[2024-01-25 17:51:05,454] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:51:05,455] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:51:05,455] [INFO] DQC Reference Directory: /var/lib/cwl/stgc1ff9d93-62a4-4c48-a01f-233cc9ddc844/dqc_reference
[2024-01-25 17:51:06,624] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:51:06,625] [INFO] Task started: Prodigal
[2024-01-25 17:51:06,625] [INFO] Running command: gunzip -c /var/lib/cwl/stg262dcd84-07a6-4218-8a11-dcde15b404ba/GCF_000175375.1_ASM17537v1_genomic.fna.gz | prodigal -d GCF_000175375.1_ASM17537v1_genomic.fna/cds.fna -a GCF_000175375.1_ASM17537v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:51:15,149] [INFO] Task succeeded: Prodigal
[2024-01-25 17:51:15,149] [INFO] Task started: HMMsearch
[2024-01-25 17:51:15,149] [INFO] Running command: hmmsearch --tblout GCF_000175375.1_ASM17537v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc1ff9d93-62a4-4c48-a01f-233cc9ddc844/dqc_reference/reference_markers.hmm GCF_000175375.1_ASM17537v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:51:15,339] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:51:15,340] [INFO] Found 6/6 markers.
[2024-01-25 17:51:15,361] [INFO] Query marker FASTA was written to GCF_000175375.1_ASM17537v1_genomic.fna/markers.fasta
[2024-01-25 17:51:15,362] [INFO] Task started: Blastn
[2024-01-25 17:51:15,362] [INFO] Running command: blastn -query GCF_000175375.1_ASM17537v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc1ff9d93-62a4-4c48-a01f-233cc9ddc844/dqc_reference/reference_markers.fasta -out GCF_000175375.1_ASM17537v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:51:16,010] [INFO] Task succeeded: Blastn
[2024-01-25 17:51:16,013] [INFO] Selected 13 target genomes.
[2024-01-25 17:51:16,014] [INFO] Target genome list was writen to GCF_000175375.1_ASM17537v1_genomic.fna/target_genomes.txt
[2024-01-25 17:51:16,021] [INFO] Task started: fastANI
[2024-01-25 17:51:16,021] [INFO] Running command: fastANI --query /var/lib/cwl/stg262dcd84-07a6-4218-8a11-dcde15b404ba/GCF_000175375.1_ASM17537v1_genomic.fna.gz --refList GCF_000175375.1_ASM17537v1_genomic.fna/target_genomes.txt --output GCF_000175375.1_ASM17537v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:51:22,884] [INFO] Task succeeded: fastANI
[2024-01-25 17:51:22,884] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc1ff9d93-62a4-4c48-a01f-233cc9ddc844/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:51:22,884] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc1ff9d93-62a4-4c48-a01f-233cc9ddc844/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:51:22,893] [INFO] Found 12 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 17:51:22,893] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:51:22,893] [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
Corynebacterium matruchotii	strain=ATCC 14266	GCA_000175375.1	43768	43768	type	True	100.0	949	949	95	conclusive
Corynebacterium matruchotii	strain=ATCC 14266	GCA_011612265.2	43768	43768	type	True	99.9895	947	949	95	conclusive
Corynebacterium matruchotii	strain=NCTC10254	GCA_900447555.1	43768	43768	type	True	99.9603	925	949	95	conclusive
Corynebacterium rouxii	strain=FRC0190	GCA_902702935.1	2719119	2719119	type	True	77.8751	61	949	95	below_threshold
Corynebacterium aquilae	strain=S-613	GCA_001941445.1	203263	203263	type	True	77.8218	118	949	95	below_threshold
Corynebacterium pseudopelargi	strain=812CH	GCA_003814005.1	2080757	2080757	type	True	77.7999	84	949	95	below_threshold
Corynebacterium diphtheriae	strain=DSM 44123	GCA_001913265.1	1717	1717	type	True	77.7499	64	949	95	below_threshold
Corynebacterium vitaeruminis	strain=DSM 20294	GCA_000550805.1	38305	38305	type	True	77.56	138	949	95	below_threshold
Corynebacterium pollutisoli	strain=VDS11	GCA_900177745.1	1610489	1610489	type	True	77.339	114	949	95	below_threshold
Corynebacterium occultum	strain=2039	GCA_009734425.1	2675219	2675219	type	True	77.1815	88	949	95	below_threshold
Corynebacterium alimapuense	strain=VA37-3	GCA_003716585.1	1576874	1576874	type	True	76.9097	55	949	95	below_threshold
Corynebacterium stationis	strain=622=DSM 20302	GCA_001941345.1	1705	1705	type	True	76.6452	50	949	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:51:22,894] [INFO] DFAST Taxonomy check result was written to GCF_000175375.1_ASM17537v1_genomic.fna/tc_result.tsv
[2024-01-25 17:51:22,895] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:51:22,895] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:51:22,895] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc1ff9d93-62a4-4c48-a01f-233cc9ddc844/dqc_reference/checkm_data
[2024-01-25 17:51:22,896] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:51:22,925] [INFO] Task started: CheckM
[2024-01-25 17:51:22,925] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000175375.1_ASM17537v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000175375.1_ASM17537v1_genomic.fna/checkm_input GCF_000175375.1_ASM17537v1_genomic.fna/checkm_result
[2024-01-25 17:51:51,131] [INFO] Task succeeded: CheckM
[2024-01-25 17:51:51,132] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:51:51,153] [INFO] ===== Completeness check finished =====
[2024-01-25 17:51:51,153] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:51:51,153] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000175375.1_ASM17537v1_genomic.fna/markers.fasta)
[2024-01-25 17:51:51,154] [INFO] Task started: Blastn
[2024-01-25 17:51:51,154] [INFO] Running command: blastn -query GCF_000175375.1_ASM17537v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc1ff9d93-62a4-4c48-a01f-233cc9ddc844/dqc_reference/reference_markers_gtdb.fasta -out GCF_000175375.1_ASM17537v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:51:52,123] [INFO] Task succeeded: Blastn
[2024-01-25 17:51:52,126] [INFO] Selected 20 target genomes.
[2024-01-25 17:51:52,126] [INFO] Target genome list was writen to GCF_000175375.1_ASM17537v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:51:52,147] [INFO] Task started: fastANI
[2024-01-25 17:51:52,148] [INFO] Running command: fastANI --query /var/lib/cwl/stg262dcd84-07a6-4218-8a11-dcde15b404ba/GCF_000175375.1_ASM17537v1_genomic.fna.gz --refList GCF_000175375.1_ASM17537v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000175375.1_ASM17537v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:52:02,798] [INFO] Task succeeded: fastANI
[2024-01-25 17:52:02,808] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:52:02,808] [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_011612265.2	s__Corynebacterium matruchotii	99.9895	947	949	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.54	97.18	0.97	0.91	9	conclusive
GCF_902702935.1	s__Corynebacterium rouxii	77.8751	61	949	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001941445.1	s__Corynebacterium aquilae	77.8218	118	949	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003814005.1	s__Corynebacterium pseudopelargi	77.7742	86	949	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000550805.1	s__Corynebacterium vitaeruminis	77.56	138	949	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.86	98.60	0.94	0.94	3	-
GCF_001457455.1	s__Corynebacterium diphtheriae	77.5151	70	949	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.05	95.03	0.92	0.83	346	-
GCF_004114895.1	s__Corynebacterium pelargi	77.35	95	949	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900177745.1	s__Corynebacterium pollutisoli	77.339	114	949	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.83	98.83	0.98	0.98	2	-
GCF_000767055.1	s__Corynebacterium doosanense	77.25	83	949	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009734425.1	s__Corynebacterium sp009734425	77.1815	88	949	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001412105.1	s__Corynebacterium oculi	76.9164	91	949	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003716585.1	s__Corynebacterium alimapuense	76.9097	55	949	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001941485.1	s__Corynebacterium frankenforstense	76.8957	100	949	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003955685.1	s__Corynebacterium sp003955685	76.8587	97	949	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176155.1	s__Corynebacterium glucuronolyticum	76.6634	55	949	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.97	98.66	0.94	0.91	8	-
GCF_001941345.1	s__Corynebacterium stationis	76.6452	50	949	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.83	97.14	0.93	0.87	11	-
--------------------------------------------------------------------------------
[2024-01-25 17:52:02,810] [INFO] GTDB search result was written to GCF_000175375.1_ASM17537v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:52:02,811] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:52:02,820] [INFO] DFAST_QC result json was written to GCF_000175375.1_ASM17537v1_genomic.fna/dqc_result.json
[2024-01-25 17:52:02,821] [INFO] DFAST_QC completed!
[2024-01-25 17:52:02,821] [INFO] Total running time: 0h0m57s