[2024-01-24 14:30:47,118] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:30:47,120] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:30:47,120] [INFO] DQC Reference Directory: /var/lib/cwl/stg18904176-7a13-4d0e-847b-0a5b91dd3f00/dqc_reference
[2024-01-24 14:30:48,397] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:30:48,398] [INFO] Task started: Prodigal
[2024-01-24 14:30:48,398] [INFO] Running command: gunzip -c /var/lib/cwl/stg0c75e06b-f2e4-437d-a377-a90caad232fa/GCF_000759775.1_ASM75977v1_genomic.fna.gz | prodigal -d GCF_000759775.1_ASM75977v1_genomic.fna/cds.fna -a GCF_000759775.1_ASM75977v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:30:58,916] [INFO] Task succeeded: Prodigal
[2024-01-24 14:30:58,916] [INFO] Task started: HMMsearch
[2024-01-24 14:30:58,917] [INFO] Running command: hmmsearch --tblout GCF_000759775.1_ASM75977v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg18904176-7a13-4d0e-847b-0a5b91dd3f00/dqc_reference/reference_markers.hmm GCF_000759775.1_ASM75977v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:30:59,263] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:30:59,265] [INFO] Found 6/6 markers.
[2024-01-24 14:30:59,306] [INFO] Query marker FASTA was written to GCF_000759775.1_ASM75977v1_genomic.fna/markers.fasta
[2024-01-24 14:30:59,307] [INFO] Task started: Blastn
[2024-01-24 14:30:59,307] [INFO] Running command: blastn -query GCF_000759775.1_ASM75977v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg18904176-7a13-4d0e-847b-0a5b91dd3f00/dqc_reference/reference_markers.fasta -out GCF_000759775.1_ASM75977v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:00,264] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:00,268] [INFO] Selected 15 target genomes.
[2024-01-24 14:31:00,268] [INFO] Target genome list was writen to GCF_000759775.1_ASM75977v1_genomic.fna/target_genomes.txt
[2024-01-24 14:31:00,287] [INFO] Task started: fastANI
[2024-01-24 14:31:00,288] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c75e06b-f2e4-437d-a377-a90caad232fa/GCF_000759775.1_ASM75977v1_genomic.fna.gz --refList GCF_000759775.1_ASM75977v1_genomic.fna/target_genomes.txt --output GCF_000759775.1_ASM75977v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:20,192] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:20,192] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg18904176-7a13-4d0e-847b-0a5b91dd3f00/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:20,192] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg18904176-7a13-4d0e-847b-0a5b91dd3f00/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:20,209] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:31:20,210] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:20,210] [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
Escherichia albertii	strain=NBRC 107761	GCA_000759775.1	208962	208962	type	True	100.0	1348	1364	95	conclusive
Escherichia albertii	strain=DSM 17582	GCA_022833075.1	208962	208962	type	True	99.9994	1364	1364	95	conclusive
Escherichia coli	strain=DSM 30083	GCA_024519395.1	562	562	neotype	True	90.4485	1134	1364	95	below_threshold
Escherichia coli	strain=ATCC 11775	GCA_000734955.1	562	562	neotype	True	90.4367	1105	1364	95	below_threshold
Escherichia coli	strain=ATCC 11775	GCA_003697165.2	562	562	neotype	True	90.4356	1133	1364	95	below_threshold
Escherichia coli	strain=DSM 30083	GCA_000690815.1	562	562	neotype	True	90.3871	1145	1364	95	below_threshold
Shigella boydii	strain=DMB SH130	GCA_003572535.1	621	621	type	True	90.1806	903	1364	95	below_threshold
Shigella sonnei	strain=ATCC 29930	GCA_002950395.1	624	624	type	True	90.1669	1097	1364	95	below_threshold
Shigella flexneri 2a	strain=ATCC 29903	GCA_002950215.1	42897	623	type	True	89.9493	1070	1364	95	below_threshold
Shigella boydii	strain=FDAARGOS_1139	GCA_016726285.1	621	621	type	True	89.9341	1044	1364	95	below_threshold
Shigella boydii	strain=NCTC12985	GCA_900457095.1	621	621	type	True	89.8841	1056	1364	95	below_threshold
Shigella dysenteriae	strain=NCTC4837	GCA_900457215.1	622	622	suspected-type	True	89.7277	1047	1364	95	below_threshold
Shigella dysenteriae	strain=ATCC 13313	GCA_002949675.1	622	622	suspected-type	True	89.6877	1055	1364	95	below_threshold
Escherichia fergusonii	strain=FDAARGOS_1499	GCA_020097475.1	564	564	type	True	88.0582	975	1364	95	below_threshold
Salmonella enterica subsp. enterica	strain=PartC-Senterica-RM8376	GCA_022869965.1	59201	28901	suspected-type	True	81.902	811	1364	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:20,212] [INFO] DFAST Taxonomy check result was written to GCF_000759775.1_ASM75977v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:20,213] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:20,213] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:20,213] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg18904176-7a13-4d0e-847b-0a5b91dd3f00/dqc_reference/checkm_data
[2024-01-24 14:31:20,215] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:20,264] [INFO] Task started: CheckM
[2024-01-24 14:31:20,264] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000759775.1_ASM75977v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000759775.1_ASM75977v1_genomic.fna/checkm_input GCF_000759775.1_ASM75977v1_genomic.fna/checkm_result
[2024-01-24 14:31:58,413] [INFO] Task succeeded: CheckM
[2024-01-24 14:31:58,414] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:31:58,433] [INFO] ===== Completeness check finished =====
[2024-01-24 14:31:58,434] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:31:58,434] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000759775.1_ASM75977v1_genomic.fna/markers.fasta)
[2024-01-24 14:31:58,435] [INFO] Task started: Blastn
[2024-01-24 14:31:58,435] [INFO] Running command: blastn -query GCF_000759775.1_ASM75977v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg18904176-7a13-4d0e-847b-0a5b91dd3f00/dqc_reference/reference_markers_gtdb.fasta -out GCF_000759775.1_ASM75977v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:59,908] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:59,915] [INFO] Selected 10 target genomes.
[2024-01-24 14:31:59,916] [INFO] Target genome list was writen to GCF_000759775.1_ASM75977v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:31:59,931] [INFO] Task started: fastANI
[2024-01-24 14:31:59,932] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c75e06b-f2e4-437d-a377-a90caad232fa/GCF_000759775.1_ASM75977v1_genomic.fna.gz --refList GCF_000759775.1_ASM75977v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000759775.1_ASM75977v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:32:11,117] [INFO] Task succeeded: fastANI
[2024-01-24 14:32:11,127] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:32:11,127] [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_000759775.1	s__Escherichia albertii	100.0	1348	1364	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	98.47	97.95	0.90	0.82	107	conclusive
GCF_003697165.2	s__Escherichia coli	90.4356	1133	1364	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	97.07	95.57	0.85	0.72	26859	-
GCF_005843885.1	s__Escherichia sp005843885	89.8904	1130	1364	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	96.83	95.39	0.87	0.80	37	-
GCF_902498915.1	s__Escherichia ruysiae	89.8002	1108	1364	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	97.82	96.45	0.94	0.86	36	-
GCF_004211955.1	s__Escherichia sp004211955	89.791	1070	1364	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001660175.1	s__Escherichia sp001660175	89.719	1114	1364	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	99.53	99.22	0.94	0.92	3	-
GCF_011881725.1	s__Escherichia coli_E	89.6672	1071	1364	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002965065.1	s__Escherichia sp002965065	89.5522	1008	1364	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002900365.1	s__Escherichia marmotae	89.3951	1113	1364	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	99.02	98.77	0.90	0.85	82	-
GCF_000026225.1	s__Escherichia fergusonii	88.01	993	1364	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	98.80	98.39	0.93	0.89	77	-
--------------------------------------------------------------------------------
[2024-01-24 14:32:11,129] [INFO] GTDB search result was written to GCF_000759775.1_ASM75977v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:32:11,130] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:32:11,133] [INFO] DFAST_QC result json was written to GCF_000759775.1_ASM75977v1_genomic.fna/dqc_result.json
[2024-01-24 14:32:11,133] [INFO] DFAST_QC completed!
[2024-01-24 14:32:11,134] [INFO] Total running time: 0h1m24s