[2023-06-16 19:26:32,684] [INFO] DFAST_QC pipeline started.
[2023-06-16 19:26:32,690] [INFO] DFAST_QC version: 0.5.7
[2023-06-16 19:26:32,691] [INFO] DQC Reference Directory: /var/lib/cwl/stg604eb1f5-e36d-4a69-88bd-b8cf62e65165/dqc_reference
[2023-06-16 19:26:35,362] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-16 19:26:35,363] [INFO] Task started: Prodigal
[2023-06-16 19:26:35,364] [INFO] Running command: gunzip -c /var/lib/cwl/stg19c329ea-e286-42cd-a46f-24523ebf0cd6/GCA_009776045.1_ASM977604v1_genomic.fna.gz | prodigal -d GCA_009776045.1_ASM977604v1_genomic.fna/cds.fna -a GCA_009776045.1_ASM977604v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-16 19:26:47,986] [INFO] Task succeeded: Prodigal
[2023-06-16 19:26:47,987] [INFO] Task started: HMMsearch
[2023-06-16 19:26:47,987] [INFO] Running command: hmmsearch --tblout GCA_009776045.1_ASM977604v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg604eb1f5-e36d-4a69-88bd-b8cf62e65165/dqc_reference/reference_markers.hmm GCA_009776045.1_ASM977604v1_genomic.fna/protein.faa > /dev/null
[2023-06-16 19:26:48,309] [INFO] Task succeeded: HMMsearch
[2023-06-16 19:26:48,310] [INFO] Found 6/6 markers.
[2023-06-16 19:26:48,367] [INFO] Query marker FASTA was written to GCA_009776045.1_ASM977604v1_genomic.fna/markers.fasta
[2023-06-16 19:26:48,367] [INFO] Task started: Blastn
[2023-06-16 19:26:48,368] [INFO] Running command: blastn -query GCA_009776045.1_ASM977604v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg604eb1f5-e36d-4a69-88bd-b8cf62e65165/dqc_reference/reference_markers.fasta -out GCA_009776045.1_ASM977604v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 19:26:49,366] [INFO] Task succeeded: Blastn
[2023-06-16 19:26:49,371] [INFO] Selected 12 target genomes.
[2023-06-16 19:26:49,371] [INFO] Target genome list was writen to GCA_009776045.1_ASM977604v1_genomic.fna/target_genomes.txt
[2023-06-16 19:26:49,372] [INFO] Task started: fastANI
[2023-06-16 19:26:49,373] [INFO] Running command: fastANI --query /var/lib/cwl/stg19c329ea-e286-42cd-a46f-24523ebf0cd6/GCA_009776045.1_ASM977604v1_genomic.fna.gz --refList GCA_009776045.1_ASM977604v1_genomic.fna/target_genomes.txt --output GCA_009776045.1_ASM977604v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-16 19:27:06,416] [INFO] Task succeeded: fastANI
[2023-06-16 19:27:06,416] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg604eb1f5-e36d-4a69-88bd-b8cf62e65165/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-16 19:27:06,417] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg604eb1f5-e36d-4a69-88bd-b8cf62e65165/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-16 19:27:06,428] [WARNING] Following organisms are indistinguishable with ANI. [Escherichia coli(562), Shigella boydii(621), Shigella dysenteriae(622), Shigella flexneri(623), Shigella sonnei(624)]
[2023-06-16 19:27:06,428] [INFO] Found 12 fastANI hits (9 hits with ANI > threshold)
[2023-06-16 19:27:06,428] [INFO] The taxonomy check result is classified as 'indistinguishable'.
[2023-06-16 19:27:06,428] [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 coli	strain=ATCC 11775	GCA_000734955.1	562	562	neotype	True	98.719	1383	1576	95	indistinguishable
Escherichia coli	strain=DSM 30083	GCA_000690815.1	562	562	neotype	True	98.6965	1412	1576	95	indistinguishable
Escherichia coli	strain=ATCC 11775	GCA_003697165.2	562	562	neotype	True	98.6813	1414	1576	95	indistinguishable
Escherichia coli	strain=DSM 30083	GCA_024519395.1	562	562	neotype	True	98.2838	1396	1576	95	indistinguishable
Shigella sonnei	strain=ATCC 29930	GCA_002950395.1	624	624	type	True	96.412	1251	1576	95	indistinguishable
Shigella flexneri 2a	strain=ATCC 29903	GCA_002950215.1	42897	623	type	True	96.344	1217	1576	95	indistinguishable
Shigella sonnei	strain=NCTC12984	GCA_900457155.1	624	624	type	True	96.3085	1271	1576	95	indistinguishable
Shigella boydii	strain=FDAARGOS_1139	GCA_016726285.1	621	621	type	True	96.2014	1194	1576	95	indistinguishable
Shigella dysenteriae	strain=ATCC 13313	GCA_002949675.1	622	622	suspected-type	True	95.9528	1149	1576	95	indistinguishable
Escherichia albertii	strain=NBRC 107761	GCA_000759775.1	208962	208962	type	True	90.0745	1093	1576	95	below_threshold
Escherichia albertii	strain=DSM 17582	GCA_022833075.1	208962	208962	type	True	89.9289	1176	1576	95	below_threshold
Pseudocitrobacter corydidari		GCA_021172065.1	2891570	2891570	type	True	81.847	834	1576	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-16 19:27:06,431] [INFO] DFAST Taxonomy check result was written to GCA_009776045.1_ASM977604v1_genomic.fna/tc_result.tsv
[2023-06-16 19:27:06,432] [INFO] ===== Taxonomy check completed =====
[2023-06-16 19:27:06,432] [INFO] ===== Start completeness check using CheckM =====
[2023-06-16 19:27:06,432] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg604eb1f5-e36d-4a69-88bd-b8cf62e65165/dqc_reference/checkm_data
[2023-06-16 19:27:06,435] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-16 19:27:06,506] [INFO] Task started: CheckM
[2023-06-16 19:27:06,506] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_009776045.1_ASM977604v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_009776045.1_ASM977604v1_genomic.fna/checkm_input GCA_009776045.1_ASM977604v1_genomic.fna/checkm_result
[2023-06-16 19:27:48,103] [INFO] Task succeeded: CheckM
[2023-06-16 19:27:48,104] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-16 19:27:48,126] [INFO] ===== Completeness check finished =====
[2023-06-16 19:27:48,126] [INFO] ===== Start GTDB Search =====
[2023-06-16 19:27:48,127] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_009776045.1_ASM977604v1_genomic.fna/markers.fasta)
[2023-06-16 19:27:48,127] [INFO] Task started: Blastn
[2023-06-16 19:27:48,127] [INFO] Running command: blastn -query GCA_009776045.1_ASM977604v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg604eb1f5-e36d-4a69-88bd-b8cf62e65165/dqc_reference/reference_markers_gtdb.fasta -out GCA_009776045.1_ASM977604v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 19:27:49,580] [INFO] Task succeeded: Blastn
[2023-06-16 19:27:49,585] [INFO] Selected 10 target genomes.
[2023-06-16 19:27:49,585] [INFO] Target genome list was writen to GCA_009776045.1_ASM977604v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-16 19:27:49,586] [INFO] Task started: fastANI
[2023-06-16 19:27:49,586] [INFO] Running command: fastANI --query /var/lib/cwl/stg19c329ea-e286-42cd-a46f-24523ebf0cd6/GCA_009776045.1_ASM977604v1_genomic.fna.gz --refList GCA_009776045.1_ASM977604v1_genomic.fna/target_genomes_gtdb.txt --output GCA_009776045.1_ASM977604v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-16 19:28:02,469] [INFO] Task succeeded: fastANI
[2023-06-16 19:28:02,479] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-16 19:28:02,479] [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_003697165.2	s__Escherichia coli	98.6813	1414	1576	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	97.07	95.57	0.85	0.72	26859	conclusive
GCF_002965065.1	s__Escherichia sp002965065	94.0824	1097	1576	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004211955.1	s__Escherichia sp004211955	92.6636	1195	1576	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_902498915.1	s__Escherichia ruysiae	92.6291	1250	1576	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	97.82	96.45	0.94	0.86	36	-
GCF_005843885.1	s__Escherichia sp005843885	92.5285	1251	1576	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	96.83	95.39	0.87	0.80	37	-
GCF_011881725.1	s__Escherichia coli_E	92.1791	1170	1576	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001660175.1	s__Escherichia sp001660175	91.823	1229	1576	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	99.53	99.22	0.94	0.92	3	-
GCF_002900365.1	s__Escherichia marmotae	90.834	1241	1576	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	90.7741	1085	1576	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	98.80	98.39	0.93	0.89	77	-
GCF_000759775.1	s__Escherichia albertii	90.0888	1092	1576	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	98.47	97.95	0.90	0.82	107	-
--------------------------------------------------------------------------------
[2023-06-16 19:28:02,481] [INFO] GTDB search result was written to GCA_009776045.1_ASM977604v1_genomic.fna/result_gtdb.tsv
[2023-06-16 19:28:02,482] [INFO] ===== GTDB Search completed =====
[2023-06-16 19:28:02,494] [INFO] DFAST_QC result json was written to GCA_009776045.1_ASM977604v1_genomic.fna/dqc_result.json
[2023-06-16 19:28:02,494] [INFO] DFAST_QC completed!
[2023-06-16 19:28:02,494] [INFO] Total running time: 0h1m30s