[2024-01-24 12:39:41,250] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:39:41,257] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:39:41,257] [INFO] DQC Reference Directory: /var/lib/cwl/stg665783a5-a541-45e9-9ef2-70364a808fd9/dqc_reference
[2024-01-24 12:39:42,682] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:39:42,683] [INFO] Task started: Prodigal
[2024-01-24 12:39:42,683] [INFO] Running command: gunzip -c /var/lib/cwl/stga05d0404-f5c6-4b72-84ec-a51d730b804c/GCF_009707705.1_ASM970770v1_genomic.fna.gz | prodigal -d GCF_009707705.1_ASM970770v1_genomic.fna/cds.fna -a GCF_009707705.1_ASM970770v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:39:54,278] [INFO] Task succeeded: Prodigal
[2024-01-24 12:39:54,279] [INFO] Task started: HMMsearch
[2024-01-24 12:39:54,279] [INFO] Running command: hmmsearch --tblout GCF_009707705.1_ASM970770v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg665783a5-a541-45e9-9ef2-70364a808fd9/dqc_reference/reference_markers.hmm GCF_009707705.1_ASM970770v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:39:54,525] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:39:54,527] [INFO] Found 6/6 markers.
[2024-01-24 12:39:54,573] [INFO] Query marker FASTA was written to GCF_009707705.1_ASM970770v1_genomic.fna/markers.fasta
[2024-01-24 12:39:54,573] [INFO] Task started: Blastn
[2024-01-24 12:39:54,573] [INFO] Running command: blastn -query GCF_009707705.1_ASM970770v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg665783a5-a541-45e9-9ef2-70364a808fd9/dqc_reference/reference_markers.fasta -out GCF_009707705.1_ASM970770v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:39:55,382] [INFO] Task succeeded: Blastn
[2024-01-24 12:39:55,386] [INFO] Selected 30 target genomes.
[2024-01-24 12:39:55,387] [INFO] Target genome list was writen to GCF_009707705.1_ASM970770v1_genomic.fna/target_genomes.txt
[2024-01-24 12:39:55,397] [INFO] Task started: fastANI
[2024-01-24 12:39:55,397] [INFO] Running command: fastANI --query /var/lib/cwl/stga05d0404-f5c6-4b72-84ec-a51d730b804c/GCF_009707705.1_ASM970770v1_genomic.fna.gz --refList GCF_009707705.1_ASM970770v1_genomic.fna/target_genomes.txt --output GCF_009707705.1_ASM970770v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:40:17,372] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:17,373] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg665783a5-a541-45e9-9ef2-70364a808fd9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:40:17,373] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg665783a5-a541-45e9-9ef2-70364a808fd9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:40:17,396] [INFO] Found 29 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:40:17,396] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:40:17,397] [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
Aquitalea aquatilis	strain=THG-DN7.12	GCA_005155025.1	1537400	1537400	type	True	80.2105	517	1115	95	below_threshold
Aquitalea denitrificans	strain=5YN1-3	GCA_009856625.1	519081	519081	type	True	80.1419	487	1115	95	below_threshold
Aquitalea magnusonii	strain=DSM 25134	GCA_003202035.1	332411	332411	suspected-type	True	79.9409	499	1115	95	below_threshold
Aquitalea pelogenes	strain=CCM 7557	GCA_001515305.1	1293573	1293573	type	True	79.777	466	1115	95	below_threshold
Chromobacterium sphagni	strain=IIBBL 14B-1	GCA_001855555.1	1903179	1903179	type	True	79.3391	384	1115	95	below_threshold
Chromobacterium violaceum	strain=ATCC 12472	GCA_000007705.1	536	536	type	True	79.2599	403	1115	95	below_threshold
Chromobacterium amazonense	strain=DSM 26508	GCA_001855565.1	1382803	1382803	type	True	79.2041	381	1115	95	below_threshold
Chromobacterium paludis	strain=IIBBL 257-1	GCA_008275125.1	2605945	2605945	type	True	79.1393	413	1115	95	below_threshold
Chromobacterium phragmitis	strain=IIBBL 112-1	GCA_003325475.1	2202141	2202141	type	True	79.137	385	1115	95	below_threshold
Chromobacterium violaceum	strain=NCTC9757	GCA_900446805.1	536	536	type	True	79.1026	409	1115	95	below_threshold
Chromobacterium aquaticum	strain=DSM 19852	GCA_021129195.1	467180	467180	type	True	79.0677	391	1115	95	below_threshold
Chromobacterium sinusclupearum	strain=MWU13-2610	GCA_002902845.1	2077146	2077146	type	True	79.0008	375	1115	95	below_threshold
Chromobacterium alkanivorans	strain=IITR-71	GCA_016937655.1	1071719	1071719	type	True	78.964	417	1115	95	below_threshold
Vogesella urethralis	strain=YM-1	GCA_007644045.2	2592656	2592656	type	True	78.9436	387	1115	95	below_threshold
Chromobacterium alticapitis	strain=MWU14-2602	GCA_002924365.1	2073169	2073169	type	True	78.8852	352	1115	95	below_threshold
Chromobacterium vaccinii	strain=MWU205	GCA_000971335.1	1108595	1108595	type	True	78.8352	378	1115	95	below_threshold
Vogesella mureinivorans	strain=389	GCA_007644035.2	657276	657276	type	True	78.6595	346	1115	95	below_threshold
Chromobacterium piscinae	strain=DSM 23278	GCA_021129175.1	686831	686831	type	True	78.624	378	1115	95	below_threshold
Rivicola pingtungensis	strain=DSM 29661	GCA_003201855.1	1054498	1054498	type	True	78.2178	252	1115	95	below_threshold
Gulbenkiania indica	strain=DSM 17901	GCA_001517245.1	375574	375574	type	True	78.0547	301	1115	95	below_threshold
Gulbenkiania indica	strain=DSM 17901	GCA_001418035.1	375574	375574	type	True	78.0547	301	1115	95	below_threshold
Aquaspirillum serpens	strain=DSM 68	GCA_000420525.1	190	190	type	True	76.7857	59	1115	95	below_threshold
Tepidimonas thermarum	strain=AA-1	GCA_007556705.1	335431	335431	type	True	76.504	67	1115	95	below_threshold
Aquabacterium soli	strain=SJQ9	GCA_003933735.1	2493092	2493092	type	True	76.3617	72	1115	95	below_threshold
Chitinibacter tainanensis	strain=DSM 15459	GCA_000429785.1	230667	230667	type	True	76.129	92	1115	95	below_threshold
Acidovorax caeni	strain=R-24608	GCA_900116825.1	343013	343013	type	True	75.9456	62	1115	95	below_threshold
Comamonas avium	strain=Sa2CVA6	GCA_014836675.1	2762231	2762231	type	True	75.9259	50	1115	95	below_threshold
Comamonas koreensis	strain=KCTC 12005	GCA_021026195.1	160825	160825	type	True	75.6827	76	1115	95	below_threshold
Acidovorax konjaci	strain=DSM 7481	GCA_900112675.1	32040	32040	type	True	75.4258	59	1115	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:40:17,398] [INFO] DFAST Taxonomy check result was written to GCF_009707705.1_ASM970770v1_genomic.fna/tc_result.tsv
[2024-01-24 12:40:17,399] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:40:17,399] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:40:17,399] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg665783a5-a541-45e9-9ef2-70364a808fd9/dqc_reference/checkm_data
[2024-01-24 12:40:17,400] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:40:17,433] [INFO] Task started: CheckM
[2024-01-24 12:40:17,433] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009707705.1_ASM970770v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009707705.1_ASM970770v1_genomic.fna/checkm_input GCF_009707705.1_ASM970770v1_genomic.fna/checkm_result
[2024-01-24 12:40:54,138] [INFO] Task succeeded: CheckM
[2024-01-24 12:40:54,140] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.20%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:40:54,165] [INFO] ===== Completeness check finished =====
[2024-01-24 12:40:54,165] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:40:54,166] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009707705.1_ASM970770v1_genomic.fna/markers.fasta)
[2024-01-24 12:40:54,166] [INFO] Task started: Blastn
[2024-01-24 12:40:54,167] [INFO] Running command: blastn -query GCF_009707705.1_ASM970770v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg665783a5-a541-45e9-9ef2-70364a808fd9/dqc_reference/reference_markers_gtdb.fasta -out GCF_009707705.1_ASM970770v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:55,350] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:55,356] [INFO] Selected 31 target genomes.
[2024-01-24 12:40:55,356] [INFO] Target genome list was writen to GCF_009707705.1_ASM970770v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:40:55,399] [INFO] Task started: fastANI
[2024-01-24 12:40:55,400] [INFO] Running command: fastANI --query /var/lib/cwl/stga05d0404-f5c6-4b72-84ec-a51d730b804c/GCF_009707705.1_ASM970770v1_genomic.fna.gz --refList GCF_009707705.1_ASM970770v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009707705.1_ASM970770v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:41:18,618] [INFO] Task succeeded: fastANI
[2024-01-24 12:41:18,641] [INFO] Found 31 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:41:18,642] [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_009707705.1	s__WLYX01 sp009707705	100.0	1114	1115	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__WLYX01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_005155025.1	s__Aquitalea aquatilis	80.2182	513	1115	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Aquitalea	95.0	99.19	99.19	0.95	0.95	2	-
GCF_002217795.2	s__Aquitalea magnusonii_B	80.1458	501	1115	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Aquitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009856625.1	s__Aquitalea denitrificans	80.1171	487	1115	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Aquitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003693445.1	s__Aquitalea sp003693445	79.9318	480	1115	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Aquitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003202035.1	s__Aquitalea magnusonii	79.9299	500	1115	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Aquitalea	95.0	99.21	98.53	0.95	0.91	3	-
GCF_001515305.1	s__Aquitalea pelogenes	79.8106	463	1115	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Aquitalea	95.0	97.38	96.32	0.89	0.86	4	-
GCF_013911085.1	s__Aquitalea magnusonii_C	79.7903	507	1115	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Aquitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013391415.1	s__Aquitalea sp013391415	79.6895	483	1115	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Aquitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001855565.1	s__Chromobacterium amazonense	79.2623	383	1115	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	97.81	97.67	0.91	0.90	4	-
GCF_001855555.1	s__Chromobacterium sphagni	79.2427	384	1115	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	99.33	99.33	0.93	0.93	2	-
GCA_002213445.1	s__Chromobacterium sp002213445	79.22	416	1115	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	99.12	99.12	0.94	0.94	2	-
GCF_000007705.1	s__Chromobacterium violaceum	79.1732	399	1115	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	98.58	98.16	0.94	0.91	26	-
GCF_900090205.1	s__Vogesella sp900090205	79.1658	392	1115	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	79.1519	385	1115	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	99.00	99.00	0.92	0.92	2	-
GCF_002848345.1	s__Chromobacterium sp002848345	79.1337	375	1115	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008275125.1	s__Chromobacterium paludis	79.0724	415	1115	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003052555.1	s__Chromobacterium sp003052555	78.9974	400	1115	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016937655.1	s__Chromobacterium alkanivorans	78.964	418	1115	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	98.67	98.67	0.95	0.95	2	-
GCF_016428945.1	s__Chromobacterium sp016428945	78.9607	378	1115	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	97.99	97.99	0.89	0.89	2	-
GCF_007644045.2	s__Vogesella urethralis	78.9485	386	1115	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Vogesella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002924365.1	s__Chromobacterium sp002924365	78.8898	352	1115	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016192025.1	s__Pseudogulbenkiania sp016192025	78.8783	313	1115	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Pseudogulbenkiania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000971335.1	s__Chromobacterium vaccinii	78.8346	378	1115	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	98.63	98.56	0.92	0.92	4	-
GCF_000711885.1	s__Chromobacterium haemolyticum	78.7957	384	1115	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	96.93	96.05	0.88	0.85	14	-
GCF_011601295.1	s__Chromobacterium vaccinii_A	78.6858	395	1115	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	95.84	95.77	0.89	0.88	3	-
GCF_018802765.1	s__Paludibacterium sp018802765	78.6383	307	1115	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Paludibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002002905.1	s__Rivicola sp002002905	78.4334	270	1115	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Aquaspirillaceae;g__Rivicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017998615.1	s__Vogesella sp017998615	78.1172	240	1115	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Vogesella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900549295.1	s__Azonexus sp900549295	76.4253	80	1115	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	99.94	99.94	0.93	0.93	2	-
GCA_003963005.1	s__Pelomonas sp003963005	75.69	55	1115	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:41:18,644] [INFO] GTDB search result was written to GCF_009707705.1_ASM970770v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:41:18,644] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:41:18,652] [INFO] DFAST_QC result json was written to GCF_009707705.1_ASM970770v1_genomic.fna/dqc_result.json
[2024-01-24 12:41:18,652] [INFO] DFAST_QC completed!
[2024-01-24 12:41:18,653] [INFO] Total running time: 0h1m37s