[2024-01-24 15:18:50,872] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:51,045] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:51,046] [INFO] DQC Reference Directory: /var/lib/cwl/stg8b5f11f2-1575-418f-af29-30c2cac3f9d9/dqc_reference
[2024-01-24 15:18:52,363] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:52,364] [INFO] Task started: Prodigal
[2024-01-24 15:18:52,365] [INFO] Running command: gunzip -c /var/lib/cwl/stg805cf499-7442-4a74-820d-8e87e552d6b0/GCF_002155265.1_ASM215526v1_genomic.fna.gz | prodigal -d GCF_002155265.1_ASM215526v1_genomic.fna/cds.fna -a GCF_002155265.1_ASM215526v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:59,291] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:59,291] [INFO] Task started: HMMsearch
[2024-01-24 15:18:59,292] [INFO] Running command: hmmsearch --tblout GCF_002155265.1_ASM215526v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8b5f11f2-1575-418f-af29-30c2cac3f9d9/dqc_reference/reference_markers.hmm GCF_002155265.1_ASM215526v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:59,521] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:59,522] [INFO] Found 6/6 markers.
[2024-01-24 15:18:59,555] [INFO] Query marker FASTA was written to GCF_002155265.1_ASM215526v1_genomic.fna/markers.fasta
[2024-01-24 15:18:59,555] [INFO] Task started: Blastn
[2024-01-24 15:18:59,555] [INFO] Running command: blastn -query GCF_002155265.1_ASM215526v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8b5f11f2-1575-418f-af29-30c2cac3f9d9/dqc_reference/reference_markers.fasta -out GCF_002155265.1_ASM215526v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:00,293] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:00,296] [INFO] Selected 8 target genomes.
[2024-01-24 15:19:00,296] [INFO] Target genome list was writen to GCF_002155265.1_ASM215526v1_genomic.fna/target_genomes.txt
[2024-01-24 15:19:00,300] [INFO] Task started: fastANI
[2024-01-24 15:19:00,300] [INFO] Running command: fastANI --query /var/lib/cwl/stg805cf499-7442-4a74-820d-8e87e552d6b0/GCF_002155265.1_ASM215526v1_genomic.fna.gz --refList GCF_002155265.1_ASM215526v1_genomic.fna/target_genomes.txt --output GCF_002155265.1_ASM215526v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:19:04,650] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:04,651] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8b5f11f2-1575-418f-af29-30c2cac3f9d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:19:04,651] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8b5f11f2-1575-418f-af29-30c2cac3f9d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:19:04,659] [INFO] Found 7 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:19:04,659] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:19:04,660] [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 pseudotuberculosis	strain=ATCC 19410	GCA_002155265.1	1719	1719	type	True	100.0	778	779	95	conclusive
Corynebacterium pseudotuberculosis	strain=DSM 20689	GCA_003634885.1	1719	1719	type	True	99.997	775	779	95	conclusive
Corynebacterium silvaticum	strain=KL0182	GCA_004382825.2	2320431	2320431	type	True	85.6554	689	779	95	below_threshold
Corynebacterium ulcerans	strain=NCTC7910	GCA_900187135.1	65058	65058	type	True	85.1818	693	779	95	below_threshold
Corynebacterium ulcerans	strain=FDAARGOS_1118	GCA_016727365.1	65058	65058	type	True	85.0772	698	779	95	below_threshold
Corynebacterium tuberculostearicum	strain=DSM 44922	GCA_013408445.1	38304	38304	type	True	78.1821	73	779	95	below_threshold
Corynebacterium tuberculostearicum	strain=FDAARGOS_1117	GCA_016728365.1	38304	38304	type	True	77.9089	70	779	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:19:04,661] [INFO] DFAST Taxonomy check result was written to GCF_002155265.1_ASM215526v1_genomic.fna/tc_result.tsv
[2024-01-24 15:19:04,662] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:19:04,662] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:19:04,662] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8b5f11f2-1575-418f-af29-30c2cac3f9d9/dqc_reference/checkm_data
[2024-01-24 15:19:04,663] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:19:04,689] [INFO] Task started: CheckM
[2024-01-24 15:19:04,689] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002155265.1_ASM215526v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002155265.1_ASM215526v1_genomic.fna/checkm_input GCF_002155265.1_ASM215526v1_genomic.fna/checkm_result
[2024-01-24 15:19:30,712] [INFO] Task succeeded: CheckM
[2024-01-24 15:19:30,714] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:19:30,735] [INFO] ===== Completeness check finished =====
[2024-01-24 15:19:30,735] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:19:30,736] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002155265.1_ASM215526v1_genomic.fna/markers.fasta)
[2024-01-24 15:19:30,736] [INFO] Task started: Blastn
[2024-01-24 15:19:30,736] [INFO] Running command: blastn -query GCF_002155265.1_ASM215526v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8b5f11f2-1575-418f-af29-30c2cac3f9d9/dqc_reference/reference_markers_gtdb.fasta -out GCF_002155265.1_ASM215526v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:31,682] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:31,685] [INFO] Selected 13 target genomes.
[2024-01-24 15:19:31,686] [INFO] Target genome list was writen to GCF_002155265.1_ASM215526v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:19:31,695] [INFO] Task started: fastANI
[2024-01-24 15:19:31,696] [INFO] Running command: fastANI --query /var/lib/cwl/stg805cf499-7442-4a74-820d-8e87e552d6b0/GCF_002155265.1_ASM215526v1_genomic.fna.gz --refList GCF_002155265.1_ASM215526v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002155265.1_ASM215526v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:19:37,922] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:37,935] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:19:37,936] [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_002155265.1	s__Corynebacterium pseudotuberculosis	100.0	778	779	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.58	98.61	0.99	0.97	131	conclusive
GCF_004382825.2	s__Corynebacterium silvaticum	85.6535	689	779	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.94	99.78	1.00	0.99	8	-
GCF_900187135.1	s__Corynebacterium ulcerans	85.1459	695	779	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.24	95.82	0.97	0.95	38	-
GCF_000011305.1	s__Corynebacterium efficiens	79.7451	70	779	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.90	99.90	0.99	0.99	2	-
GCF_001277995.1	s__Corynebacterium deserti	79.7434	73	779	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902702935.1	s__Corynebacterium rouxii	79.49	147	779	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001457455.1	s__Corynebacterium diphtheriae	79.2264	161	779	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.05	95.03	0.92	0.83	346	-
GCF_016127015.1	s__Corynebacterium aurimucosum_E	78.2528	79	779	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	96.91	96.45	0.92	0.89	6	-
GCF_016894265.1	s__Corynebacterium tuberculostearicum_D	78.0266	67	779	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.1108	N/A	N/A	N/A	N/A	1	-
GCF_013408445.1	s__Corynebacterium tuberculostearicum	78.0025	72	779	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	96.3332	98.29	96.59	0.96	0.92	3	-
GCA_900539985.1	s__Corynebacterium sp900539985	77.3001	59	779	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.98	99.98	0.92	0.92	2	-
GCF_001412105.1	s__Corynebacterium oculi	76.8008	63	779	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:19:37,938] [INFO] GTDB search result was written to GCF_002155265.1_ASM215526v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:19:37,938] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:19:37,941] [INFO] DFAST_QC result json was written to GCF_002155265.1_ASM215526v1_genomic.fna/dqc_result.json
[2024-01-24 15:19:37,942] [INFO] DFAST_QC completed!
[2024-01-24 15:19:37,942] [INFO] Total running time: 0h0m47s