[2024-01-24 11:44:05,464] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:44:05,465] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:44:05,465] [INFO] DQC Reference Directory: /var/lib/cwl/stga5708de5-b598-4e1b-b46f-829a1d97870a/dqc_reference
[2024-01-24 11:44:08,838] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:44:08,839] [INFO] Task started: Prodigal
[2024-01-24 11:44:08,839] [INFO] Running command: gunzip -c /var/lib/cwl/stg47fb4c08-5871-4bdf-b3dc-e57a5a940501/GCF_001525545.2_ASM152554v2_genomic.fna.gz | prodigal -d GCF_001525545.2_ASM152554v2_genomic.fna/cds.fna -a GCF_001525545.2_ASM152554v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:24,004] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:24,005] [INFO] Task started: HMMsearch
[2024-01-24 11:44:24,005] [INFO] Running command: hmmsearch --tblout GCF_001525545.2_ASM152554v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga5708de5-b598-4e1b-b46f-829a1d97870a/dqc_reference/reference_markers.hmm GCF_001525545.2_ASM152554v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:24,296] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:24,298] [INFO] Found 6/6 markers.
[2024-01-24 11:44:24,338] [INFO] Query marker FASTA was written to GCF_001525545.2_ASM152554v2_genomic.fna/markers.fasta
[2024-01-24 11:44:24,338] [INFO] Task started: Blastn
[2024-01-24 11:44:24,338] [INFO] Running command: blastn -query GCF_001525545.2_ASM152554v2_genomic.fna/markers.fasta -db /var/lib/cwl/stga5708de5-b598-4e1b-b46f-829a1d97870a/dqc_reference/reference_markers.fasta -out GCF_001525545.2_ASM152554v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:25,450] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:25,454] [INFO] Selected 12 target genomes.
[2024-01-24 11:44:25,454] [INFO] Target genome list was writen to GCF_001525545.2_ASM152554v2_genomic.fna/target_genomes.txt
[2024-01-24 11:44:25,464] [INFO] Task started: fastANI
[2024-01-24 11:44:25,464] [INFO] Running command: fastANI --query /var/lib/cwl/stg47fb4c08-5871-4bdf-b3dc-e57a5a940501/GCF_001525545.2_ASM152554v2_genomic.fna.gz --refList GCF_001525545.2_ASM152554v2_genomic.fna/target_genomes.txt --output GCF_001525545.2_ASM152554v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:43,376] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:43,377] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga5708de5-b598-4e1b-b46f-829a1d97870a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:43,377] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga5708de5-b598-4e1b-b46f-829a1d97870a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:43,388] [INFO] Found 12 fastANI hits (8 hits with ANI > threshold)
[2024-01-24 11:44:43,388] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 11:44:43,388] [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
Bordetella parapertussis	strain=FDAARGOS_177	GCA_001525545.2	519	519	suspected-type	True	100.0	1598	1600	95	inconclusive
Bordetella parapertussis	strain=NCTC5952	GCA_900445785.1	519	519	suspected-type	True	99.9975	1588	1600	95	inconclusive
Bordetella parapertussis	strain=FDAARGOS_1541	GCA_020735925.1	519	519	suspected-type	True	99.9968	1590	1600	95	inconclusive
Bordetella bronchiseptica	strain=NCTC452	GCA_900445725.1	518	518	suspected-type	True	98.9791	1547	1600	95	inconclusive
Bordetella bronchiseptica	strain=NBRC 13691	GCA_001598655.1	518	518	suspected-type	True	98.9041	1443	1600	95	inconclusive
Bordetella bronchiseptica	strain=CCUG 219	GCA_021391275.1	518	518	suspected-type	True	98.8852	1387	1600	95	inconclusive
Bordetella pertussis	strain=18323	GCA_000306945.1	520	520	type	True	98.1554	1230	1600	95	inconclusive
Bordetella pertussis	strain=FDAARGOS_1543	GCA_020736265.1	520	520	type	True	98.1088	1236	1600	95	inconclusive
Achromobacter xylosoxidans	strain=PartM-Axylosoxidans-RM8376	GCA_022870085.1	85698	85698	type	True	82.9955	996	1600	95	below_threshold
Achromobacter insolitus	strain=NCTC 13520	GCA_024168865.1	217204	217204	type	True	81.7665	899	1600	95	below_threshold
Eoetvoesia caeni	strain=PB3-7B	GCA_022688825.1	645616	645616	type	True	77.714	329	1600	95	below_threshold
Cupriavidus numazuensis	strain=LMG 26411	GCA_905397435.1	221992	221992	type	True	77.2948	485	1600	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:43,390] [INFO] DFAST Taxonomy check result was written to GCF_001525545.2_ASM152554v2_genomic.fna/tc_result.tsv
[2024-01-24 11:44:43,390] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:43,390] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:43,390] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga5708de5-b598-4e1b-b46f-829a1d97870a/dqc_reference/checkm_data
[2024-01-24 11:44:43,391] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:43,436] [INFO] Task started: CheckM
[2024-01-24 11:44:43,436] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001525545.2_ASM152554v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001525545.2_ASM152554v2_genomic.fna/checkm_input GCF_001525545.2_ASM152554v2_genomic.fna/checkm_result
[2024-01-24 11:45:33,186] [INFO] Task succeeded: CheckM
[2024-01-24 11:45:33,188] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:45:33,210] [INFO] ===== Completeness check finished =====
[2024-01-24 11:45:33,211] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:45:33,211] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001525545.2_ASM152554v2_genomic.fna/markers.fasta)
[2024-01-24 11:45:33,211] [INFO] Task started: Blastn
[2024-01-24 11:45:33,212] [INFO] Running command: blastn -query GCF_001525545.2_ASM152554v2_genomic.fna/markers.fasta -db /var/lib/cwl/stga5708de5-b598-4e1b-b46f-829a1d97870a/dqc_reference/reference_markers_gtdb.fasta -out GCF_001525545.2_ASM152554v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:45:35,482] [INFO] Task succeeded: Blastn
[2024-01-24 11:45:35,485] [INFO] Selected 20 target genomes.
[2024-01-24 11:45:35,486] [INFO] Target genome list was writen to GCF_001525545.2_ASM152554v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:45:35,500] [INFO] Task started: fastANI
[2024-01-24 11:45:35,500] [INFO] Running command: fastANI --query /var/lib/cwl/stg47fb4c08-5871-4bdf-b3dc-e57a5a940501/GCF_001525545.2_ASM152554v2_genomic.fna.gz --refList GCF_001525545.2_ASM152554v2_genomic.fna/target_genomes_gtdb.txt --output GCF_001525545.2_ASM152554v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:46:01,694] [INFO] Task succeeded: fastANI
[2024-01-24 11:46:01,714] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:46:01,714] [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_000306945.1	s__Bordetella pertussis	98.1941	1227	1600	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella	95.0	99.42	95.13	0.93	0.83	983	conclusive
GCF_002261345.1	s__Bordetella_A sp002261345	83.2632	937	1600	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_A	95.0	99.26	99.26	0.94	0.94	2	-
GCF_017356245.1	s__Bordetella_A petrii_D	83.1522	918	1600	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002885955.2	s__Achromobacter pulmonis_A	83.1348	1019	1600	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	98.97	98.79	0.92	0.89	3	-
GCF_002902905.1	s__Achromobacter sp002902905	83.117	957	1600	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	96.15	96.15	0.87	0.87	2	-
GCF_016127315.1	s__Achromobacter insuavis_A	83.0817	978	1600	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.6014	97.14	97.13	0.90	0.90	4	-
GCF_902859695.1	s__Achromobacter ruhlandii	83.0371	945	1600	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0063	98.29	97.95	0.91	0.85	19	-
GCF_001457475.1	s__Achromobacter xylosoxidans	83.0055	997	1600	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	98.72	96.70	0.93	0.87	75	-
GCF_902859745.1	s__Achromobacter dolens	82.9566	937	1600	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0063	99.05	99.03	0.93	0.90	8	-
GCF_902859645.1	s__Achromobacter insuavis	82.9341	958	1600	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.6014	99.48	98.86	0.95	0.90	7	-
GCF_001270295.1	s__Achromobacter sp001270295	82.7643	746	1600	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014490035.1	s__Achromobacter bronchisepticus_A	82.6915	949	1600	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0106	99.75	98.99	0.98	0.93	5	-
GCF_017745595.1	s__Bordetella_A petrii_C	82.646	868	1600	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902859735.1	s__Achromobacter aegrifaciens	82.6383	942	1600	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0106	99.14	98.95	0.96	0.93	10	-
GCF_007679965.1	s__Bordetella_B sp007679965	82.6281	905	1600	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001571365.1	s__Achromobacter denitrificans	82.5851	972	1600	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	99.42	98.61	0.95	0.90	14	-
GCF_900496975.1	s__Achromobacter veterisilvae	82.5125	963	1600	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014170305.1	s__Achromobacter sp014170305	82.3687	929	1600	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000757485.1	s__Achromobacter sp000757485	82.1474	956	1600	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002261475.1	s__Bordetella sp002261475	82.1172	904	1600	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella	95.0	99.06	99.06	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:46:01,716] [INFO] GTDB search result was written to GCF_001525545.2_ASM152554v2_genomic.fna/result_gtdb.tsv
[2024-01-24 11:46:01,717] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:46:01,720] [INFO] DFAST_QC result json was written to GCF_001525545.2_ASM152554v2_genomic.fna/dqc_result.json
[2024-01-24 11:46:01,721] [INFO] DFAST_QC completed!
[2024-01-24 11:46:01,721] [INFO] Total running time: 0h1m56s