[2024-01-24 13:19:01,542] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:19:01,543] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:19:01,543] [INFO] DQC Reference Directory: /var/lib/cwl/stgb463c78b-4f58-4ec1-989e-b19893c0a0bd/dqc_reference
[2024-01-24 13:19:02,802] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:19:02,803] [INFO] Task started: Prodigal
[2024-01-24 13:19:02,803] [INFO] Running command: gunzip -c /var/lib/cwl/stg91efc088-e96e-4eee-9a73-34cc23b06199/GCF_007644045.2_ASM764404v2_genomic.fna.gz | prodigal -d GCF_007644045.2_ASM764404v2_genomic.fna/cds.fna -a GCF_007644045.2_ASM764404v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:19:16,294] [INFO] Task succeeded: Prodigal
[2024-01-24 13:19:16,295] [INFO] Task started: HMMsearch
[2024-01-24 13:19:16,295] [INFO] Running command: hmmsearch --tblout GCF_007644045.2_ASM764404v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb463c78b-4f58-4ec1-989e-b19893c0a0bd/dqc_reference/reference_markers.hmm GCF_007644045.2_ASM764404v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:16,649] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:16,651] [INFO] Found 6/6 markers.
[2024-01-24 13:19:16,689] [INFO] Query marker FASTA was written to GCF_007644045.2_ASM764404v2_genomic.fna/markers.fasta
[2024-01-24 13:19:16,689] [INFO] Task started: Blastn
[2024-01-24 13:19:16,689] [INFO] Running command: blastn -query GCF_007644045.2_ASM764404v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgb463c78b-4f58-4ec1-989e-b19893c0a0bd/dqc_reference/reference_markers.fasta -out GCF_007644045.2_ASM764404v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:17,741] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:17,744] [INFO] Selected 14 target genomes.
[2024-01-24 13:19:17,745] [INFO] Target genome list was writen to GCF_007644045.2_ASM764404v2_genomic.fna/target_genomes.txt
[2024-01-24 13:19:17,770] [INFO] Task started: fastANI
[2024-01-24 13:19:17,770] [INFO] Running command: fastANI --query /var/lib/cwl/stg91efc088-e96e-4eee-9a73-34cc23b06199/GCF_007644045.2_ASM764404v2_genomic.fna.gz --refList GCF_007644045.2_ASM764404v2_genomic.fna/target_genomes.txt --output GCF_007644045.2_ASM764404v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:31,690] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:31,690] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb463c78b-4f58-4ec1-989e-b19893c0a0bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:31,691] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb463c78b-4f58-4ec1-989e-b19893c0a0bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:31,704] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:19:31,704] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:19:31,704] [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
Vogesella urethralis	strain=YM-1	GCA_007644045.2	2592656	2592656	type	True	100.0	1305	1308	95	conclusive
Vogesella mureinivorans	strain=389	GCA_007644035.2	657276	657276	type	True	87.2415	990	1308	95	below_threshold
Vogesella alkaliphila	strain=KCTC 32041	GCA_014652475.1	1193621	1193621	type	True	83.5548	783	1308	95	below_threshold
Vogesella fluminis	strain=KCTC 23713	GCA_014652335.1	1069161	1069161	type	True	83.1544	708	1308	95	below_threshold
Vogesella indigofera	strain=DSM 3303	GCA_003633895.1	45465	45465	type	True	83.0747	784	1308	95	below_threshold
Chromobacterium phragmitis	strain=IIBBL 112-1	GCA_003325475.1	2202141	2202141	type	True	80.2394	577	1308	95	below_threshold
Chromobacterium sinusclupearum	strain=MWU13-2610	GCA_002902845.1	2077146	2077146	type	True	80.1589	575	1308	95	below_threshold
Chromobacterium alticapitis	strain=MWU14-2602	GCA_002924365.1	2073169	2073169	type	True	80.1288	558	1308	95	below_threshold
Chromobacterium piscinae	strain=DSM 23278	GCA_021129175.1	686831	686831	type	True	80.1268	596	1308	95	below_threshold
Chromobacterium amazonense	strain=DSM 26508	GCA_001855565.1	1382803	1382803	type	True	80.1152	541	1308	95	below_threshold
Chromobacterium alkanivorans	strain=IITR-71	GCA_016937655.1	1071719	1071719	type	True	79.916	648	1308	95	below_threshold
Chromobacterium aquaticum	strain=DSM 19852	GCA_021129195.1	467180	467180	type	True	79.8163	580	1308	95	below_threshold
Chromobacterium haemolyticum	strain=DSM 19808	GCA_000711885.1	394935	394935	type	True	79.5908	534	1308	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	76.1715	257	1308	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:31,706] [INFO] DFAST Taxonomy check result was written to GCF_007644045.2_ASM764404v2_genomic.fna/tc_result.tsv
[2024-01-24 13:19:31,707] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:31,707] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:31,707] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb463c78b-4f58-4ec1-989e-b19893c0a0bd/dqc_reference/checkm_data
[2024-01-24 13:19:31,708] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:31,750] [INFO] Task started: CheckM
[2024-01-24 13:19:31,750] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007644045.2_ASM764404v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007644045.2_ASM764404v2_genomic.fna/checkm_input GCF_007644045.2_ASM764404v2_genomic.fna/checkm_result
[2024-01-24 13:20:13,457] [INFO] Task succeeded: CheckM
[2024-01-24 13:20:13,458] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:20:13,473] [INFO] ===== Completeness check finished =====
[2024-01-24 13:20:13,473] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:20:13,474] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007644045.2_ASM764404v2_genomic.fna/markers.fasta)
[2024-01-24 13:20:13,474] [INFO] Task started: Blastn
[2024-01-24 13:20:13,474] [INFO] Running command: blastn -query GCF_007644045.2_ASM764404v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgb463c78b-4f58-4ec1-989e-b19893c0a0bd/dqc_reference/reference_markers_gtdb.fasta -out GCF_007644045.2_ASM764404v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:20:15,467] [INFO] Task succeeded: Blastn
[2024-01-24 13:20:15,471] [INFO] Selected 10 target genomes.
[2024-01-24 13:20:15,471] [INFO] Target genome list was writen to GCF_007644045.2_ASM764404v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:20:15,486] [INFO] Task started: fastANI
[2024-01-24 13:20:15,487] [INFO] Running command: fastANI --query /var/lib/cwl/stg91efc088-e96e-4eee-9a73-34cc23b06199/GCF_007644045.2_ASM764404v2_genomic.fna.gz --refList GCF_007644045.2_ASM764404v2_genomic.fna/target_genomes_gtdb.txt --output GCF_007644045.2_ASM764404v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:20:25,552] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:25,564] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:20:25,565] [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_007644045.2	s__Vogesella urethralis	100.0	1305	1308	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Vogesella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_000335715.1	s__Vogesella sp000335715	88.2686	988	1308	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Vogesella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017998615.1	s__Vogesella sp017998615	87.9258	666	1308	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Vogesella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900090205.1	s__Vogesella sp900090205	83.6387	827	1308	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Vogesella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652475.1	s__Vogesella alkaliphila	83.5722	781	1308	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Vogesella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652335.1	s__Vogesella fluminis	83.1404	709	1308	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Vogesella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902829295.1	s__Vogesella oryzae	83.1398	734	1308	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Vogesella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003633895.1	s__Vogesella indigofera	83.0761	784	1308	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Vogesella	95.0	97.25	97.21	0.95	0.93	3	-
GCF_016428945.1	s__Chromobacterium sp016428945	80.1721	560	1308	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	97.99	97.99	0.89	0.89	2	-
GCF_001043555.1	s__Chromobacterium sp001043555	79.7649	602	1308	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:20:25,566] [INFO] GTDB search result was written to GCF_007644045.2_ASM764404v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:20:25,567] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:20:25,570] [INFO] DFAST_QC result json was written to GCF_007644045.2_ASM764404v2_genomic.fna/dqc_result.json
[2024-01-24 13:20:25,570] [INFO] DFAST_QC completed!
[2024-01-24 13:20:25,570] [INFO] Total running time: 0h1m24s