[2024-01-24 12:34:20,371] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:34:20,373] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:34:20,373] [INFO] DQC Reference Directory: /var/lib/cwl/stgd4e29139-0c51-4c73-b793-d2a8be97011f/dqc_reference
[2024-01-24 12:34:21,617] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:34:21,617] [INFO] Task started: Prodigal
[2024-01-24 12:34:21,618] [INFO] Running command: gunzip -c /var/lib/cwl/stg98b2026f-4994-41ab-a826-58510d3cc1f5/GCF_016937655.1_ASM1693765v1_genomic.fna.gz | prodigal -d GCF_016937655.1_ASM1693765v1_genomic.fna/cds.fna -a GCF_016937655.1_ASM1693765v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:34:37,075] [INFO] Task succeeded: Prodigal
[2024-01-24 12:34:37,076] [INFO] Task started: HMMsearch
[2024-01-24 12:34:37,076] [INFO] Running command: hmmsearch --tblout GCF_016937655.1_ASM1693765v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd4e29139-0c51-4c73-b793-d2a8be97011f/dqc_reference/reference_markers.hmm GCF_016937655.1_ASM1693765v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:34:37,379] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:34:37,381] [INFO] Found 6/6 markers.
[2024-01-24 12:34:37,427] [INFO] Query marker FASTA was written to GCF_016937655.1_ASM1693765v1_genomic.fna/markers.fasta
[2024-01-24 12:34:37,428] [INFO] Task started: Blastn
[2024-01-24 12:34:37,428] [INFO] Running command: blastn -query GCF_016937655.1_ASM1693765v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd4e29139-0c51-4c73-b793-d2a8be97011f/dqc_reference/reference_markers.fasta -out GCF_016937655.1_ASM1693765v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:34:38,432] [INFO] Task succeeded: Blastn
[2024-01-24 12:34:38,437] [INFO] Selected 13 target genomes.
[2024-01-24 12:34:38,437] [INFO] Target genome list was writen to GCF_016937655.1_ASM1693765v1_genomic.fna/target_genomes.txt
[2024-01-24 12:34:38,442] [INFO] Task started: fastANI
[2024-01-24 12:34:38,442] [INFO] Running command: fastANI --query /var/lib/cwl/stg98b2026f-4994-41ab-a826-58510d3cc1f5/GCF_016937655.1_ASM1693765v1_genomic.fna.gz --refList GCF_016937655.1_ASM1693765v1_genomic.fna/target_genomes.txt --output GCF_016937655.1_ASM1693765v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:34:53,682] [INFO] Task succeeded: fastANI
[2024-01-24 12:34:53,683] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd4e29139-0c51-4c73-b793-d2a8be97011f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:34:53,683] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd4e29139-0c51-4c73-b793-d2a8be97011f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:34:53,699] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:34:53,699] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:34:53,699] [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
Chromobacterium alkanivorans	strain=IITR-71	GCA_016937655.1	1071719	1071719	type	True	100.0	1725	1726	95	conclusive
Chromobacterium haemolyticum	strain=DSM 19808	GCA_000711885.1	394935	394935	type	True	91.9544	1397	1726	95	below_threshold
Chromobacterium aquaticum	strain=DSM 19852	GCA_021129195.1	467180	467180	type	True	91.0689	1298	1726	95	below_threshold
Chromobacterium violaceum	strain=ATCC 12472	GCA_000007705.1	536	536	type	True	83.9327	990	1726	95	below_threshold
Chromobacterium subtsugae	strain=PRAA4-1	GCA_001676875.1	251747	251747	type	True	83.7368	988	1726	95	below_threshold
Chromobacterium vaccinii	strain=MWU205	GCA_000971335.1	1108595	1108595	type	True	83.6694	964	1726	95	below_threshold
Chromobacterium piscinae	strain=DSM 23278	GCA_021129175.1	686831	686831	type	True	83.5629	929	1726	95	below_threshold
Chromobacterium sphagni	strain=IIBBL 14B-1	GCA_001855555.1	1903179	1903179	type	True	83.4903	925	1726	95	below_threshold
Chromobacterium alticapitis	strain=MWU14-2602	GCA_002924365.1	2073169	2073169	type	True	83.2676	898	1726	95	below_threshold
Chromobacterium amazonense	strain=DSM 26508	GCA_001855565.1	1382803	1382803	type	True	83.2482	880	1726	95	below_threshold
Chromobacterium sinusclupearum	strain=MWU13-2610	GCA_002902845.1	2077146	2077146	type	True	83.0607	914	1726	95	below_threshold
Crenobacter intestini	strain=GY 70310	GCA_004919095.1	2563443	2563443	type	True	79.9956	555	1726	95	below_threshold
Kingella potus	strain=NCTC13336	GCA_900451175.1	265175	265175	type	True	76.5845	103	1726	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:34:53,701] [INFO] DFAST Taxonomy check result was written to GCF_016937655.1_ASM1693765v1_genomic.fna/tc_result.tsv
[2024-01-24 12:34:53,701] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:34:53,701] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:34:53,702] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd4e29139-0c51-4c73-b793-d2a8be97011f/dqc_reference/checkm_data
[2024-01-24 12:34:53,703] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:34:53,752] [INFO] Task started: CheckM
[2024-01-24 12:34:53,753] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016937655.1_ASM1693765v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016937655.1_ASM1693765v1_genomic.fna/checkm_input GCF_016937655.1_ASM1693765v1_genomic.fna/checkm_result
[2024-01-24 12:35:38,578] [INFO] Task succeeded: CheckM
[2024-01-24 12:35:38,580] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:35:38,608] [INFO] ===== Completeness check finished =====
[2024-01-24 12:35:38,609] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:35:38,609] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016937655.1_ASM1693765v1_genomic.fna/markers.fasta)
[2024-01-24 12:35:38,610] [INFO] Task started: Blastn
[2024-01-24 12:35:38,610] [INFO] Running command: blastn -query GCF_016937655.1_ASM1693765v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd4e29139-0c51-4c73-b793-d2a8be97011f/dqc_reference/reference_markers_gtdb.fasta -out GCF_016937655.1_ASM1693765v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:35:40,603] [INFO] Task succeeded: Blastn
[2024-01-24 12:35:40,609] [INFO] Selected 5 target genomes.
[2024-01-24 12:35:40,609] [INFO] Target genome list was writen to GCF_016937655.1_ASM1693765v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:35:40,615] [INFO] Task started: fastANI
[2024-01-24 12:35:40,615] [INFO] Running command: fastANI --query /var/lib/cwl/stg98b2026f-4994-41ab-a826-58510d3cc1f5/GCF_016937655.1_ASM1693765v1_genomic.fna.gz --refList GCF_016937655.1_ASM1693765v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016937655.1_ASM1693765v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:35:49,979] [INFO] Task succeeded: fastANI
[2024-01-24 12:35:49,989] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:35:49,990] [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_016937655.1	s__Chromobacterium alkanivorans	100.0	1725	1726	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	98.67	98.67	0.95	0.95	2	conclusive
GCF_003052555.1	s__Chromobacterium sp003052555	93.6835	1515	1726	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002081825.1	s__Chromobacterium haemolyticum_A	92.5218	1466	1726	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	97.46	97.46	0.88	0.88	2	-
GCF_000711885.1	s__Chromobacterium haemolyticum	91.9592	1397	1726	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	96.93	96.05	0.88	0.85	14	-
GCF_001043555.1	s__Chromobacterium sp001043555	91.2076	1404	1726	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 12:35:49,992] [INFO] GTDB search result was written to GCF_016937655.1_ASM1693765v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:35:49,993] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:35:49,996] [INFO] DFAST_QC result json was written to GCF_016937655.1_ASM1693765v1_genomic.fna/dqc_result.json
[2024-01-24 12:35:49,996] [INFO] DFAST_QC completed!
[2024-01-24 12:35:49,996] [INFO] Total running time: 0h1m30s