[2024-01-24 13:49:30,465] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:30,467] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:30,467] [INFO] DQC Reference Directory: /var/lib/cwl/stg635f1802-35a7-4458-ba4d-59ff392bdd58/dqc_reference
[2024-01-24 13:49:31,833] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:31,835] [INFO] Task started: Prodigal
[2024-01-24 13:49:31,835] [INFO] Running command: gunzip -c /var/lib/cwl/stg20e41475-f276-4502-9950-c7466243d335/GCF_001020985.1_ASM102098v1_genomic.fna.gz | prodigal -d GCF_001020985.1_ASM102098v1_genomic.fna/cds.fna -a GCF_001020985.1_ASM102098v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:42,774] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:42,775] [INFO] Task started: HMMsearch
[2024-01-24 13:49:42,775] [INFO] Running command: hmmsearch --tblout GCF_001020985.1_ASM102098v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg635f1802-35a7-4458-ba4d-59ff392bdd58/dqc_reference/reference_markers.hmm GCF_001020985.1_ASM102098v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:43,097] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:43,098] [INFO] Found 6/6 markers.
[2024-01-24 13:49:43,132] [INFO] Query marker FASTA was written to GCF_001020985.1_ASM102098v1_genomic.fna/markers.fasta
[2024-01-24 13:49:43,133] [INFO] Task started: Blastn
[2024-01-24 13:49:43,133] [INFO] Running command: blastn -query GCF_001020985.1_ASM102098v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg635f1802-35a7-4458-ba4d-59ff392bdd58/dqc_reference/reference_markers.fasta -out GCF_001020985.1_ASM102098v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:43,905] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:43,909] [INFO] Selected 23 target genomes.
[2024-01-24 13:49:43,910] [INFO] Target genome list was writen to GCF_001020985.1_ASM102098v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:43,939] [INFO] Task started: fastANI
[2024-01-24 13:49:43,939] [INFO] Running command: fastANI --query /var/lib/cwl/stg20e41475-f276-4502-9950-c7466243d335/GCF_001020985.1_ASM102098v1_genomic.fna.gz --refList GCF_001020985.1_ASM102098v1_genomic.fna/target_genomes.txt --output GCF_001020985.1_ASM102098v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:57,317] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:57,317] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg635f1802-35a7-4458-ba4d-59ff392bdd58/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:57,317] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg635f1802-35a7-4458-ba4d-59ff392bdd58/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:57,328] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:49:57,328] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:57,329] [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 mustelae	strain=DSM 45274	GCA_001020985.1	571915	571915	type	True	100.0	1149	1157	95	conclusive
Corynebacterium ulcerans	strain=NCTC7910	GCA_900187135.1	65058	65058	type	True	79.555	76	1157	95	below_threshold
Corynebacterium ulcerans	strain=FDAARGOS_1118	GCA_016727365.1	65058	65058	type	True	79.5074	74	1157	95	below_threshold
Corynebacterium diphtheriae	strain=NCTC11397	GCA_001457455.1	1717	1717	type	True	79.1979	91	1157	95	below_threshold
Corynebacterium diphtheriae		GCA_902809765.1	1717	1717	type	True	79.1089	91	1157	95	below_threshold
Corynebacterium diphtheriae subsp. diphtheriae	strain=FDAARGOS_1554	GCA_020736085.1	2315257	1717	type	True	79.076	88	1157	95	below_threshold
Corynebacterium vitaeruminis	strain=DSM 20294	GCA_000550805.1	38305	38305	type	True	78.7133	100	1157	95	below_threshold
Corynebacterium rouxii	strain=FRC0190	GCA_902702935.1	2719119	2719119	type	True	78.3172	92	1157	95	below_threshold
Corynebacterium diphtheriae	strain=DSM 44123	GCA_001913265.1	1717	1717	type	True	78.077	84	1157	95	below_threshold
Corynebacterium silvaticum	strain=KL0182	GCA_004382825.2	2320431	2320431	type	True	77.8071	73	1157	95	below_threshold
Corynebacterium matruchotii	strain=ATCC 14266	GCA_000175375.1	43768	43768	type	True	77.5146	113	1157	95	below_threshold
Corynebacterium phoceense	strain=MC1	GCA_900092335.1	1686286	1686286	type	True	77.4701	55	1157	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:57,330] [INFO] DFAST Taxonomy check result was written to GCF_001020985.1_ASM102098v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:57,331] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:57,331] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:57,331] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg635f1802-35a7-4458-ba4d-59ff392bdd58/dqc_reference/checkm_data
[2024-01-24 13:49:57,333] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:57,386] [INFO] Task started: CheckM
[2024-01-24 13:49:57,386] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001020985.1_ASM102098v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001020985.1_ASM102098v1_genomic.fna/checkm_input GCF_001020985.1_ASM102098v1_genomic.fna/checkm_result
[2024-01-24 13:50:34,658] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:34,659] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:34,694] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:34,695] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:34,695] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001020985.1_ASM102098v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:34,696] [INFO] Task started: Blastn
[2024-01-24 13:50:34,696] [INFO] Running command: blastn -query GCF_001020985.1_ASM102098v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg635f1802-35a7-4458-ba4d-59ff392bdd58/dqc_reference/reference_markers_gtdb.fasta -out GCF_001020985.1_ASM102098v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:35,695] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:35,699] [INFO] Selected 20 target genomes.
[2024-01-24 13:50:35,699] [INFO] Target genome list was writen to GCF_001020985.1_ASM102098v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:35,713] [INFO] Task started: fastANI
[2024-01-24 13:50:35,714] [INFO] Running command: fastANI --query /var/lib/cwl/stg20e41475-f276-4502-9950-c7466243d335/GCF_001020985.1_ASM102098v1_genomic.fna.gz --refList GCF_001020985.1_ASM102098v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001020985.1_ASM102098v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:45,849] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:45,865] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:45,866] [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_001020985.1	s__Corynebacterium mustelae	100.0	1145	1157	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900187135.1	s__Corynebacterium ulcerans	79.6122	74	1157	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.24	95.82	0.97	0.95	38	-
GCF_001457455.1	s__Corynebacterium diphtheriae	79.2012	92	1157	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.05	95.03	0.92	0.83	346	-
GCF_002355155.1	s__Corynebacterium suranareeae	79.1028	69	1157	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002563965.1	s__Corynebacterium renale	79.048	65	1157	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.02	98.07	0.97	0.94	5	-
GCF_001586215.1	s__Corynebacterium simulans	78.768	67	1157	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.78	97.47	0.94	0.92	11	-
GCF_000011325.1	s__Corynebacterium glutamicum	78.7414	74	1157	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.67	97.34	0.92	0.85	76	-
GCF_000550805.1	s__Corynebacterium vitaeruminis	78.6272	100	1157	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.86	98.60	0.94	0.94	3	-
GCF_902702935.1	s__Corynebacterium rouxii	78.5587	91	1157	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004114895.1	s__Corynebacterium pelargi	78.4915	94	1157	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004382825.2	s__Corynebacterium silvaticum	77.8528	72	1157	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.94	99.78	1.00	0.99	8	-
GCF_900092335.1	s__Corynebacterium phoceense	77.4667	55	1157	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.96	96.08	0.95	0.92	11	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:45,868] [INFO] GTDB search result was written to GCF_001020985.1_ASM102098v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:45,868] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:45,871] [INFO] DFAST_QC result json was written to GCF_001020985.1_ASM102098v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:45,872] [INFO] DFAST_QC completed!
[2024-01-24 13:50:45,872] [INFO] Total running time: 0h1m15s