[2024-01-24 12:14:48,331] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:48,332] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:48,333] [INFO] DQC Reference Directory: /var/lib/cwl/stg6f2454c8-d629-4d1f-aa91-e9e883758eb0/dqc_reference
[2024-01-24 12:14:49,587] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:49,588] [INFO] Task started: Prodigal
[2024-01-24 12:14:49,588] [INFO] Running command: gunzip -c /var/lib/cwl/stg253313c4-2b48-428e-b230-ae22a254fe1d/GCF_018802605.1_ASM1880260v1_genomic.fna.gz | prodigal -d GCF_018802605.1_ASM1880260v1_genomic.fna/cds.fna -a GCF_018802605.1_ASM1880260v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:15:03,549] [INFO] Task succeeded: Prodigal
[2024-01-24 12:15:03,549] [INFO] Task started: HMMsearch
[2024-01-24 12:15:03,549] [INFO] Running command: hmmsearch --tblout GCF_018802605.1_ASM1880260v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6f2454c8-d629-4d1f-aa91-e9e883758eb0/dqc_reference/reference_markers.hmm GCF_018802605.1_ASM1880260v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:15:03,834] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:15:03,836] [INFO] Found 6/6 markers.
[2024-01-24 12:15:03,883] [INFO] Query marker FASTA was written to GCF_018802605.1_ASM1880260v1_genomic.fna/markers.fasta
[2024-01-24 12:15:03,884] [INFO] Task started: Blastn
[2024-01-24 12:15:03,884] [INFO] Running command: blastn -query GCF_018802605.1_ASM1880260v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6f2454c8-d629-4d1f-aa91-e9e883758eb0/dqc_reference/reference_markers.fasta -out GCF_018802605.1_ASM1880260v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:04,904] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:04,911] [INFO] Selected 19 target genomes.
[2024-01-24 12:15:04,912] [INFO] Target genome list was writen to GCF_018802605.1_ASM1880260v1_genomic.fna/target_genomes.txt
[2024-01-24 12:15:04,920] [INFO] Task started: fastANI
[2024-01-24 12:15:04,921] [INFO] Running command: fastANI --query /var/lib/cwl/stg253313c4-2b48-428e-b230-ae22a254fe1d/GCF_018802605.1_ASM1880260v1_genomic.fna.gz --refList GCF_018802605.1_ASM1880260v1_genomic.fna/target_genomes.txt --output GCF_018802605.1_ASM1880260v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:19,648] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:19,649] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6f2454c8-d629-4d1f-aa91-e9e883758eb0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:19,649] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6f2454c8-d629-4d1f-aa91-e9e883758eb0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:19,669] [INFO] Found 19 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:15:19,669] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:15:19,669] [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 paludis	strain=BCRC 80514	GCA_018802605.1	1225769	1225769	type	True	100.0	1354	1356	95	conclusive
Paludibacterium paludis	strain=KCTC 32182	GCA_014652495.1	1225769	1225769	type	True	99.9695	1308	1356	95	conclusive
Chromobacterium violaceum	strain=NCTC9757	GCA_900446805.1	536	536	type	True	79.7875	496	1356	95	below_threshold
Chromobacterium violaceum	strain=ATCC 12472	GCA_000007705.1	536	536	type	True	79.7597	501	1356	95	below_threshold
Chromobacterium amazonense	strain=DSM 26508	GCA_001855565.1	1382803	1382803	type	True	79.4713	445	1356	95	below_threshold
Chromobacterium phragmitis	strain=IIBBL 112-1	GCA_003325475.1	2202141	2202141	type	True	79.2795	473	1356	95	below_threshold
Crenobacter cavernae	strain=K1W11S-77	GCA_003355495.1	2290923	2290923	type	True	79.2465	365	1356	95	below_threshold
Chromobacterium sinusclupearum	strain=MWU13-2610	GCA_002902845.1	2077146	2077146	type	True	79.1916	442	1356	95	below_threshold
Crenobacter luteus	strain=DSM 27258	GCA_004345725.1	1452487	1452487	type	True	79.1066	397	1356	95	below_threshold
Chromobacterium alkanivorans	strain=IITR-71	GCA_016937655.1	1071719	1071719	type	True	79.0905	507	1356	95	below_threshold
Chromobacterium piscinae	strain=DSM 23278	GCA_021129175.1	686831	686831	type	True	79.0873	470	1356	95	below_threshold
Chromobacterium sphagni	strain=IIBBL 14B-1	GCA_001855555.1	1903179	1903179	type	True	79.0804	489	1356	95	below_threshold
Chromobacterium vaccinii	strain=MWU205	GCA_000971335.1	1108595	1108595	type	True	79.0175	487	1356	95	below_threshold
Chromobacterium aquaticum	strain=DSM 19852	GCA_021129195.1	467180	467180	type	True	79.004	459	1356	95	below_threshold
Paludibacterium purpuratum	strain=CECT 8976	GCA_004363805.1	1144873	1144873	type	True	78.8152	370	1356	95	below_threshold
Chromobacterium alticapitis	strain=MWU14-2602	GCA_002924365.1	2073169	2073169	type	True	78.7928	441	1356	95	below_threshold
Paludibacterium yongneupense	strain=DSM 18731	GCA_000422925.1	400061	400061	type	True	78.5877	337	1356	95	below_threshold
Gulbenkiania indica	strain=DSM 17901	GCA_001418035.1	375574	375574	type	True	78.2737	321	1356	95	below_threshold
Massilia terrae	strain=JCM 31606	GCA_024753145.1	1811224	1811224	type	True	76.4714	198	1356	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:19,674] [INFO] DFAST Taxonomy check result was written to GCF_018802605.1_ASM1880260v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:19,675] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:19,675] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:19,675] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6f2454c8-d629-4d1f-aa91-e9e883758eb0/dqc_reference/checkm_data
[2024-01-24 12:15:19,676] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:19,721] [INFO] Task started: CheckM
[2024-01-24 12:15:19,722] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018802605.1_ASM1880260v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018802605.1_ASM1880260v1_genomic.fna/checkm_input GCF_018802605.1_ASM1880260v1_genomic.fna/checkm_result
[2024-01-24 12:16:02,427] [INFO] Task succeeded: CheckM
[2024-01-24 12:16:02,428] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:16:02,452] [INFO] ===== Completeness check finished =====
[2024-01-24 12:16:02,453] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:16:02,453] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018802605.1_ASM1880260v1_genomic.fna/markers.fasta)
[2024-01-24 12:16:02,453] [INFO] Task started: Blastn
[2024-01-24 12:16:02,454] [INFO] Running command: blastn -query GCF_018802605.1_ASM1880260v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6f2454c8-d629-4d1f-aa91-e9e883758eb0/dqc_reference/reference_markers_gtdb.fasta -out GCF_018802605.1_ASM1880260v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:04,342] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:04,348] [INFO] Selected 19 target genomes.
[2024-01-24 12:16:04,349] [INFO] Target genome list was writen to GCF_018802605.1_ASM1880260v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:16:04,363] [INFO] Task started: fastANI
[2024-01-24 12:16:04,363] [INFO] Running command: fastANI --query /var/lib/cwl/stg253313c4-2b48-428e-b230-ae22a254fe1d/GCF_018802605.1_ASM1880260v1_genomic.fna.gz --refList GCF_018802605.1_ASM1880260v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018802605.1_ASM1880260v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:19,705] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:19,734] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:16:19,734] [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_018802605.1	s__Paludibacterium paludis	100.0	1353	1356	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Paludibacterium	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCA_018260425.1	s__Paludibacterium sp018260425	80.0253	606	1356	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Paludibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000007705.1	s__Chromobacterium violaceum	79.7173	503	1356	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	98.58	98.16	0.94	0.91	26	-
GCF_008275125.1	s__Chromobacterium paludis	79.5677	468	1356	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000527175.1	s__Pseudogulbenkiania sp000527175	79.5522	440	1356	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Pseudogulbenkiania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003325475.1	s__Chromobacterium phragmitis	79.2947	475	1356	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	99.00	99.00	0.92	0.92	2	-
GCF_003355495.1	s__Crenobacter cavernae	79.2232	367	1356	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Crenobacter	95.0	96.17	96.17	0.93	0.93	2	-
GCA_002213445.1	s__Chromobacterium sp002213445	79.1907	479	1356	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	99.12	99.12	0.94	0.94	2	-
GCF_900177275.1	s__Pseudogulbenkiania subflava	79.1861	409	1356	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Pseudogulbenkiania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004345725.1	s__Crenobacter luteus	79.1302	395	1356	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Crenobacter	95.0	98.88	98.88	0.93	0.93	2	-
GCF_000174355.1	s__Pseudogulbenkiania ferrooxidans_A	79.0808	426	1356	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Pseudogulbenkiania	95.0	97.29	97.29	0.89	0.89	2	-
GCF_011601295.1	s__Chromobacterium vaccinii_A	79.0428	489	1356	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	95.84	95.77	0.89	0.88	3	-
GCF_001855555.1	s__Chromobacterium sphagni	79.0377	497	1356	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	99.33	99.33	0.93	0.93	2	-
GCF_000971335.1	s__Chromobacterium vaccinii	79.0318	484	1356	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	98.63	98.56	0.92	0.92	4	-
GCF_003052555.1	s__Chromobacterium sp003052555	79.0003	480	1356	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001676875.1	s__Chromobacterium subtsugae	78.9819	508	1356	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	99.12	98.52	0.94	0.91	9	-
GCF_004363805.1	s__Paludibacterium purpuratum	78.8332	369	1356	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Paludibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422925.1	s__Paludibacterium yongneupense	78.5877	337	1356	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Paludibacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCA_004346645.1	s__Gulbenkiania mobilis	78.3508	309	1356	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Gulbenkiania	95.0	99.11	99.06	0.93	0.92	4	-
--------------------------------------------------------------------------------
[2024-01-24 12:16:19,736] [INFO] GTDB search result was written to GCF_018802605.1_ASM1880260v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:19,738] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:19,743] [INFO] DFAST_QC result json was written to GCF_018802605.1_ASM1880260v1_genomic.fna/dqc_result.json
[2024-01-24 12:16:19,743] [INFO] DFAST_QC completed!
[2024-01-24 12:16:19,743] [INFO] Total running time: 0h1m31s