[2024-01-24 12:54:39,443] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:54:39,445] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:54:39,445] [INFO] DQC Reference Directory: /var/lib/cwl/stg3df882cf-7d5e-4a04-8bda-3d1d3fd5a63a/dqc_reference
[2024-01-24 12:54:41,001] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:54:41,002] [INFO] Task started: Prodigal
[2024-01-24 12:54:41,002] [INFO] Running command: gunzip -c /var/lib/cwl/stgac0859b6-83ae-408c-8761-7f9d8bf354f0/GCF_002902845.1_ASM290284v1_genomic.fna.gz | prodigal -d GCF_002902845.1_ASM290284v1_genomic.fna/cds.fna -a GCF_002902845.1_ASM290284v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:54:54,791] [INFO] Task succeeded: Prodigal
[2024-01-24 12:54:54,792] [INFO] Task started: HMMsearch
[2024-01-24 12:54:54,792] [INFO] Running command: hmmsearch --tblout GCF_002902845.1_ASM290284v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3df882cf-7d5e-4a04-8bda-3d1d3fd5a63a/dqc_reference/reference_markers.hmm GCF_002902845.1_ASM290284v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:54:55,108] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:54:55,110] [INFO] Found 6/6 markers.
[2024-01-24 12:54:55,148] [INFO] Query marker FASTA was written to GCF_002902845.1_ASM290284v1_genomic.fna/markers.fasta
[2024-01-24 12:54:55,148] [INFO] Task started: Blastn
[2024-01-24 12:54:55,148] [INFO] Running command: blastn -query GCF_002902845.1_ASM290284v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3df882cf-7d5e-4a04-8bda-3d1d3fd5a63a/dqc_reference/reference_markers.fasta -out GCF_002902845.1_ASM290284v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:56,191] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:56,194] [INFO] Selected 12 target genomes.
[2024-01-24 12:54:56,195] [INFO] Target genome list was writen to GCF_002902845.1_ASM290284v1_genomic.fna/target_genomes.txt
[2024-01-24 12:54:56,201] [INFO] Task started: fastANI
[2024-01-24 12:54:56,201] [INFO] Running command: fastANI --query /var/lib/cwl/stgac0859b6-83ae-408c-8761-7f9d8bf354f0/GCF_002902845.1_ASM290284v1_genomic.fna.gz --refList GCF_002902845.1_ASM290284v1_genomic.fna/target_genomes.txt --output GCF_002902845.1_ASM290284v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:55:09,875] [INFO] Task succeeded: fastANI
[2024-01-24 12:55:09,876] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3df882cf-7d5e-4a04-8bda-3d1d3fd5a63a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:55:09,877] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3df882cf-7d5e-4a04-8bda-3d1d3fd5a63a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:55:09,893] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:55:09,893] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:55:09,893] [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 sinusclupearum	strain=MWU13-2610	GCA_002902845.1	2077146	2077146	type	True	100.0	1411	1416	95	conclusive
Chromobacterium amazonense	strain=DSM 26508	GCA_001855565.1	1382803	1382803	type	True	94.9584	1167	1416	95	below_threshold
Chromobacterium paludis	strain=IIBBL 257-1	GCA_008275125.1	2605945	2605945	type	True	87.5368	1072	1416	95	below_threshold
Chromobacterium alticapitis	strain=MWU14-2602	GCA_002924365.1	2073169	2073169	type	True	87.3261	1054	1416	95	below_threshold
Chromobacterium violaceum	strain=ATCC 12472	GCA_000007705.1	536	536	type	True	86.8978	1072	1416	95	below_threshold
Chromobacterium violaceum	strain=NCTC9757	GCA_900446805.1	536	536	type	True	86.8725	1079	1416	95	below_threshold
Chromobacterium vaccinii	strain=MWU205	GCA_000971335.1	1108595	1108595	type	True	86.6736	1065	1416	95	below_threshold
Chromobacterium subtsugae	strain=PRAA4-1	GCA_001676875.1	251747	251747	type	True	86.5879	1063	1416	95	below_threshold
Chromobacterium piscinae	strain=DSM 23278	GCA_021129175.1	686831	686831	type	True	86.3893	1031	1416	95	below_threshold
Chromobacterium phragmitis	strain=IIBBL 112-1	GCA_003325475.1	2202141	2202141	type	True	86.1247	1064	1416	95	below_threshold
Chromobacterium aquaticum	strain=DSM 19852	GCA_021129195.1	467180	467180	type	True	82.9244	854	1416	95	below_threshold
Rugamonas brunnea	strain=LX20W	GCA_014042345.1	2758569	2758569	type	True	76.8598	327	1416	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:55:09,895] [INFO] DFAST Taxonomy check result was written to GCF_002902845.1_ASM290284v1_genomic.fna/tc_result.tsv
[2024-01-24 12:55:09,896] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:55:09,896] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:55:09,896] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3df882cf-7d5e-4a04-8bda-3d1d3fd5a63a/dqc_reference/checkm_data
[2024-01-24 12:55:09,897] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:55:09,947] [INFO] Task started: CheckM
[2024-01-24 12:55:09,948] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002902845.1_ASM290284v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002902845.1_ASM290284v1_genomic.fna/checkm_input GCF_002902845.1_ASM290284v1_genomic.fna/checkm_result
[2024-01-24 12:55:50,748] [INFO] Task succeeded: CheckM
[2024-01-24 12:55:50,750] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:55:50,768] [INFO] ===== Completeness check finished =====
[2024-01-24 12:55:50,769] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:55:50,769] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002902845.1_ASM290284v1_genomic.fna/markers.fasta)
[2024-01-24 12:55:50,769] [INFO] Task started: Blastn
[2024-01-24 12:55:50,769] [INFO] Running command: blastn -query GCF_002902845.1_ASM290284v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3df882cf-7d5e-4a04-8bda-3d1d3fd5a63a/dqc_reference/reference_markers_gtdb.fasta -out GCF_002902845.1_ASM290284v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:55:52,892] [INFO] Task succeeded: Blastn
[2024-01-24 12:55:52,895] [INFO] Selected 9 target genomes.
[2024-01-24 12:55:52,896] [INFO] Target genome list was writen to GCF_002902845.1_ASM290284v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:55:52,905] [INFO] Task started: fastANI
[2024-01-24 12:55:52,905] [INFO] Running command: fastANI --query /var/lib/cwl/stgac0859b6-83ae-408c-8761-7f9d8bf354f0/GCF_002902845.1_ASM290284v1_genomic.fna.gz --refList GCF_002902845.1_ASM290284v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002902845.1_ASM290284v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:56:03,528] [INFO] Task succeeded: fastANI
[2024-01-24 12:56:03,536] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:56:03,536] [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_016428945.1	s__Chromobacterium sp016428945	97.9882	1259	1416	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	97.99	97.99	0.89	0.89	2	conclusive
GCF_001855565.1	s__Chromobacterium amazonense	94.9466	1167	1416	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	97.81	97.67	0.91	0.90	4	-
GCF_008275125.1	s__Chromobacterium paludis	87.5309	1073	1416	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002924365.1	s__Chromobacterium sp002924365	87.3195	1055	1416	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000007705.1	s__Chromobacterium violaceum	86.9035	1072	1416	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	98.58	98.16	0.94	0.91	26	-
GCF_000971335.1	s__Chromobacterium vaccinii	86.6681	1066	1416	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	98.63	98.56	0.92	0.92	4	-
GCF_001676875.1	s__Chromobacterium subtsugae	86.5652	1065	1416	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	99.12	98.52	0.94	0.91	9	-
GCF_011601295.1	s__Chromobacterium vaccinii_A	86.4074	1079	1416	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	95.84	95.77	0.89	0.88	3	-
GCF_003325475.1	s__Chromobacterium phragmitis	86.1016	1067	1416	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	99.00	99.00	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:56:03,539] [INFO] GTDB search result was written to GCF_002902845.1_ASM290284v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:56:03,539] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:56:03,543] [INFO] DFAST_QC result json was written to GCF_002902845.1_ASM290284v1_genomic.fna/dqc_result.json
[2024-01-24 12:56:03,543] [INFO] DFAST_QC completed!
[2024-01-24 12:56:03,543] [INFO] Total running time: 0h1m24s