[2024-01-24 12:44:10,101] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:10,103] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:10,103] [INFO] DQC Reference Directory: /var/lib/cwl/stg6b2dba20-cbca-42d2-a093-d809b92073e9/dqc_reference
[2024-01-24 12:44:11,496] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:11,497] [INFO] Task started: Prodigal
[2024-01-24 12:44:11,497] [INFO] Running command: gunzip -c /var/lib/cwl/stg8ef7709d-ed54-4430-af5b-69212c7052fe/GCF_030408755.1_ASM3040875v1_genomic.fna.gz | prodigal -d GCF_030408755.1_ASM3040875v1_genomic.fna/cds.fna -a GCF_030408755.1_ASM3040875v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:44:22,895] [INFO] Task succeeded: Prodigal
[2024-01-24 12:44:22,896] [INFO] Task started: HMMsearch
[2024-01-24 12:44:22,896] [INFO] Running command: hmmsearch --tblout GCF_030408755.1_ASM3040875v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6b2dba20-cbca-42d2-a093-d809b92073e9/dqc_reference/reference_markers.hmm GCF_030408755.1_ASM3040875v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:44:23,196] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:44:23,197] [INFO] Found 6/6 markers.
[2024-01-24 12:44:23,226] [INFO] Query marker FASTA was written to GCF_030408755.1_ASM3040875v1_genomic.fna/markers.fasta
[2024-01-24 12:44:23,227] [INFO] Task started: Blastn
[2024-01-24 12:44:23,227] [INFO] Running command: blastn -query GCF_030408755.1_ASM3040875v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6b2dba20-cbca-42d2-a093-d809b92073e9/dqc_reference/reference_markers.fasta -out GCF_030408755.1_ASM3040875v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:23,988] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:23,992] [INFO] Selected 23 target genomes.
[2024-01-24 12:44:23,993] [INFO] Target genome list was writen to GCF_030408755.1_ASM3040875v1_genomic.fna/target_genomes.txt
[2024-01-24 12:44:24,015] [INFO] Task started: fastANI
[2024-01-24 12:44:24,016] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ef7709d-ed54-4430-af5b-69212c7052fe/GCF_030408755.1_ASM3040875v1_genomic.fna.gz --refList GCF_030408755.1_ASM3040875v1_genomic.fna/target_genomes.txt --output GCF_030408755.1_ASM3040875v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:44:33,491] [INFO] Task succeeded: fastANI
[2024-01-24 12:44:33,492] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6b2dba20-cbca-42d2-a093-d809b92073e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:44:33,492] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6b2dba20-cbca-42d2-a093-d809b92073e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:44:33,509] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:44:33,510] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:44:33,510] [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	79.3372	147	1078	95	below_threshold
Corynebacterium epidermidicanis	strain=DSM 45586	GCA_001021025.1	1050174	1050174	type	True	79.2221	92	1078	95	below_threshold
Corynebacterium diphtheriae		GCA_902809765.1	1717	1717	type	True	79.181	126	1078	95	below_threshold
Corynebacterium diphtheriae	strain=NCTC11397	GCA_001457455.1	1717	1717	type	True	79.1497	125	1078	95	below_threshold
Corynebacterium striatum	strain=FDAARGOS_1054	GCA_016403285.1	43770	43770	type	True	79.0091	101	1078	95	below_threshold
Corynebacterium halotolerans	strain=YIM 70093 = DSM 44683	GCA_000341345.1	225326	225326	type	True	78.8941	112	1078	95	below_threshold
Corynebacterium glutamicum	strain=ATCC 13032 substr. K051	GCA_000382905.1	1718	1718	type	True	78.826	133	1078	95	below_threshold
Corynebacterium hindlerae	strain=NML 93-0612	GCA_014117265.1	699041	699041	type	True	78.7571	122	1078	95	below_threshold
Corynebacterium rouxii	strain=FRC0190	GCA_902702935.1	2719119	2719119	type	True	78.7559	122	1078	95	below_threshold
Corynebacterium glutamicum	strain=ATCC 13032	GCA_000011325.1	1718	1718	type	True	78.7463	129	1078	95	below_threshold
Corynebacterium striatum	strain=NCTC764	GCA_900447675.1	43770	43770	type	True	78.6628	98	1078	95	below_threshold
Corynebacterium gerontici	strain=W8	GCA_003813985.1	2079234	2079234	type	True	78.626	115	1078	95	below_threshold
Corynebacterium vitaeruminis	strain=DSM 20294	GCA_000550805.1	38305	38305	type	True	78.5934	163	1078	95	below_threshold
Corynebacterium glutamicum	strain=ATCC 13032	GCA_002847405.1	1718	1718	type	True	78.4664	129	1078	95	below_threshold
Corynebacterium diphtheriae	strain=DSM 44123	GCA_001913265.1	1717	1717	type	True	78.4584	117	1078	95	below_threshold
Corynebacterium maris	strain=DSM 45190	GCA_000442645.1	575200	575200	type	True	78.4383	88	1078	95	below_threshold
Corynebacterium striatum	strain=NBRC 15291	GCA_006538485.1	43770	43770	type	True	78.393	98	1078	95	below_threshold
Corynebacterium glutamicum	strain=ATCC 13032	GCA_011761195.1	1718	1718	type	True	78.392	137	1078	95	below_threshold
Corynebacterium silvaticum	strain=KL0182	GCA_004382825.2	2320431	2320431	type	True	78.1339	99	1078	95	below_threshold
Corynebacterium frankenforstense	strain=ST18	GCA_001941485.1	1230998	1230998	type	True	77.7543	91	1078	95	below_threshold
Corynebacterium halotolerans	strain=DSM 44683	GCA_000688435.1	225326	225326	type	True	77.6916	104	1078	95	below_threshold
Corynebacterium spheniscorum	strain=CCUG 45512	GCA_008693095.1	185761	185761	type	True	77.5993	92	1078	95	below_threshold
Corynebacterium pollutisoli	strain=VDS11	GCA_900177745.1	1610489	1610489	type	True	77.5979	111	1078	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:44:33,512] [INFO] DFAST Taxonomy check result was written to GCF_030408755.1_ASM3040875v1_genomic.fna/tc_result.tsv
[2024-01-24 12:44:33,512] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:44:33,512] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:44:33,513] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6b2dba20-cbca-42d2-a093-d809b92073e9/dqc_reference/checkm_data
[2024-01-24 12:44:33,514] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:44:33,550] [INFO] Task started: CheckM
[2024-01-24 12:44:33,550] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030408755.1_ASM3040875v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030408755.1_ASM3040875v1_genomic.fna/checkm_input GCF_030408755.1_ASM3040875v1_genomic.fna/checkm_result
[2024-01-24 12:45:11,395] [INFO] Task succeeded: CheckM
[2024-01-24 12:45:11,396] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:45:11,432] [INFO] ===== Completeness check finished =====
[2024-01-24 12:45:11,432] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:45:11,432] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030408755.1_ASM3040875v1_genomic.fna/markers.fasta)
[2024-01-24 12:45:11,433] [INFO] Task started: Blastn
[2024-01-24 12:45:11,433] [INFO] Running command: blastn -query GCF_030408755.1_ASM3040875v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6b2dba20-cbca-42d2-a093-d809b92073e9/dqc_reference/reference_markers_gtdb.fasta -out GCF_030408755.1_ASM3040875v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:12,437] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:12,442] [INFO] Selected 23 target genomes.
[2024-01-24 12:45:12,442] [INFO] Target genome list was writen to GCF_030408755.1_ASM3040875v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:45:12,500] [INFO] Task started: fastANI
[2024-01-24 12:45:12,500] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ef7709d-ed54-4430-af5b-69212c7052fe/GCF_030408755.1_ASM3040875v1_genomic.fna.gz --refList GCF_030408755.1_ASM3040875v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030408755.1_ASM3040875v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:45:22,218] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:22,242] [INFO] Found 23 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:45:22,243] [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_001021025.1	s__Corynebacterium epidermidicanis	79.6008	92	1078	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	79.473	128	1078	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.05	95.03	0.92	0.83	346	-
GCF_004795735.1	s__Corynebacterium endometrii	79.427	83	1078	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900187135.1	s__Corynebacterium ulcerans	79.285	108	1078	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.24	95.82	0.97	0.95	38	-
GCF_001020985.1	s__Corynebacterium mustelae	79.1068	146	1078	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	78.798	125	1078	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014117265.1	s__Corynebacterium sp014117265	78.7953	122	1078	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.31	97.31	0.93	0.93	2	-
GCF_003813985.1	s__Corynebacterium geronticis	78.7213	115	1078	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	78.7166	164	1078	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.86	98.60	0.94	0.94	3	-
GCF_000341345.1	s__Corynebacterium halotolerans	78.6597	110	1078	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000833575.1	s__Corynebacterium singulare	78.6222	86	1078	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.05	96.95	0.89	0.88	3	-
GCF_000980815.1	s__Corynebacterium camporealensis	78.6108	110	1078	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.96	99.96	1.00	1.00	2	-
GCF_000011325.1	s__Corynebacterium glutamicum	78.5994	131	1078	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.67	97.34	0.92	0.85	76	-
GCF_000442645.1	s__Corynebacterium maris	78.2416	85	1078	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004382825.2	s__Corynebacterium silvaticum	78.1766	98	1078	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.94	99.78	1.00	0.99	8	-
GCF_001941485.1	s__Corynebacterium frankenforstense	78.1557	93	1078	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001021045.1	s__Corynebacterium testudinoris	78.0301	108	1078	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002861385.1	s__Corynebacterium aurimucosum_C	77.936	85	1078	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.04	96.50	0.91	0.89	28	-
GCF_000159135.1	s__Corynebacterium striatum	77.8628	91	1078	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.44	95.19	0.92	0.85	41	-
GCF_001836165.1	s__Corynebacterium sp001836165	77.8571	76	1078	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.96	97.92	0.93	0.93	3	-
GCF_900113445.1	s__Corynebacterium spheniscorum	77.6471	94	1078	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.99	99.99	0.98	0.98	2	-
GCF_900177745.1	s__Corynebacterium pollutisoli	77.5979	111	1078	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.83	98.83	0.98	0.98	2	-
GCF_003955685.1	s__Corynebacterium sp003955685	77.5453	101	1078	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 12:45:22,244] [INFO] GTDB search result was written to GCF_030408755.1_ASM3040875v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:45:22,245] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:45:22,250] [INFO] DFAST_QC result json was written to GCF_030408755.1_ASM3040875v1_genomic.fna/dqc_result.json
[2024-01-24 12:45:22,250] [INFO] DFAST_QC completed!
[2024-01-24 12:45:22,250] [INFO] Total running time: 0h1m12s