[2023-06-13 08:07:47,574] [INFO] DFAST_QC pipeline started.
[2023-06-13 08:07:47,578] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 08:07:47,578] [INFO] DQC Reference Directory: /var/lib/cwl/stgc92fc2c9-8865-4251-b66e-2d3ff25311ae/dqc_reference
[2023-06-13 08:07:48,896] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 08:07:48,897] [INFO] Task started: Prodigal
[2023-06-13 08:07:48,898] [INFO] Running command: gunzip -c /var/lib/cwl/stg177e6249-eb29-4e17-8a02-aeb2e8c54ea2/GCA_022749335.1_ASM2274933v1_genomic.fna.gz | prodigal -d GCA_022749335.1_ASM2274933v1_genomic.fna/cds.fna -a GCA_022749335.1_ASM2274933v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 08:07:57,549] [INFO] Task succeeded: Prodigal
[2023-06-13 08:07:57,550] [INFO] Task started: HMMsearch
[2023-06-13 08:07:57,550] [INFO] Running command: hmmsearch --tblout GCA_022749335.1_ASM2274933v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc92fc2c9-8865-4251-b66e-2d3ff25311ae/dqc_reference/reference_markers.hmm GCA_022749335.1_ASM2274933v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 08:07:57,884] [INFO] Task succeeded: HMMsearch
[2023-06-13 08:07:57,885] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg177e6249-eb29-4e17-8a02-aeb2e8c54ea2/GCA_022749335.1_ASM2274933v1_genomic.fna.gz]
[2023-06-13 08:07:57,920] [INFO] Query marker FASTA was written to GCA_022749335.1_ASM2274933v1_genomic.fna/markers.fasta
[2023-06-13 08:07:57,920] [INFO] Task started: Blastn
[2023-06-13 08:07:57,920] [INFO] Running command: blastn -query GCA_022749335.1_ASM2274933v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc92fc2c9-8865-4251-b66e-2d3ff25311ae/dqc_reference/reference_markers.fasta -out GCA_022749335.1_ASM2274933v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 08:07:58,814] [INFO] Task succeeded: Blastn
[2023-06-13 08:07:58,819] [INFO] Selected 15 target genomes.
[2023-06-13 08:07:58,820] [INFO] Target genome list was writen to GCA_022749335.1_ASM2274933v1_genomic.fna/target_genomes.txt
[2023-06-13 08:07:58,827] [INFO] Task started: fastANI
[2023-06-13 08:07:58,827] [INFO] Running command: fastANI --query /var/lib/cwl/stg177e6249-eb29-4e17-8a02-aeb2e8c54ea2/GCA_022749335.1_ASM2274933v1_genomic.fna.gz --refList GCA_022749335.1_ASM2274933v1_genomic.fna/target_genomes.txt --output GCA_022749335.1_ASM2274933v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 08:08:13,515] [INFO] Task succeeded: fastANI
[2023-06-13 08:08:13,516] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc92fc2c9-8865-4251-b66e-2d3ff25311ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 08:08:13,516] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc92fc2c9-8865-4251-b66e-2d3ff25311ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 08:08:13,535] [WARNING] Following organisms are indistinguishable with ANI. [Escherichia coli(562), Shigella boydii(621), Shigella dysenteriae(622), Shigella flexneri(623), Shigella sonnei(624)]
[2023-06-13 08:08:13,536] [INFO] Found 15 fastANI hits (12 hits with ANI > threshold)
[2023-06-13 08:08:13,536] [INFO] The taxonomy check result is classified as 'indistinguishable'.
[2023-06-13 08:08:13,536] [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
Shigella sonnei	strain=ATCC 29930	GCA_002950395.1	624	624	type	True	98.5149	961	1034	95	indistinguishable
Shigella boydii	strain=DMB SH130	GCA_003572535.1	621	621	type	True	98.4915	808	1034	95	indistinguishable
Shigella sonnei	strain=NCTC12984	GCA_900457155.1	624	624	type	True	98.4742	956	1034	95	indistinguishable
Shigella boydii	strain=FDAARGOS_1139	GCA_016726285.1	621	621	type	True	98.4579	936	1034	95	indistinguishable
Shigella boydii	strain=NCTC12985	GCA_900457095.1	621	621	type	True	98.4368	938	1034	95	indistinguishable
Shigella flexneri 2a	strain=ATCC 29903	GCA_002950215.1	42897	623	type	True	98.1927	948	1034	95	indistinguishable
Shigella dysenteriae	strain=NCTC4837	GCA_900457215.1	622	622	suspected-type	True	97.3541	879	1034	95	indistinguishable
Shigella dysenteriae	strain=ATCC 13313	GCA_002949675.1	622	622	suspected-type	True	97.3191	883	1034	95	indistinguishable
Escherichia coli	strain=DSM 30083	GCA_024519395.1	562	562	neotype	True	97.1072	960	1034	95	indistinguishable
Escherichia coli	strain=ATCC 11775	GCA_003697165.2	562	562	neotype	True	97.095	967	1034	95	indistinguishable
Escherichia coli	strain=DSM 30083	GCA_000690815.1	562	562	neotype	True	97.0909	965	1034	95	indistinguishable
Escherichia coli	strain=ATCC 11775	GCA_000734955.1	562	562	neotype	True	97.0604	951	1034	95	indistinguishable
Escherichia albertii	strain=NBRC 107761	GCA_000759775.1	208962	208962	type	True	90.4841	815	1034	95	below_threshold
Escherichia albertii	strain=DSM 17582	GCA_022833075.1	208962	208962	type	True	90.412	866	1034	95	below_threshold
Pseudocitrobacter corydidari		GCA_021172065.1	2891570	2891570	type	True	81.7813	654	1034	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 08:08:13,538] [INFO] DFAST Taxonomy check result was written to GCA_022749335.1_ASM2274933v1_genomic.fna/tc_result.tsv
[2023-06-13 08:08:13,539] [INFO] ===== Taxonomy check completed =====
[2023-06-13 08:08:13,540] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 08:08:13,540] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc92fc2c9-8865-4251-b66e-2d3ff25311ae/dqc_reference/checkm_data
[2023-06-13 08:08:13,541] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 08:08:13,585] [INFO] Task started: CheckM
[2023-06-13 08:08:13,585] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022749335.1_ASM2274933v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022749335.1_ASM2274933v1_genomic.fna/checkm_input GCA_022749335.1_ASM2274933v1_genomic.fna/checkm_result
[2023-06-13 08:08:45,115] [INFO] Task succeeded: CheckM
[2023-06-13 08:08:45,117] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.42%
Contamintation: 5.59%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-13 08:08:45,155] [INFO] ===== Completeness check finished =====
[2023-06-13 08:08:45,155] [INFO] ===== Start GTDB Search =====
[2023-06-13 08:08:45,156] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022749335.1_ASM2274933v1_genomic.fna/markers.fasta)
[2023-06-13 08:08:45,156] [INFO] Task started: Blastn
[2023-06-13 08:08:45,156] [INFO] Running command: blastn -query GCA_022749335.1_ASM2274933v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc92fc2c9-8865-4251-b66e-2d3ff25311ae/dqc_reference/reference_markers_gtdb.fasta -out GCA_022749335.1_ASM2274933v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 08:08:46,412] [INFO] Task succeeded: Blastn
[2023-06-13 08:08:46,417] [INFO] Selected 10 target genomes.
[2023-06-13 08:08:46,417] [INFO] Target genome list was writen to GCA_022749335.1_ASM2274933v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 08:08:46,418] [INFO] Task started: fastANI
[2023-06-13 08:08:46,419] [INFO] Running command: fastANI --query /var/lib/cwl/stg177e6249-eb29-4e17-8a02-aeb2e8c54ea2/GCA_022749335.1_ASM2274933v1_genomic.fna.gz --refList GCA_022749335.1_ASM2274933v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022749335.1_ASM2274933v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 08:08:55,979] [INFO] Task succeeded: fastANI
[2023-06-13 08:08:55,993] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 08:08:55,994] [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	97.095	967	1034	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	94.8209	837	1034	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	93.1879	941	1034	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	93.0784	937	1034	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	92.9017	949	1034	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	92.5125	889	1034	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	92.0957	951	1034	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	91.2668	912	1034	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	90.964	798	1034	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	90.4727	816	1034	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	98.47	97.95	0.90	0.82	107	-
--------------------------------------------------------------------------------
[2023-06-13 08:08:55,996] [INFO] GTDB search result was written to GCA_022749335.1_ASM2274933v1_genomic.fna/result_gtdb.tsv
[2023-06-13 08:08:55,996] [INFO] ===== GTDB Search completed =====
[2023-06-13 08:08:56,000] [INFO] DFAST_QC result json was written to GCA_022749335.1_ASM2274933v1_genomic.fna/dqc_result.json
[2023-06-13 08:08:56,000] [INFO] DFAST_QC completed!
[2023-06-13 08:08:56,000] [INFO] Total running time: 0h1m8s