[2024-01-25 19:43:35,524] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:43:35,527] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:43:35,528] [INFO] DQC Reference Directory: /var/lib/cwl/stg154fa4cf-0c1c-40f7-a930-15b6bf705ea1/dqc_reference
[2024-01-25 19:43:36,618] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:43:36,619] [INFO] Task started: Prodigal
[2024-01-25 19:43:36,619] [INFO] Running command: gunzip -c /var/lib/cwl/stg518ce0b0-6dfb-45be-99c5-47266222cfde/GCF_000007705.1_ASM770v1_genomic.fna.gz | prodigal -d GCF_000007705.1_ASM770v1_genomic.fna/cds.fna -a GCF_000007705.1_ASM770v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:43:51,393] [INFO] Task succeeded: Prodigal
[2024-01-25 19:43:51,393] [INFO] Task started: HMMsearch
[2024-01-25 19:43:51,393] [INFO] Running command: hmmsearch --tblout GCF_000007705.1_ASM770v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg154fa4cf-0c1c-40f7-a930-15b6bf705ea1/dqc_reference/reference_markers.hmm GCF_000007705.1_ASM770v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:43:51,632] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:43:51,633] [INFO] Found 6/6 markers.
[2024-01-25 19:43:51,669] [INFO] Query marker FASTA was written to GCF_000007705.1_ASM770v1_genomic.fna/markers.fasta
[2024-01-25 19:43:51,669] [INFO] Task started: Blastn
[2024-01-25 19:43:51,669] [INFO] Running command: blastn -query GCF_000007705.1_ASM770v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg154fa4cf-0c1c-40f7-a930-15b6bf705ea1/dqc_reference/reference_markers.fasta -out GCF_000007705.1_ASM770v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:43:52,695] [INFO] Task succeeded: Blastn
[2024-01-25 19:43:52,698] [INFO] Selected 12 target genomes.
[2024-01-25 19:43:52,698] [INFO] Target genome list was writen to GCF_000007705.1_ASM770v1_genomic.fna/target_genomes.txt
[2024-01-25 19:43:52,700] [INFO] Task started: fastANI
[2024-01-25 19:43:52,700] [INFO] Running command: fastANI --query /var/lib/cwl/stg518ce0b0-6dfb-45be-99c5-47266222cfde/GCF_000007705.1_ASM770v1_genomic.fna.gz --refList GCF_000007705.1_ASM770v1_genomic.fna/target_genomes.txt --output GCF_000007705.1_ASM770v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:44:07,500] [INFO] Task succeeded: fastANI
[2024-01-25 19:44:07,501] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg154fa4cf-0c1c-40f7-a930-15b6bf705ea1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:44:07,501] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg154fa4cf-0c1c-40f7-a930-15b6bf705ea1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:44:07,509] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:44:07,510] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:44:07,510] [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 violaceum	strain=ATCC 12472	GCA_000007705.1	536	536	type	True	100.0	1581	1583	95	conclusive
Chromobacterium violaceum	strain=NCTC9757	GCA_900446805.1	536	536	type	True	99.9931	1575	1583	95	conclusive
Chromobacterium vaccinii	strain=MWU205	GCA_000971335.1	1108595	1108595	type	True	91.1858	1279	1583	95	below_threshold
Chromobacterium piscinae	strain=DSM 23278	GCA_021129175.1	686831	686831	type	True	91.1475	1252	1583	95	below_threshold
Chromobacterium phragmitis	strain=IIBBL 112-1	GCA_003325475.1	2202141	2202141	type	True	89.3662	1282	1583	95	below_threshold
Chromobacterium subtsugae	strain=PRAA4-1	GCA_001676875.1	251747	251747	type	True	87.9538	1181	1583	95	below_threshold
Chromobacterium amazonense	strain=DSM 26508	GCA_001855565.1	1382803	1382803	type	True	87.3609	1068	1583	95	below_threshold
Chromobacterium paludis	strain=IIBBL 257-1	GCA_008275125.1	2605945	2605945	type	True	87.0438	1089	1583	95	below_threshold
Chromobacterium alticapitis	strain=MWU14-2602	GCA_002924365.1	2073169	2073169	type	True	86.8791	1071	1583	95	below_threshold
Chromobacterium sinusclupearum	strain=MWU13-2610	GCA_002902845.1	2077146	2077146	type	True	86.7429	1094	1583	95	below_threshold
Chromobacterium aquaticum	strain=DSM 19852	GCA_021129195.1	467180	467180	type	True	83.6348	923	1583	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	76.7558	438	1583	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:44:07,511] [INFO] DFAST Taxonomy check result was written to GCF_000007705.1_ASM770v1_genomic.fna/tc_result.tsv
[2024-01-25 19:44:07,512] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:44:07,512] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:44:07,512] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg154fa4cf-0c1c-40f7-a930-15b6bf705ea1/dqc_reference/checkm_data
[2024-01-25 19:44:07,513] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:44:07,559] [INFO] Task started: CheckM
[2024-01-25 19:44:07,559] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000007705.1_ASM770v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000007705.1_ASM770v1_genomic.fna/checkm_input GCF_000007705.1_ASM770v1_genomic.fna/checkm_result
[2024-01-25 19:44:55,354] [INFO] Task succeeded: CheckM
[2024-01-25 19:44:55,355] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:44:55,397] [INFO] ===== Completeness check finished =====
[2024-01-25 19:44:55,397] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:44:55,397] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000007705.1_ASM770v1_genomic.fna/markers.fasta)
[2024-01-25 19:44:55,397] [INFO] Task started: Blastn
[2024-01-25 19:44:55,398] [INFO] Running command: blastn -query GCF_000007705.1_ASM770v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg154fa4cf-0c1c-40f7-a930-15b6bf705ea1/dqc_reference/reference_markers_gtdb.fasta -out GCF_000007705.1_ASM770v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:44:57,522] [INFO] Task succeeded: Blastn
[2024-01-25 19:44:57,528] [INFO] Selected 11 target genomes.
[2024-01-25 19:44:57,528] [INFO] Target genome list was writen to GCF_000007705.1_ASM770v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:44:57,529] [INFO] Task started: fastANI
[2024-01-25 19:44:57,529] [INFO] Running command: fastANI --query /var/lib/cwl/stg518ce0b0-6dfb-45be-99c5-47266222cfde/GCF_000007705.1_ASM770v1_genomic.fna.gz --refList GCF_000007705.1_ASM770v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000007705.1_ASM770v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:45:11,753] [INFO] Task succeeded: fastANI
[2024-01-25 19:45:11,760] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:45:11,760] [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_000007705.1	s__Chromobacterium violaceum	100.0	1581	1583	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	98.58	98.16	0.94	0.91	26	conclusive
GCF_000971335.1	s__Chromobacterium vaccinii	91.2154	1276	1583	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	98.63	98.56	0.92	0.92	4	-
GCF_011601295.1	s__Chromobacterium vaccinii_A	91.1234	1325	1583	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	89.3574	1282	1583	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	88.1108	1222	1583	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	87.9502	1181	1583	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	99.12	98.52	0.94	0.91	9	-
GCF_001855565.1	s__Chromobacterium amazonense	87.3499	1068	1583	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	87.08	1089	1583	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	86.8852	1070	1583	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016428945.1	s__Chromobacterium sp016428945	86.8148	1054	1583	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	97.99	97.99	0.89	0.89	2	-
GCF_001855555.1	s__Chromobacterium sphagni	86.663	1104	1583	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	99.33	99.33	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:45:11,762] [INFO] GTDB search result was written to GCF_000007705.1_ASM770v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:45:11,762] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:45:11,765] [INFO] DFAST_QC result json was written to GCF_000007705.1_ASM770v1_genomic.fna/dqc_result.json
[2024-01-25 19:45:11,765] [INFO] DFAST_QC completed!
[2024-01-25 19:45:11,765] [INFO] Total running time: 0h1m36s