[2024-01-24 11:05:24,599] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:24,607] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:24,607] [INFO] DQC Reference Directory: /var/lib/cwl/stgb15f0a74-4626-4d33-a4df-be557cd0081b/dqc_reference
[2024-01-24 11:05:26,215] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:26,216] [INFO] Task started: Prodigal
[2024-01-24 11:05:26,216] [INFO] Running command: gunzip -c /var/lib/cwl/stgc5fa8f53-b2ac-4bbe-ab78-b71e7fe1c137/GCF_027570165.1_ASM2757016v1_genomic.fna.gz | prodigal -d GCF_027570165.1_ASM2757016v1_genomic.fna/cds.fna -a GCF_027570165.1_ASM2757016v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:33,097] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:33,098] [INFO] Task started: HMMsearch
[2024-01-24 11:05:33,098] [INFO] Running command: hmmsearch --tblout GCF_027570165.1_ASM2757016v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb15f0a74-4626-4d33-a4df-be557cd0081b/dqc_reference/reference_markers.hmm GCF_027570165.1_ASM2757016v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:33,334] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:33,336] [INFO] Found 6/6 markers.
[2024-01-24 11:05:33,363] [INFO] Query marker FASTA was written to GCF_027570165.1_ASM2757016v1_genomic.fna/markers.fasta
[2024-01-24 11:05:33,363] [INFO] Task started: Blastn
[2024-01-24 11:05:33,363] [INFO] Running command: blastn -query GCF_027570165.1_ASM2757016v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb15f0a74-4626-4d33-a4df-be557cd0081b/dqc_reference/reference_markers.fasta -out GCF_027570165.1_ASM2757016v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:34,331] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:34,337] [INFO] Selected 13 target genomes.
[2024-01-24 11:05:34,337] [INFO] Target genome list was writen to GCF_027570165.1_ASM2757016v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:34,341] [INFO] Task started: fastANI
[2024-01-24 11:05:34,341] [INFO] Running command: fastANI --query /var/lib/cwl/stgc5fa8f53-b2ac-4bbe-ab78-b71e7fe1c137/GCF_027570165.1_ASM2757016v1_genomic.fna.gz --refList GCF_027570165.1_ASM2757016v1_genomic.fna/target_genomes.txt --output GCF_027570165.1_ASM2757016v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:05:40,605] [INFO] Task succeeded: fastANI
[2024-01-24 11:05:40,606] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb15f0a74-4626-4d33-a4df-be557cd0081b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:05:40,606] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb15f0a74-4626-4d33-a4df-be557cd0081b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:05:40,616] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:05:40,616] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:05:40,616] [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	87.2614	645	743	95	below_threshold
Corynebacterium jeikeium	strain=ATCC 43734	GCA_001999385.1	38289	38289	suspected-type	True	87.2584	620	743	95	below_threshold
Corynebacterium jeikeium	strain=ATCC 43734	GCA_000163435.1	38289	38289	suspected-type	True	87.1949	639	743	95	below_threshold
Corynebacterium falsenii	strain=FDAARGOS_1494	GCA_020099275.1	108486	108486	type	True	80.1903	347	743	95	below_threshold
Corynebacterium urealyticum	strain=NCTC12011	GCA_900187235.1	43771	43771	type	True	79.9935	294	743	95	below_threshold
Corynebacterium urealyticum	strain=FDAARGOS_994	GCA_016127975.1	43771	43771	type	True	79.8876	291	743	95	below_threshold
Corynebacterium zhongnanshanii	strain=zg-320	GCA_014490575.1	2768834	2768834	type	True	78.7991	240	743	95	below_threshold
Corynebacterium auriscanis	strain=CIP 106629	GCA_000767255.1	99807	99807	type	True	78.4706	199	743	95	below_threshold
Corynebacterium suicordis	strain=DSM 45110	GCA_015351405.1	203264	203264	type	True	78.1045	250	743	95	below_threshold
Corynebacterium gallinarum	strain=Sa1YVA5	GCA_014837045.1	2762214	2762214	type	True	77.5917	166	743	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:05:40,618] [INFO] DFAST Taxonomy check result was written to GCF_027570165.1_ASM2757016v1_genomic.fna/tc_result.tsv
[2024-01-24 11:05:40,619] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:05:40,619] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:05:40,620] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb15f0a74-4626-4d33-a4df-be557cd0081b/dqc_reference/checkm_data
[2024-01-24 11:05:40,621] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:05:40,650] [INFO] Task started: CheckM
[2024-01-24 11:05:40,650] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_027570165.1_ASM2757016v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_027570165.1_ASM2757016v1_genomic.fna/checkm_input GCF_027570165.1_ASM2757016v1_genomic.fna/checkm_result
[2024-01-24 11:06:06,106] [INFO] Task succeeded: CheckM
[2024-01-24 11:06:06,108] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:06:06,129] [INFO] ===== Completeness check finished =====
[2024-01-24 11:06:06,130] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:06:06,130] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_027570165.1_ASM2757016v1_genomic.fna/markers.fasta)
[2024-01-24 11:06:06,131] [INFO] Task started: Blastn
[2024-01-24 11:06:06,131] [INFO] Running command: blastn -query GCF_027570165.1_ASM2757016v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb15f0a74-4626-4d33-a4df-be557cd0081b/dqc_reference/reference_markers_gtdb.fasta -out GCF_027570165.1_ASM2757016v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:07,546] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:07,550] [INFO] Selected 10 target genomes.
[2024-01-24 11:06:07,551] [INFO] Target genome list was writen to GCF_027570165.1_ASM2757016v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:06:07,561] [INFO] Task started: fastANI
[2024-01-24 11:06:07,561] [INFO] Running command: fastANI --query /var/lib/cwl/stgc5fa8f53-b2ac-4bbe-ab78-b71e7fe1c137/GCF_027570165.1_ASM2757016v1_genomic.fna.gz --refList GCF_027570165.1_ASM2757016v1_genomic.fna/target_genomes_gtdb.txt --output GCF_027570165.1_ASM2757016v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:06:12,645] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:12,657] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:06:12,657] [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_000738265.1	s__Corynebacterium jeikeium_A	97.9498	703	743	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.92	97.52	0.95	0.93	11	conclusive
GCF_000738175.1	s__Corynebacterium jeikeium_C	87.7942	663	743	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	87.5314	636	743	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.83	97.75	0.93	0.93	3	-
GCF_000163435.1	s__Corynebacterium jeikeium	87.1949	639	743	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.68	96.00	0.93	0.90	9	-
GCA_000525655.1	s__Corynebacterium falsenii	80.0912	356	743	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.72	98.72	0.95	0.95	2	-
GCF_001815985.1	s__Corynebacterium sp001815985	79.9733	298	743	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	96.95	96.87	0.95	0.94	3	-
GCA_019114175.1	s__Corynebacterium gallistercoris	79.4397	288	743	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	78.7993	239	743	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.40	97.50	0.99	0.97	7	-
GCF_000767255.1	s__Corynebacterium auriscanis	78.4706	199	743	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.87	97.87	0.94	0.94	2	-
GCF_014837045.1	s__Corynebacterium sp014837045	77.5917	166	743	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 11:06:12,659] [INFO] GTDB search result was written to GCF_027570165.1_ASM2757016v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:06:12,659] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:06:12,663] [INFO] DFAST_QC result json was written to GCF_027570165.1_ASM2757016v1_genomic.fna/dqc_result.json
[2024-01-24 11:06:12,663] [INFO] DFAST_QC completed!
[2024-01-24 11:06:12,663] [INFO] Total running time: 0h0m48s