[2024-01-24 14:07:30,272] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:07:30,274] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:07:30,274] [INFO] DQC Reference Directory: /var/lib/cwl/stgc44b02d9-02e2-4d28-a739-99e4263e6238/dqc_reference
[2024-01-24 14:07:31,513] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:07:31,514] [INFO] Task started: Prodigal
[2024-01-24 14:07:31,514] [INFO] Running command: gunzip -c /var/lib/cwl/stg2d6e38b2-c04c-47fd-89d9-a8f3c6f5fcc5/GCF_900461185.1_48853_B02_genomic.fna.gz | prodigal -d GCF_900461185.1_48853_B02_genomic.fna/cds.fna -a GCF_900461185.1_48853_B02_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:07:39,221] [INFO] Task succeeded: Prodigal
[2024-01-24 14:07:39,222] [INFO] Task started: HMMsearch
[2024-01-24 14:07:39,222] [INFO] Running command: hmmsearch --tblout GCF_900461185.1_48853_B02_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc44b02d9-02e2-4d28-a739-99e4263e6238/dqc_reference/reference_markers.hmm GCF_900461185.1_48853_B02_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:07:39,465] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:07:39,466] [INFO] Found 6/6 markers.
[2024-01-24 14:07:39,491] [INFO] Query marker FASTA was written to GCF_900461185.1_48853_B02_genomic.fna/markers.fasta
[2024-01-24 14:07:39,492] [INFO] Task started: Blastn
[2024-01-24 14:07:39,492] [INFO] Running command: blastn -query GCF_900461185.1_48853_B02_genomic.fna/markers.fasta -db /var/lib/cwl/stgc44b02d9-02e2-4d28-a739-99e4263e6238/dqc_reference/reference_markers.fasta -out GCF_900461185.1_48853_B02_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:40,430] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:40,433] [INFO] Selected 11 target genomes.
[2024-01-24 14:07:40,433] [INFO] Target genome list was writen to GCF_900461185.1_48853_B02_genomic.fna/target_genomes.txt
[2024-01-24 14:07:40,439] [INFO] Task started: fastANI
[2024-01-24 14:07:40,439] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d6e38b2-c04c-47fd-89d9-a8f3c6f5fcc5/GCF_900461185.1_48853_B02_genomic.fna.gz --refList GCF_900461185.1_48853_B02_genomic.fna/target_genomes.txt --output GCF_900461185.1_48853_B02_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:07:46,201] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:46,202] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc44b02d9-02e2-4d28-a739-99e4263e6238/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:07:46,202] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc44b02d9-02e2-4d28-a739-99e4263e6238/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:07:46,212] [INFO] Found 11 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:07:46,212] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:07:46,213] [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 jeikeium	strain=NCTC11913	GCA_900461185.1	38289	38289	suspected-type	True	100.0	838	841	95	conclusive
Corynebacterium jeikeium	strain=ATCC 43734	GCA_001999385.1	38289	38289	suspected-type	True	99.948	769	841	95	conclusive
Corynebacterium jeikeium	strain=ATCC 43734	GCA_000163435.1	38289	38289	suspected-type	True	99.8598	813	841	95	conclusive
Corynebacterium urealyticum	strain=NCTC12011	GCA_900187235.1	43771	43771	type	True	81.1978	320	841	95	below_threshold
Corynebacterium urealyticum	strain=FDAARGOS_994	GCA_016127975.1	43771	43771	type	True	81.0812	318	841	95	below_threshold
Corynebacterium falsenii	strain=FDAARGOS_1494	GCA_020099275.1	108486	108486	type	True	79.7329	373	841	95	below_threshold
Corynebacterium dentalis	strain=Marseille-P4122	GCA_900232865.1	2014528	2014528	type	True	79.2278	261	841	95	below_threshold
Corynebacterium zhongnanshanii	strain=zg-320	GCA_014490575.1	2768834	2768834	type	True	78.7767	245	841	95	below_threshold
Corynebacterium glyciniphilum	strain=AJ 3170	GCA_000626675.1	1404244	1404244	type	True	78.2542	166	841	95	below_threshold
Corynebacterium xerosis	strain=NBRC 16721	GCA_001552415.1	1725	1725	suspected-type	True	78.0462	219	841	95	below_threshold
Corynebacterium yudongzhengii	strain=2183	GCA_003065405.1	2080740	2080740	type	True	78.0258	165	841	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:07:46,214] [INFO] DFAST Taxonomy check result was written to GCF_900461185.1_48853_B02_genomic.fna/tc_result.tsv
[2024-01-24 14:07:46,215] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:07:46,215] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:07:46,215] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc44b02d9-02e2-4d28-a739-99e4263e6238/dqc_reference/checkm_data
[2024-01-24 14:07:46,216] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:07:46,245] [INFO] Task started: CheckM
[2024-01-24 14:07:46,245] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900461185.1_48853_B02_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900461185.1_48853_B02_genomic.fna/checkm_input GCF_900461185.1_48853_B02_genomic.fna/checkm_result
[2024-01-24 14:08:14,321] [INFO] Task succeeded: CheckM
[2024-01-24 14:08:14,322] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:08:14,339] [INFO] ===== Completeness check finished =====
[2024-01-24 14:08:14,339] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:08:14,339] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900461185.1_48853_B02_genomic.fna/markers.fasta)
[2024-01-24 14:08:14,340] [INFO] Task started: Blastn
[2024-01-24 14:08:14,340] [INFO] Running command: blastn -query GCF_900461185.1_48853_B02_genomic.fna/markers.fasta -db /var/lib/cwl/stgc44b02d9-02e2-4d28-a739-99e4263e6238/dqc_reference/reference_markers_gtdb.fasta -out GCF_900461185.1_48853_B02_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:08:15,783] [INFO] Task succeeded: Blastn
[2024-01-24 14:08:15,786] [INFO] Selected 9 target genomes.
[2024-01-24 14:08:15,786] [INFO] Target genome list was writen to GCF_900461185.1_48853_B02_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:08:15,794] [INFO] Task started: fastANI
[2024-01-24 14:08:15,794] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d6e38b2-c04c-47fd-89d9-a8f3c6f5fcc5/GCF_900461185.1_48853_B02_genomic.fna.gz --refList GCF_900461185.1_48853_B02_genomic.fna/target_genomes_gtdb.txt --output GCF_900461185.1_48853_B02_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:08:20,731] [INFO] Task succeeded: fastANI
[2024-01-24 14:08:20,740] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:08:20,740] [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_000163435.1	s__Corynebacterium jeikeium	99.8598	813	841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.68	96.00	0.93	0.90	9	conclusive
GCF_000738175.1	s__Corynebacterium jeikeium_C	92.4438	708	841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001807485.1	s__Corynebacterium sp001807485	92.2907	676	841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.83	97.75	0.93	0.93	3	-
GCF_000738265.1	s__Corynebacterium jeikeium_A	87.0138	665	841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.92	97.52	0.95	0.93	11	-
GCA_000525655.1	s__Corynebacterium falsenii	79.781	366	841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.72	98.72	0.95	0.95	2	-
GCA_019120635.1	s__Corynebacterium intestinavium	79.3572	273	841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019114175.1	s__Corynebacterium gallistercoris	79.2867	296	841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014490575.1	s__Corynebacterium sp014490575	78.8896	243	841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.40	97.50	0.99	0.97	7	-
GCF_001056295.1	s__Corynebacterium halotolerans_A	77.8747	227	841	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 14:08:20,742] [INFO] GTDB search result was written to GCF_900461185.1_48853_B02_genomic.fna/result_gtdb.tsv
[2024-01-24 14:08:20,743] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:08:20,746] [INFO] DFAST_QC result json was written to GCF_900461185.1_48853_B02_genomic.fna/dqc_result.json
[2024-01-24 14:08:20,746] [INFO] DFAST_QC completed!
[2024-01-24 14:08:20,746] [INFO] Total running time: 0h0m50s