[2024-01-25 20:20:05,889] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:20:05,890] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:20:05,891] [INFO] DQC Reference Directory: /var/lib/cwl/stgd24b22dc-469f-400e-ad41-40f5b2fda84b/dqc_reference
[2024-01-25 20:20:07,240] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:20:07,243] [INFO] Task started: Prodigal
[2024-01-25 20:20:07,243] [INFO] Running command: gunzip -c /var/lib/cwl/stg6b01dfe8-cb8e-40ad-b100-cec1badaf429/GCF_000411375.1_Cory_pyru_17730_V1_genomic.fna.gz | prodigal -d GCF_000411375.1_Cory_pyru_17730_V1_genomic.fna/cds.fna -a GCF_000411375.1_Cory_pyru_17730_V1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:20:15,390] [INFO] Task succeeded: Prodigal
[2024-01-25 20:20:15,391] [INFO] Task started: HMMsearch
[2024-01-25 20:20:15,391] [INFO] Running command: hmmsearch --tblout GCF_000411375.1_Cory_pyru_17730_V1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd24b22dc-469f-400e-ad41-40f5b2fda84b/dqc_reference/reference_markers.hmm GCF_000411375.1_Cory_pyru_17730_V1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:20:15,576] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:20:15,578] [INFO] Found 6/6 markers.
[2024-01-25 20:20:15,601] [INFO] Query marker FASTA was written to GCF_000411375.1_Cory_pyru_17730_V1_genomic.fna/markers.fasta
[2024-01-25 20:20:15,601] [INFO] Task started: Blastn
[2024-01-25 20:20:15,601] [INFO] Running command: blastn -query GCF_000411375.1_Cory_pyru_17730_V1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd24b22dc-469f-400e-ad41-40f5b2fda84b/dqc_reference/reference_markers.fasta -out GCF_000411375.1_Cory_pyru_17730_V1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:20:16,454] [INFO] Task succeeded: Blastn
[2024-01-25 20:20:16,456] [INFO] Selected 11 target genomes.
[2024-01-25 20:20:16,457] [INFO] Target genome list was writen to GCF_000411375.1_Cory_pyru_17730_V1_genomic.fna/target_genomes.txt
[2024-01-25 20:20:16,469] [INFO] Task started: fastANI
[2024-01-25 20:20:16,469] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b01dfe8-cb8e-40ad-b100-cec1badaf429/GCF_000411375.1_Cory_pyru_17730_V1_genomic.fna.gz --refList GCF_000411375.1_Cory_pyru_17730_V1_genomic.fna/target_genomes.txt --output GCF_000411375.1_Cory_pyru_17730_V1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:20:22,507] [INFO] Task succeeded: fastANI
[2024-01-25 20:20:22,507] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd24b22dc-469f-400e-ad41-40f5b2fda84b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:20:22,507] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd24b22dc-469f-400e-ad41-40f5b2fda84b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:20:22,515] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:20:22,516] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:20:22,516] [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 pyruviciproducens	strain=ATCC BAA-1742	GCA_000411375.1	598660	598660	type	True	99.9987	901	906	95	conclusive
Corynebacterium glucuronolyticum	strain=FDAARGOS_1053	GCA_016127395.1	39791	39791	type	True	82.722	550	906	95	below_threshold
Corynebacterium glucuronolyticum	strain=DSM 44120	GCA_900176155.1	39791	39791	type	True	82.4239	540	906	95	below_threshold
Corynebacterium glucuronolyticum	strain=DSM 44120	GCA_019633635.1	39791	39791	type	True	82.4237	541	906	95	below_threshold
Corynebacterium jeikeium	strain=NCTC11913	GCA_900461185.1	38289	38289	suspected-type	True	78.4278	124	906	95	below_threshold
Corynebacterium vitaeruminis	strain=DSM 20294	GCA_000550805.1	38305	38305	type	True	78.4088	219	906	95	below_threshold
Corynebacterium jeikeium	strain=ATCC 43734	GCA_000163435.1	38289	38289	suspected-type	True	78.1148	125	906	95	below_threshold
Corynebacterium doosanense	strain=CAU 212	GCA_000767055.1	1121358	1121358	type	True	78.0529	191	906	95	below_threshold
Corynebacterium jeikeium	strain=ATCC 43734	GCA_001999385.1	38289	38289	suspected-type	True	78.0295	118	906	95	below_threshold
Corynebacterium humireducens	strain=NBRC 106098	GCA_001571025.1	1223514	1223514	type	True	77.877	198	906	95	below_threshold
Streptomyces gougerotii	strain=JCM 4136	GCA_014648955.1	53448	53448	suspected-type	True	75.5729	73	906	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:20:22,517] [INFO] DFAST Taxonomy check result was written to GCF_000411375.1_Cory_pyru_17730_V1_genomic.fna/tc_result.tsv
[2024-01-25 20:20:22,518] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:20:22,518] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:20:22,518] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd24b22dc-469f-400e-ad41-40f5b2fda84b/dqc_reference/checkm_data
[2024-01-25 20:20:22,519] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:20:22,547] [INFO] Task started: CheckM
[2024-01-25 20:20:22,547] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000411375.1_Cory_pyru_17730_V1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000411375.1_Cory_pyru_17730_V1_genomic.fna/checkm_input GCF_000411375.1_Cory_pyru_17730_V1_genomic.fna/checkm_result
[2024-01-25 20:20:48,774] [INFO] Task succeeded: CheckM
[2024-01-25 20:20:48,775] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:20:48,794] [INFO] ===== Completeness check finished =====
[2024-01-25 20:20:48,795] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:20:48,795] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000411375.1_Cory_pyru_17730_V1_genomic.fna/markers.fasta)
[2024-01-25 20:20:48,795] [INFO] Task started: Blastn
[2024-01-25 20:20:48,795] [INFO] Running command: blastn -query GCF_000411375.1_Cory_pyru_17730_V1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd24b22dc-469f-400e-ad41-40f5b2fda84b/dqc_reference/reference_markers_gtdb.fasta -out GCF_000411375.1_Cory_pyru_17730_V1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:20:50,081] [INFO] Task succeeded: Blastn
[2024-01-25 20:20:50,086] [INFO] Selected 15 target genomes.
[2024-01-25 20:20:50,086] [INFO] Target genome list was writen to GCF_000411375.1_Cory_pyru_17730_V1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:20:50,102] [INFO] Task started: fastANI
[2024-01-25 20:20:50,103] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b01dfe8-cb8e-40ad-b100-cec1badaf429/GCF_000411375.1_Cory_pyru_17730_V1_genomic.fna.gz --refList GCF_000411375.1_Cory_pyru_17730_V1_genomic.fna/target_genomes_gtdb.txt --output GCF_000411375.1_Cory_pyru_17730_V1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:20:59,015] [INFO] Task succeeded: fastANI
[2024-01-25 20:20:59,024] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:20:59,025] [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_000411375.1	s__Corynebacterium pyruviciproducens	99.9987	901	906	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.67	97.67	0.91	0.91	2	conclusive
GCF_900176155.1	s__Corynebacterium glucuronolyticum	82.4239	540	906	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.97	98.66	0.94	0.91	8	-
GCF_000550805.1	s__Corynebacterium vitaeruminis	78.4459	220	906	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.86	98.60	0.94	0.94	3	-
GCF_000819445.1	s__Corynebacterium humireducens	78.2289	206	906	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.80	97.60	0.97	0.93	3	-
GCF_001941485.1	s__Corynebacterium frankenforstense	78.168	204	906	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	78.1131	125	906	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.68	96.00	0.93	0.90	9	-
GCF_000767055.1	s__Corynebacterium doosanense	78.1055	193	906	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001941445.1	s__Corynebacterium aquilae	78.0589	132	906	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016728705.1	s__Corynebacterium sp001807205	77.7968	145	906	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.15	96.83	0.93	0.90	8	-
GCF_001807485.1	s__Corynebacterium sp001807485	77.7885	126	906	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.83	97.75	0.93	0.93	3	-
GCF_002994655.1	s__Corynebacterium sp002994655	77.756	163	906	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_903645305.1	s__Corynebacterium sp001764565	77.6449	167	906	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.10	98.10	0.96	0.96	2	-
GCF_011170125.1	s__Streptomyces diastaticus	76.3047	77	906	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.51	98.72	0.93	0.90	11	-
GCF_014648195.1	s__Streptomyces purpureus	75.7449	75	906	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.54	99.54	0.95	0.95	2	-
GCF_001426585.1	s__Streptomyces sp001426585	75.6558	77	906	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.07	96.69	0.91	0.88	3	-
--------------------------------------------------------------------------------
[2024-01-25 20:20:59,026] [INFO] GTDB search result was written to GCF_000411375.1_Cory_pyru_17730_V1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:20:59,027] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:20:59,030] [INFO] DFAST_QC result json was written to GCF_000411375.1_Cory_pyru_17730_V1_genomic.fna/dqc_result.json
[2024-01-25 20:20:59,031] [INFO] DFAST_QC completed!
[2024-01-25 20:20:59,031] [INFO] Total running time: 0h0m53s