[2023-06-04 20:24:03,616] [INFO] DFAST_QC pipeline started.
[2023-06-04 20:24:03,626] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 20:24:03,626] [INFO] DQC Reference Directory: /var/lib/cwl/stgebed152b-17e6-484e-9126-209c76b4e5f7/dqc_reference
[2023-06-04 20:24:05,386] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 20:24:05,389] [INFO] Task started: Prodigal
[2023-06-04 20:24:05,389] [INFO] Running command: gunzip -c /var/lib/cwl/stga434f46d-7661-4724-8151-fc5e9a631ac2/GCA_934277795.1_ERR7738662_bin.86_genomic.fna.gz | prodigal -d GCA_934277795.1_ERR7738662_bin.86_genomic.fna/cds.fna -a GCA_934277795.1_ERR7738662_bin.86_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 20:24:16,641] [INFO] Task succeeded: Prodigal
[2023-06-04 20:24:16,642] [INFO] Task started: HMMsearch
[2023-06-04 20:24:16,642] [INFO] Running command: hmmsearch --tblout GCA_934277795.1_ERR7738662_bin.86_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgebed152b-17e6-484e-9126-209c76b4e5f7/dqc_reference/reference_markers.hmm GCA_934277795.1_ERR7738662_bin.86_genomic.fna/protein.faa > /dev/null
[2023-06-04 20:24:16,931] [INFO] Task succeeded: HMMsearch
[2023-06-04 20:24:16,935] [INFO] Found 6/6 markers.
[2023-06-04 20:24:16,980] [INFO] Query marker FASTA was written to GCA_934277795.1_ERR7738662_bin.86_genomic.fna/markers.fasta
[2023-06-04 20:24:16,981] [INFO] Task started: Blastn
[2023-06-04 20:24:16,981] [INFO] Running command: blastn -query GCA_934277795.1_ERR7738662_bin.86_genomic.fna/markers.fasta -db /var/lib/cwl/stgebed152b-17e6-484e-9126-209c76b4e5f7/dqc_reference/reference_markers.fasta -out GCA_934277795.1_ERR7738662_bin.86_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 20:24:17,927] [INFO] Task succeeded: Blastn
[2023-06-04 20:24:17,933] [INFO] Selected 15 target genomes.
[2023-06-04 20:24:17,934] [INFO] Target genome list was writen to GCA_934277795.1_ERR7738662_bin.86_genomic.fna/target_genomes.txt
[2023-06-04 20:24:17,939] [INFO] Task started: fastANI
[2023-06-04 20:24:17,940] [INFO] Running command: fastANI --query /var/lib/cwl/stga434f46d-7661-4724-8151-fc5e9a631ac2/GCA_934277795.1_ERR7738662_bin.86_genomic.fna.gz --refList GCA_934277795.1_ERR7738662_bin.86_genomic.fna/target_genomes.txt --output GCA_934277795.1_ERR7738662_bin.86_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 20:24:37,577] [INFO] Task succeeded: fastANI
[2023-06-04 20:24:37,578] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgebed152b-17e6-484e-9126-209c76b4e5f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 20:24:37,578] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgebed152b-17e6-484e-9126-209c76b4e5f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 20:24:37,595] [WARNING] Following organisms are indistinguishable with ANI. [Escherichia coli(562), Shigella boydii(621), Shigella dysenteriae(622), Shigella flexneri(623), Shigella sonnei(624)]
[2023-06-04 20:24:37,596] [INFO] Found 15 fastANI hits (12 hits with ANI > threshold)
[2023-06-04 20:24:37,596] [INFO] The taxonomy check result is classified as 'indistinguishable'.
[2023-06-04 20:24:37,596] [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 boydii	strain=DMB SH130	GCA_003572535.1	621	621	type	True	98.203	974	1372	95	indistinguishable
Shigella sonnei	strain=ATCC 29930	GCA_002950395.1	624	624	type	True	98.0817	1240	1372	95	indistinguishable
Shigella sonnei	strain=NCTC12984	GCA_900457155.1	624	624	type	True	98.0473	1239	1372	95	indistinguishable
Shigella boydii	strain=NCTC12985	GCA_900457095.1	621	621	type	True	98.0143	1152	1372	95	indistinguishable
Shigella boydii	strain=FDAARGOS_1139	GCA_016726285.1	621	621	type	True	98.0047	1154	1372	95	indistinguishable
Shigella flexneri 2a	strain=ATCC 29903	GCA_002950215.1	42897	623	type	True	97.8557	1210	1372	95	indistinguishable
Shigella dysenteriae	strain=NCTC4837	GCA_900457215.1	622	622	suspected-type	True	97.2471	1123	1372	95	indistinguishable
Shigella dysenteriae	strain=ATCC 13313	GCA_002949675.1	622	622	suspected-type	True	97.1995	1131	1372	95	indistinguishable
Escherichia coli	strain=DSM 30083	GCA_024519395.1	562	562	neotype	True	96.9237	1229	1372	95	indistinguishable
Escherichia coli	strain=ATCC 11775	GCA_000734955.1	562	562	neotype	True	96.8948	1223	1372	95	indistinguishable
Escherichia coli	strain=DSM 30083	GCA_000690815.1	562	562	neotype	True	96.8911	1241	1372	95	indistinguishable
Escherichia coli	strain=ATCC 11775	GCA_003697165.2	562	562	neotype	True	96.8766	1239	1372	95	indistinguishable
Escherichia albertii	strain=NBRC 107761	GCA_000759775.1	208962	208962	type	True	90.0886	1026	1372	95	below_threshold
Escherichia albertii	strain=DSM 17582	GCA_022833075.1	208962	208962	type	True	89.9291	1100	1372	95	below_threshold
Salmonella enterica subsp. enterica	strain=PartC-Senterica-RM8376	GCA_022869965.1	59201	28901	suspected-type	True	82.147	860	1372	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-04 20:24:37,598] [INFO] DFAST Taxonomy check result was written to GCA_934277795.1_ERR7738662_bin.86_genomic.fna/tc_result.tsv
[2023-06-04 20:24:37,599] [INFO] ===== Taxonomy check completed =====
[2023-06-04 20:24:37,599] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 20:24:37,599] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgebed152b-17e6-484e-9126-209c76b4e5f7/dqc_reference/checkm_data
[2023-06-04 20:24:37,600] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 20:24:37,652] [INFO] Task started: CheckM
[2023-06-04 20:24:37,653] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934277795.1_ERR7738662_bin.86_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934277795.1_ERR7738662_bin.86_genomic.fna/checkm_input GCA_934277795.1_ERR7738662_bin.86_genomic.fna/checkm_result
[2023-06-04 20:25:14,448] [INFO] Task succeeded: CheckM
[2023-06-04 20:25:14,450] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 20:25:14,476] [INFO] ===== Completeness check finished =====
[2023-06-04 20:25:14,476] [INFO] ===== Start GTDB Search =====
[2023-06-04 20:25:14,477] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934277795.1_ERR7738662_bin.86_genomic.fna/markers.fasta)
[2023-06-04 20:25:14,477] [INFO] Task started: Blastn
[2023-06-04 20:25:14,477] [INFO] Running command: blastn -query GCA_934277795.1_ERR7738662_bin.86_genomic.fna/markers.fasta -db /var/lib/cwl/stgebed152b-17e6-484e-9126-209c76b4e5f7/dqc_reference/reference_markers_gtdb.fasta -out GCA_934277795.1_ERR7738662_bin.86_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 20:25:15,855] [INFO] Task succeeded: Blastn
[2023-06-04 20:25:15,860] [INFO] Selected 10 target genomes.
[2023-06-04 20:25:15,861] [INFO] Target genome list was writen to GCA_934277795.1_ERR7738662_bin.86_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 20:25:15,872] [INFO] Task started: fastANI
[2023-06-04 20:25:15,873] [INFO] Running command: fastANI --query /var/lib/cwl/stga434f46d-7661-4724-8151-fc5e9a631ac2/GCA_934277795.1_ERR7738662_bin.86_genomic.fna.gz --refList GCA_934277795.1_ERR7738662_bin.86_genomic.fna/target_genomes_gtdb.txt --output GCA_934277795.1_ERR7738662_bin.86_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 20:25:27,210] [INFO] Task succeeded: fastANI
[2023-06-04 20:25:27,223] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 20:25:27,224] [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	96.8766	1239	1372	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	94.5488	1026	1372	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	92.9822	1181	1372	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	92.9232	1159	1372	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	92.7855	1190	1372	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	92.29	1134	1372	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	91.7681	1202	1372	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	91.0896	1167	1372	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	90.6705	1034	1372	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	90.123	1024	1372	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	98.47	97.95	0.90	0.82	107	-
--------------------------------------------------------------------------------
[2023-06-04 20:25:27,226] [INFO] GTDB search result was written to GCA_934277795.1_ERR7738662_bin.86_genomic.fna/result_gtdb.tsv
[2023-06-04 20:25:27,226] [INFO] ===== GTDB Search completed =====
[2023-06-04 20:25:27,231] [INFO] DFAST_QC result json was written to GCA_934277795.1_ERR7738662_bin.86_genomic.fna/dqc_result.json
[2023-06-04 20:25:27,231] [INFO] DFAST_QC completed!
[2023-06-04 20:25:27,231] [INFO] Total running time: 0h1m24s