[2024-01-25 18:39:35,691] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:39:35,692] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:39:35,692] [INFO] DQC Reference Directory: /var/lib/cwl/stg17116e20-6ae8-4c0e-b595-c4f58bc342ec/dqc_reference
[2024-01-25 18:39:36,811] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:39:36,811] [INFO] Task started: Prodigal
[2024-01-25 18:39:36,812] [INFO] Running command: gunzip -c /var/lib/cwl/stg3f5e5fbe-ec9f-437f-b3c1-2dadb431a406/GCF_014490575.1_ASM1449057v1_genomic.fna.gz | prodigal -d GCF_014490575.1_ASM1449057v1_genomic.fna/cds.fna -a GCF_014490575.1_ASM1449057v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:39:43,251] [INFO] Task succeeded: Prodigal
[2024-01-25 18:39:43,251] [INFO] Task started: HMMsearch
[2024-01-25 18:39:43,251] [INFO] Running command: hmmsearch --tblout GCF_014490575.1_ASM1449057v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg17116e20-6ae8-4c0e-b595-c4f58bc342ec/dqc_reference/reference_markers.hmm GCF_014490575.1_ASM1449057v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:39:43,429] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:39:43,430] [INFO] Found 6/6 markers.
[2024-01-25 18:39:43,451] [INFO] Query marker FASTA was written to GCF_014490575.1_ASM1449057v1_genomic.fna/markers.fasta
[2024-01-25 18:39:43,451] [INFO] Task started: Blastn
[2024-01-25 18:39:43,451] [INFO] Running command: blastn -query GCF_014490575.1_ASM1449057v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg17116e20-6ae8-4c0e-b595-c4f58bc342ec/dqc_reference/reference_markers.fasta -out GCF_014490575.1_ASM1449057v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:39:44,258] [INFO] Task succeeded: Blastn
[2024-01-25 18:39:44,260] [INFO] Selected 11 target genomes.
[2024-01-25 18:39:44,261] [INFO] Target genome list was writen to GCF_014490575.1_ASM1449057v1_genomic.fna/target_genomes.txt
[2024-01-25 18:39:44,272] [INFO] Task started: fastANI
[2024-01-25 18:39:44,273] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f5e5fbe-ec9f-437f-b3c1-2dadb431a406/GCF_014490575.1_ASM1449057v1_genomic.fna.gz --refList GCF_014490575.1_ASM1449057v1_genomic.fna/target_genomes.txt --output GCF_014490575.1_ASM1449057v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:39:48,891] [INFO] Task succeeded: fastANI
[2024-01-25 18:39:48,891] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg17116e20-6ae8-4c0e-b595-c4f58bc342ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:39:48,891] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg17116e20-6ae8-4c0e-b595-c4f58bc342ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:39:48,899] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:39:48,899] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:39:48,899] [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 zhongnanshanii	strain=zg-320	GCA_014490575.1	2768834	2768834	type	True	100.0	735	735	95	conclusive
Corynebacterium falsenii	strain=FDAARGOS_1494	GCA_020099275.1	108486	108486	type	True	79.3888	243	735	95	below_threshold
Corynebacterium resistens	strain=DSM 45100	GCA_000177535.2	258224	258224	type	True	79.2491	148	735	95	below_threshold
Corynebacterium urogenitale	strain=LMM-1652	GCA_009026825.1	2487892	2487892	type	True	79.232	192	735	95	below_threshold
Corynebacterium jeikeium	strain=NCTC11913	GCA_900461185.1	38289	38289	suspected-type	True	79.0218	252	735	95	below_threshold
Corynebacterium jeikeium	strain=ATCC 43734	GCA_001999385.1	38289	38289	suspected-type	True	78.7893	238	735	95	below_threshold
Corynebacterium jeikeium	strain=ATCC 43734	GCA_000163435.1	38289	38289	suspected-type	True	78.7715	250	735	95	below_threshold
Corynebacterium dentalis	strain=Marseille-P4122	GCA_900232865.1	2014528	2014528	type	True	78.594	212	735	95	below_threshold
Corynebacterium suicordis	strain=DSM 45110	GCA_015351405.1	203264	203264	type	True	78.5578	208	735	95	below_threshold
Corynebacterium heidelbergense	strain=DSM 104638	GCA_003285565.1	2055947	2055947	type	True	77.9519	151	735	95	below_threshold
Corynebacterium atypicum	strain=R2070	GCA_000732945.1	191610	191610	type	True	77.38	69	735	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:39:48,901] [INFO] DFAST Taxonomy check result was written to GCF_014490575.1_ASM1449057v1_genomic.fna/tc_result.tsv
[2024-01-25 18:39:48,902] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:39:48,902] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:39:48,902] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg17116e20-6ae8-4c0e-b595-c4f58bc342ec/dqc_reference/checkm_data
[2024-01-25 18:39:48,903] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:39:48,928] [INFO] Task started: CheckM
[2024-01-25 18:39:48,928] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014490575.1_ASM1449057v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014490575.1_ASM1449057v1_genomic.fna/checkm_input GCF_014490575.1_ASM1449057v1_genomic.fna/checkm_result
[2024-01-25 18:40:11,861] [INFO] Task succeeded: CheckM
[2024-01-25 18:40:11,862] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:40:11,878] [INFO] ===== Completeness check finished =====
[2024-01-25 18:40:11,878] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:40:11,879] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014490575.1_ASM1449057v1_genomic.fna/markers.fasta)
[2024-01-25 18:40:11,879] [INFO] Task started: Blastn
[2024-01-25 18:40:11,880] [INFO] Running command: blastn -query GCF_014490575.1_ASM1449057v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg17116e20-6ae8-4c0e-b595-c4f58bc342ec/dqc_reference/reference_markers_gtdb.fasta -out GCF_014490575.1_ASM1449057v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:40:13,027] [INFO] Task succeeded: Blastn
[2024-01-25 18:40:13,030] [INFO] Selected 15 target genomes.
[2024-01-25 18:40:13,030] [INFO] Target genome list was writen to GCF_014490575.1_ASM1449057v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:40:13,050] [INFO] Task started: fastANI
[2024-01-25 18:40:13,050] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f5e5fbe-ec9f-437f-b3c1-2dadb431a406/GCF_014490575.1_ASM1449057v1_genomic.fna.gz --refList GCF_014490575.1_ASM1449057v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014490575.1_ASM1449057v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:40:19,816] [INFO] Task succeeded: fastANI
[2024-01-25 18:40:19,826] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:40:19,826] [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_014490575.1	s__Corynebacterium sp014490575	100.0	735	735	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.40	97.50	0.99	0.97	7	conclusive
GCA_000525655.1	s__Corynebacterium falsenii	79.4539	243	735	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.72	98.72	0.95	0.95	2	-
GCF_009026825.1	s__Corynebacterium sp009026825	79.1933	190	735	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	79.1838	257	735	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.83	97.75	0.93	0.93	3	-
GCF_000738175.1	s__Corynebacterium jeikeium_C	79.1725	264	735	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000177535.2	s__Corynebacterium resistens	79.142	147	735	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000738265.1	s__Corynebacterium jeikeium_A	79.1099	246	735	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.92	97.52	0.95	0.93	11	-
GCA_019114175.1	s__Corynebacterium gallistercoris	78.8424	221	735	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000163435.1	s__Corynebacterium jeikeium	78.7892	249	735	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.68	96.00	0.93	0.90	9	-
GCF_900232865.1	s__Corynebacterium dentalis	78.594	212	735	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.56	98.56	0.96	0.96	2	-
GCF_015351405.1	s__Corynebacterium sp015351405	78.5776	207	735	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003285565.1	s__Corynebacterium heidelbergense	77.9519	151	735	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	96.29	96.29	0.86	0.86	2	-
GCA_019120175.1	s__Corynebacterium faecigallinarum	77.5385	203	735	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000732945.1	s__Corynebacterium atypicum	77.4014	69	735	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002101885.1	s__Mycobacterium senuense	76.3479	50	735	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:40:19,828] [INFO] GTDB search result was written to GCF_014490575.1_ASM1449057v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:40:19,829] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:40:19,831] [INFO] DFAST_QC result json was written to GCF_014490575.1_ASM1449057v1_genomic.fna/dqc_result.json
[2024-01-25 18:40:19,832] [INFO] DFAST_QC completed!
[2024-01-25 18:40:19,832] [INFO] Total running time: 0h0m44s