[2024-01-24 13:26:11,390] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:26:11,392] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:26:11,392] [INFO] DQC Reference Directory: /var/lib/cwl/stg9c3ecd6c-420a-4a18-a81b-8f96f56a18ac/dqc_reference
[2024-01-24 13:26:12,765] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:26:12,766] [INFO] Task started: Prodigal
[2024-01-24 13:26:12,766] [INFO] Running command: gunzip -c /var/lib/cwl/stg403ef3b2-b4ef-4879-a0d4-f48a067c66b3/GCF_003572535.1_ASM357253v1_genomic.fna.gz | prodigal -d GCF_003572535.1_ASM357253v1_genomic.fna/cds.fna -a GCF_003572535.1_ASM357253v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:26:22,344] [INFO] Task succeeded: Prodigal
[2024-01-24 13:26:22,345] [INFO] Task started: HMMsearch
[2024-01-24 13:26:22,345] [INFO] Running command: hmmsearch --tblout GCF_003572535.1_ASM357253v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9c3ecd6c-420a-4a18-a81b-8f96f56a18ac/dqc_reference/reference_markers.hmm GCF_003572535.1_ASM357253v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:26:22,658] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:26:22,663] [INFO] Found 6/6 markers.
[2024-01-24 13:26:22,711] [INFO] Query marker FASTA was written to GCF_003572535.1_ASM357253v1_genomic.fna/markers.fasta
[2024-01-24 13:26:22,711] [INFO] Task started: Blastn
[2024-01-24 13:26:22,712] [INFO] Running command: blastn -query GCF_003572535.1_ASM357253v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9c3ecd6c-420a-4a18-a81b-8f96f56a18ac/dqc_reference/reference_markers.fasta -out GCF_003572535.1_ASM357253v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:23,621] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:23,625] [INFO] Selected 12 target genomes.
[2024-01-24 13:26:23,626] [INFO] Target genome list was writen to GCF_003572535.1_ASM357253v1_genomic.fna/target_genomes.txt
[2024-01-24 13:26:23,636] [INFO] Task started: fastANI
[2024-01-24 13:26:23,636] [INFO] Running command: fastANI --query /var/lib/cwl/stg403ef3b2-b4ef-4879-a0d4-f48a067c66b3/GCF_003572535.1_ASM357253v1_genomic.fna.gz --refList GCF_003572535.1_ASM357253v1_genomic.fna/target_genomes.txt --output GCF_003572535.1_ASM357253v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:26:49,598] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:49,599] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9c3ecd6c-420a-4a18-a81b-8f96f56a18ac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:26:49,600] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9c3ecd6c-420a-4a18-a81b-8f96f56a18ac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:26:49,614] [WARNING] Following organisms are indistinguishable with ANI. [Escherichia coli(562), Shigella boydii(621), Shigella dysenteriae(622), Shigella flexneri(623), Shigella sonnei(624)]
[2024-01-24 13:26:49,614] [INFO] Found 12 fastANI hits (9 hits with ANI > threshold)
[2024-01-24 13:26:49,614] [INFO] The taxonomy check result is classified as 'indistinguishable'.
[2024-01-24 13:26:49,614] [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	100.0	1091	1104	95	indistinguishable
Shigella boydii	strain=FDAARGOS_1139	GCA_016726285.1	621	621	type	True	99.9941	1104	1104	95	indistinguishable
Shigella boydii	strain=NCTC12985	GCA_900457095.1	621	621	type	True	99.9869	1100	1104	95	indistinguishable
Shigella sonnei	strain=ATCC 29930	GCA_002950395.1	624	624	type	True	98.4865	1046	1104	95	indistinguishable
Shigella sonnei	strain=NCTC12984	GCA_900457155.1	624	624	type	True	98.4469	1045	1104	95	indistinguishable
Shigella flexneri 2a	strain=ATCC 29903	GCA_002950215.1	42897	623	type	True	97.8572	1031	1104	95	indistinguishable
Escherichia coli	strain=ATCC 11775	GCA_003697165.2	562	562	neotype	True	96.7894	1025	1104	95	indistinguishable
Escherichia coli	strain=ATCC 11775	GCA_000734955.1	562	562	neotype	True	96.7889	1011	1104	95	indistinguishable
Escherichia coli	strain=DSM 30083	GCA_024519395.1	562	562	neotype	True	96.7575	1019	1104	95	indistinguishable
Escherichia albertii	strain=NBRC 107761	GCA_000759775.1	208962	208962	type	True	90.3643	891	1104	95	below_threshold
Escherichia albertii	strain=DSM 17582	GCA_022833075.1	208962	208962	type	True	90.1986	942	1104	95	below_threshold
Pseudocitrobacter corydidari		GCA_021172065.1	2891570	2891570	type	True	82.3392	708	1104	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:26:49,616] [INFO] DFAST Taxonomy check result was written to GCF_003572535.1_ASM357253v1_genomic.fna/tc_result.tsv
[2024-01-24 13:26:49,617] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:26:49,617] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:26:49,617] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9c3ecd6c-420a-4a18-a81b-8f96f56a18ac/dqc_reference/checkm_data
[2024-01-24 13:26:49,618] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:26:49,658] [INFO] Task started: CheckM
[2024-01-24 13:26:49,658] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003572535.1_ASM357253v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003572535.1_ASM357253v1_genomic.fna/checkm_input GCF_003572535.1_ASM357253v1_genomic.fna/checkm_result
[2024-01-24 13:27:22,656] [INFO] Task succeeded: CheckM
[2024-01-24 13:27:22,658] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:27:22,686] [INFO] ===== Completeness check finished =====
[2024-01-24 13:27:22,687] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:27:22,687] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003572535.1_ASM357253v1_genomic.fna/markers.fasta)
[2024-01-24 13:27:22,688] [INFO] Task started: Blastn
[2024-01-24 13:27:22,688] [INFO] Running command: blastn -query GCF_003572535.1_ASM357253v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9c3ecd6c-420a-4a18-a81b-8f96f56a18ac/dqc_reference/reference_markers_gtdb.fasta -out GCF_003572535.1_ASM357253v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:27:24,272] [INFO] Task succeeded: Blastn
[2024-01-24 13:27:24,277] [INFO] Selected 10 target genomes.
[2024-01-24 13:27:24,277] [INFO] Target genome list was writen to GCF_003572535.1_ASM357253v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:27:24,287] [INFO] Task started: fastANI
[2024-01-24 13:27:24,287] [INFO] Running command: fastANI --query /var/lib/cwl/stg403ef3b2-b4ef-4879-a0d4-f48a067c66b3/GCF_003572535.1_ASM357253v1_genomic.fna.gz --refList GCF_003572535.1_ASM357253v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003572535.1_ASM357253v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:27:34,598] [INFO] Task succeeded: fastANI
[2024-01-24 13:27:34,612] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:27:34,612] [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	96.7894	1025	1104	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	94.5012	903	1104	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	93.1577	984	1104	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	93.0061	983	1104	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	92.9573	988	1104	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	92.4835	952	1104	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	91.9995	978	1104	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	99.53	99.22	0.94	0.92	3	-
GCF_000026225.1	s__Escherichia fergusonii	91.2673	870	1104	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	98.80	98.39	0.93	0.89	77	-
GCF_002900365.1	s__Escherichia marmotae	91.1614	989	1104	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	90.355	892	1104	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	98.47	97.95	0.90	0.82	107	-
--------------------------------------------------------------------------------
[2024-01-24 13:27:34,614] [INFO] GTDB search result was written to GCF_003572535.1_ASM357253v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:27:34,614] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:27:34,617] [INFO] DFAST_QC result json was written to GCF_003572535.1_ASM357253v1_genomic.fna/dqc_result.json
[2024-01-24 13:27:34,617] [INFO] DFAST_QC completed!
[2024-01-24 13:27:34,618] [INFO] Total running time: 0h1m23s