GCF_001418035.1_ASM141803v1_genomic.fna/cds.fna -a GCF_001418035.1_ASM141803v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:20,522] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:20,522] [INFO] Task started: HMMsearch
[2024-01-24 12:14:20,522] [INFO] Running command: hmmsearch --tblout GCF_001418035.1_ASM141803v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8b2158db-50b8-44ce-9410-d04a8933413b/dqc_reference/reference_markers.hmm GCF_001418035.1_ASM141803v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:20,851] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:20,852] [INFO] Found 6/6 markers.
[2024-01-24 12:14:20,891] [INFO] Query marker FASTA was written to GCF_001418035.1_ASM141803v1_genomic.fna/markers.fasta
[2024-01-24 12:14:20,891] [INFO] Task started: Blastn
[2024-01-24 12:14:20,891] [INFO] Running command: blastn -query GCF_001418035.1_ASM141803v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8b2158db-50b8-44ce-9410-d04a8933413b/dqc_reference/reference_markers.fasta -out GCF_001418035.1_ASM141803v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:21,822] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:21,826] [INFO] Selected 19 target genomes.
[2024-01-24 12:14:21,826] [INFO] Target genome list was writen to GCF_001418035.1_ASM141803v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:21,842] [INFO] Task started: fastANI
[2024-01-24 12:14:21,842] [INFO] Running command: fastANI --query /var/lib/cwl/stgc92e75cf-91ae-47d8-a51b-423f376eba86/GCF_001418035.1_ASM141803v1_genomic.fna.gz --refList GCF_001418035.1_ASM141803v1_genomic.fna/target_genomes.txt --output GCF_001418035.1_ASM141803v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:37,215] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:37,215] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8b2158db-50b8-44ce-9410-d04a8933413b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:37,216] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8b2158db-50b8-44ce-9410-d04a8933413b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:37,231] [INFO] Found 19 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:14:37,231] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:14:37,231] [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
Gulbenkiania indica	strain=DSM 17901	GCA_001418035.1	375574	375574	type	True	100.0	938	940	95	conclusive
Gulbenkiania indica	strain=DSM 17901	GCA_001517245.1	375574	375574	type	True	100.0	938	940	95	conclusive
Chromobacterium violaceum	strain=NCTC9757	GCA_900446805.1	536	536	type	True	79.7186	465	940	95	below_threshold
Chromobacterium violaceum	strain=ATCC 12472	GCA_000007705.1	536	536	type	True	79.6808	461	940	95	below_threshold
Crenobacter luteus	strain=DSM 27258	GCA_004345725.1	1452487	1452487	type	True	79.3202	408	940	95	below_threshold
Chromobacterium alkanivorans	strain=IITR-71	GCA_016937655.1	1071719	1071719	type	True	79.2629	485	940	95	below_threshold
Chromobacterium sphagni	strain=IIBBL 14B-1	GCA_001855555.1	1903179	1903179	type	True	79.2465	443	940	95	below_threshold
Chromobacterium amazonense	strain=DSM 26508	GCA_001855565.1	1382803	1382803	type	True	79.219	406	940	95	below_threshold
Chromobacterium sinusclupearum	strain=MWU13-2610	GCA_002902845.1	2077146	2077146	type	True	79.2155	425	940	95	below_threshold
Chromobacterium subtsugae	strain=PRAA4-1	GCA_001676875.1	251747	251747	type	True	79.2137	468	940	95	below_threshold
Chromobacterium piscinae	strain=DSM 23278	GCA_021129175.1	686831	686831	type	True	79.1806	418	940	95	below_threshold
Chromobacterium aquaticum	strain=DSM 19852	GCA_021129195.1	467180	467180	type	True	79.0853	439	940	95	below_threshold
Crenobacter sedimenti	strain=HX-7-9	GCA_010435965.1	2705474	2705474	type	True	79.0328	397	940	95	below_threshold
Crenobacter intestini	strain=GY 70310	GCA_004919095.1	2563443	2563443	type	True	78.8403	400	940	95	below_threshold
Chromobacterium alticapitis	strain=MWU14-2602	GCA_002924365.1	2073169	2073169	type	True	78.8305	406	940	95	below_threshold
Paludibacterium paludis	strain=BCRC 80514	GCA_018802605.1	1225769	1225769	type	True	78.1394	318	940	95	below_threshold
Paludibacterium paludis	strain=KCTC 32182	GCA_014652495.1	1225769	1225769	type	True	78.1281	318	940	95	below_threshold
Paludibacterium yongneupense	strain=DSM 18731	GCA_000422925.1	400061	400061	type	True	77.7661	242	940	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	76.4247	147	940	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:37,234] [INFO] DFAST Taxonomy check result was written to GCF_001418035.1_ASM141803v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:37,235] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:37,235] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:37,235] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8b2158db-50b8-44ce-9410-d04a8933413b/dqc_reference/checkm_data
[2024-01-24 12:14:37,236] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:37,283] [INFO] Task started: CheckM
[2024-01-24 12:14:37,284] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001418035.1_ASM141803v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001418035.1_ASM141803v1_genomic.fna/checkm_input GCF_001418035.1_ASM141803v1_genomic.fna/checkm_result
[2024-01-24 12:15:08,818] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:08,820] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:08,839] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:08,839] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:08,840] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001418035.1_ASM141803v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:08,840] [INFO] Task started: Blastn
[2024-01-24 12:15:08,840] [INFO] Running command: blastn -query GCF_001418035.1_ASM141803v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8b2158db-50b8-44ce-9410-d04a8933413b/dqc_reference/reference_markers_gtdb.fasta -out GCF_001418035.1_ASM141803v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:10,641] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:10,646] [INFO] Selected 23 target genomes.
[2024-01-24 12:15:10,646] [INFO] Target genome list was writen to GCF_001418035.1_ASM141803v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:10,674] [INFO] Task started: fastANI
[2024-01-24 12:15:10,675] [INFO] Running command: fastANI --query /var/lib/cwl/stgc92e75cf-91ae-47d8-a51b-423f376eba86/GCF_001418035.1_ASM141803v1_genomic.fna.gz --refList GCF_001418035.1_ASM141803v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001418035.1_ASM141803v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:27,729] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:27,751] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:15:27,751] [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_004346645.1	s__Gulbenkiania mobilis	99.1176	880	940	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Gulbenkiania	95.0	99.11	99.06	0.93	0.92	4	conclusive
GCF_000007705.1	s__Chromobacterium violaceum	79.7025	460	940	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	98.58	98.16	0.94	0.91	26	-
GCF_000527175.1	s__Pseudogulbenkiania sp000527175	79.6747	485	940	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Pseudogulbenkiania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900090205.1	s__Vogesella sp900090205	79.4921	460	940	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Vogesella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002213445.1	s__Chromobacterium sp002213445	79.4785	443	940	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	99.12	99.12	0.94	0.94	2	-
GCF_000174355.1	s__Pseudogulbenkiania ferrooxidans_A	79.4531	467	940	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Pseudogulbenkiania	95.0	97.29	97.29	0.89	0.89	2	-
GCA_016192025.1	s__Pseudogulbenkiania sp016192025	79.2828	373	940	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Pseudogulbenkiania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016937655.1	s__Chromobacterium alkanivorans	79.2822	483	940	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	98.67	98.67	0.95	0.95	2	-
GCF_001676875.1	s__Chromobacterium subtsugae	79.2413	466	940	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	99.12	98.52	0.94	0.91	9	-
GCF_001855555.1	s__Chromobacterium sphagni	79.2355	444	940	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	99.33	99.33	0.93	0.93	2	-
GCF_002848345.1	s__Chromobacterium sp002848345	79.2353	452	940	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001855565.1	s__Chromobacterium amazonense	79.208	409	940	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	97.81	97.67	0.91	0.90	4	-
GCF_016428945.1	s__Chromobacterium sp016428945	79.1241	420	940	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	97.99	97.99	0.89	0.89	2	-
GCF_003052555.1	s__Chromobacterium sp003052555	79.0966	461	940	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001043555.1	s__Chromobacterium sp001043555	79.0356	451	940	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010435965.1	s__STGJ01 sp010435965	79.0117	399	940	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__STGJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007644045.2	s__Vogesella urethralis	78.999	417	940	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Vogesella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003325475.1	s__Chromobacterium phragmitis	78.9204	446	940	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	99.00	99.00	0.92	0.92	2	-
GCF_004919095.1	s__STGJ01 sp004919095	78.8211	398	940	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__STGJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018802765.1	s__Paludibacterium sp018802765	78.3235	309	940	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Paludibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018802605.1	s__Paludibacterium paludis	78.1502	317	940	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Paludibacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_018055005.1	s__Laribacter sp018055005	77.8565	206	940	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Aquaspirillaceae;g__Laribacter	95.0	99.59	99.59	0.84	0.84	2	-
GCF_000422925.1	s__Paludibacterium yongneupense	77.7314	242	940	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Paludibacterium	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:15:27,753] [INFO] GTDB search result was written to GCF_001418035.1_ASM141803v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:27,754] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:27,758] [INFO] DFAST_QC result json was written to GCF_001418035.1_ASM141803v1_genomic.fna/dqc_result.json
[2024-01-24 12:15:27,758] [INFO] DFAST_QC completed!
[2024-01-24 12:15:27,759] [INFO] Total running time: 0h1m18s