[2023-06-19 15:25:44,105] [INFO] DFAST_QC pipeline started.
[2023-06-19 15:25:44,110] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 15:25:44,110] [INFO] DQC Reference Directory: /var/lib/cwl/stgd53e8112-fe48-43f0-a933-51d12ab9ffb0/dqc_reference
[2023-06-19 15:25:45,647] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 15:25:45,649] [INFO] Task started: Prodigal
[2023-06-19 15:25:45,650] [INFO] Running command: gunzip -c /var/lib/cwl/stg2c5615b0-5dcf-4b64-8f60-5c08255eec8b/GCA_018005215.1_ASM1800521v1_genomic.fna.gz | prodigal -d GCA_018005215.1_ASM1800521v1_genomic.fna/cds.fna -a GCA_018005215.1_ASM1800521v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 15:25:49,652] [INFO] Task succeeded: Prodigal
[2023-06-19 15:25:49,652] [INFO] Task started: HMMsearch
[2023-06-19 15:25:49,652] [INFO] Running command: hmmsearch --tblout GCA_018005215.1_ASM1800521v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd53e8112-fe48-43f0-a933-51d12ab9ffb0/dqc_reference/reference_markers.hmm GCA_018005215.1_ASM1800521v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 15:25:49,883] [INFO] Task succeeded: HMMsearch
[2023-06-19 15:25:49,885] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg2c5615b0-5dcf-4b64-8f60-5c08255eec8b/GCA_018005215.1_ASM1800521v1_genomic.fna.gz]
[2023-06-19 15:25:49,908] [INFO] Query marker FASTA was written to GCA_018005215.1_ASM1800521v1_genomic.fna/markers.fasta
[2023-06-19 15:25:49,908] [INFO] Task started: Blastn
[2023-06-19 15:25:49,908] [INFO] Running command: blastn -query GCA_018005215.1_ASM1800521v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd53e8112-fe48-43f0-a933-51d12ab9ffb0/dqc_reference/reference_markers.fasta -out GCA_018005215.1_ASM1800521v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 15:25:50,701] [INFO] Task succeeded: Blastn
[2023-06-19 15:25:50,705] [INFO] Selected 14 target genomes.
[2023-06-19 15:25:50,705] [INFO] Target genome list was writen to GCA_018005215.1_ASM1800521v1_genomic.fna/target_genomes.txt
[2023-06-19 15:25:50,711] [INFO] Task started: fastANI
[2023-06-19 15:25:50,711] [INFO] Running command: fastANI --query /var/lib/cwl/stg2c5615b0-5dcf-4b64-8f60-5c08255eec8b/GCA_018005215.1_ASM1800521v1_genomic.fna.gz --refList GCA_018005215.1_ASM1800521v1_genomic.fna/target_genomes.txt --output GCA_018005215.1_ASM1800521v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 15:26:01,040] [INFO] Task succeeded: fastANI
[2023-06-19 15:26:01,041] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd53e8112-fe48-43f0-a933-51d12ab9ffb0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 15:26:01,041] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd53e8112-fe48-43f0-a933-51d12ab9ffb0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 15:26:01,054] [WARNING] Following organisms are indistinguishable with ANI. [Escherichia coli(562), Shigella boydii(621), Shigella dysenteriae(622), Shigella flexneri(623), Shigella sonnei(624)]
[2023-06-19 15:26:01,054] [INFO] Found 14 fastANI hits (11 hits with ANI > threshold)
[2023-06-19 15:26:01,054] [INFO] The taxonomy check result is classified as 'indistinguishable'.
[2023-06-19 15:26:01,055] [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	98.6209	443	461	95	indistinguishable
Shigella sonnei	strain=NCTC12984	GCA_900457155.1	624	624	type	True	98.5512	446	461	95	indistinguishable
Shigella flexneri 2a	strain=ATCC 29903	GCA_002950215.1	42897	623	type	True	98.3737	433	461	95	indistinguishable
Shigella boydii	strain=NCTC12985	GCA_900457095.1	621	621	type	True	98.2807	430	461	95	indistinguishable
Shigella boydii	strain=FDAARGOS_1139	GCA_016726285.1	621	621	type	True	98.2225	428	461	95	indistinguishable
Shigella boydii	strain=DMB SH130	GCA_003572535.1	621	621	type	True	98.1769	378	461	95	indistinguishable
Escherichia coli	strain=ATCC 11775	GCA_000734955.1	562	562	neotype	True	97.6857	436	461	95	indistinguishable
Escherichia coli	strain=ATCC 11775	GCA_003697165.2	562	562	neotype	True	97.6721	445	461	95	indistinguishable
Shigella dysenteriae	strain=ATCC 13313	GCA_002949675.1	622	622	suspected-type	True	97.6615	398	461	95	indistinguishable
Escherichia coli	strain=DSM 30083	GCA_000690815.1	562	562	neotype	True	97.6547	445	461	95	indistinguishable
Escherichia coli	strain=DSM 30083	GCA_024519395.1	562	562	neotype	True	97.5293	445	461	95	indistinguishable
Escherichia albertii	strain=DSM 17582	GCA_022833075.1	208962	208962	type	True	89.8883	401	461	95	below_threshold
Escherichia albertii	strain=NBRC 107761	GCA_000759775.1	208962	208962	type	True	89.886	389	461	95	below_threshold
Salmonella enterica subsp. enterica	strain=PartC-Senterica-RM8376	GCA_022869965.1	59201	28901	suspected-type	True	81.9674	329	461	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 15:26:01,058] [INFO] DFAST Taxonomy check result was written to GCA_018005215.1_ASM1800521v1_genomic.fna/tc_result.tsv
[2023-06-19 15:26:01,059] [INFO] ===== Taxonomy check completed =====
[2023-06-19 15:26:01,059] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 15:26:01,060] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd53e8112-fe48-43f0-a933-51d12ab9ffb0/dqc_reference/checkm_data
[2023-06-19 15:26:01,061] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 15:26:01,083] [INFO] Task started: CheckM
[2023-06-19 15:26:01,083] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018005215.1_ASM1800521v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018005215.1_ASM1800521v1_genomic.fna/checkm_input GCA_018005215.1_ASM1800521v1_genomic.fna/checkm_result
[2023-06-19 15:26:21,785] [INFO] Task succeeded: CheckM
[2023-06-19 15:26:21,786] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 12.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 15:26:21,812] [INFO] ===== Completeness check finished =====
[2023-06-19 15:26:21,812] [INFO] ===== Start GTDB Search =====
[2023-06-19 15:26:21,812] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018005215.1_ASM1800521v1_genomic.fna/markers.fasta)
[2023-06-19 15:26:21,812] [INFO] Task started: Blastn
[2023-06-19 15:26:21,813] [INFO] Running command: blastn -query GCA_018005215.1_ASM1800521v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd53e8112-fe48-43f0-a933-51d12ab9ffb0/dqc_reference/reference_markers_gtdb.fasta -out GCA_018005215.1_ASM1800521v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 15:26:22,870] [INFO] Task succeeded: Blastn
[2023-06-19 15:26:22,875] [INFO] Selected 10 target genomes.
[2023-06-19 15:26:22,875] [INFO] Target genome list was writen to GCA_018005215.1_ASM1800521v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 15:26:22,881] [INFO] Task started: fastANI
[2023-06-19 15:26:22,881] [INFO] Running command: fastANI --query /var/lib/cwl/stg2c5615b0-5dcf-4b64-8f60-5c08255eec8b/GCA_018005215.1_ASM1800521v1_genomic.fna.gz --refList GCA_018005215.1_ASM1800521v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018005215.1_ASM1800521v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 15:26:30,882] [INFO] Task succeeded: fastANI
[2023-06-19 15:26:30,895] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 15:26:30,896] [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	97.6721	445	461	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	94.7777	395	461	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902498915.1	s__Escherichia ruysiae	92.921	429	461	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	92.7098	427	461	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_005843885.1	s__Escherichia sp005843885	92.635	434	461	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	92.1362	413	461	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	91.8807	428	461	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	91.1275	420	461	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	99.02	98.77	0.90	0.85	82	-
GCF_000759775.1	s__Escherichia albertii	89.8462	390	461	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	98.47	97.95	0.90	0.82	107	-
GCF_000026225.1	s__Escherichia fergusonii	89.3235	358	461	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	98.80	98.39	0.93	0.89	77	-
--------------------------------------------------------------------------------
[2023-06-19 15:26:30,898] [INFO] GTDB search result was written to GCA_018005215.1_ASM1800521v1_genomic.fna/result_gtdb.tsv
[2023-06-19 15:26:30,899] [INFO] ===== GTDB Search completed =====
[2023-06-19 15:26:30,903] [INFO] DFAST_QC result json was written to GCA_018005215.1_ASM1800521v1_genomic.fna/dqc_result.json
[2023-06-19 15:26:30,904] [INFO] DFAST_QC completed!
[2023-06-19 15:26:30,904] [INFO] Total running time: 0h0m47s