[2024-01-24 12:36:24,858] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:36:24,860] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:36:24,860] [INFO] DQC Reference Directory: /var/lib/cwl/stg288a1050-8d99-4006-ab96-48c282e59a97/dqc_reference
[2024-01-24 12:36:26,202] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:36:26,203] [INFO] Task started: Prodigal
[2024-01-24 12:36:26,203] [INFO] Running command: gunzip -c /var/lib/cwl/stg563d9405-5d6b-4aa2-8069-c520f4c76c7f/GCF_016342275.1_ASM1634227v1_genomic.fna.gz | prodigal -d GCF_016342275.1_ASM1634227v1_genomic.fna/cds.fna -a GCF_016342275.1_ASM1634227v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:36:34,657] [INFO] Task succeeded: Prodigal
[2024-01-24 12:36:34,658] [INFO] Task started: HMMsearch
[2024-01-24 12:36:34,658] [INFO] Running command: hmmsearch --tblout GCF_016342275.1_ASM1634227v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg288a1050-8d99-4006-ab96-48c282e59a97/dqc_reference/reference_markers.hmm GCF_016342275.1_ASM1634227v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:36:34,900] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:36:34,901] [INFO] Found 6/6 markers.
[2024-01-24 12:36:34,936] [INFO] Query marker FASTA was written to GCF_016342275.1_ASM1634227v1_genomic.fna/markers.fasta
[2024-01-24 12:36:34,936] [INFO] Task started: Blastn
[2024-01-24 12:36:34,936] [INFO] Running command: blastn -query GCF_016342275.1_ASM1634227v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg288a1050-8d99-4006-ab96-48c282e59a97/dqc_reference/reference_markers.fasta -out GCF_016342275.1_ASM1634227v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:36:35,892] [INFO] Task succeeded: Blastn
[2024-01-24 12:36:35,896] [INFO] Selected 22 target genomes.
[2024-01-24 12:36:35,896] [INFO] Target genome list was writen to GCF_016342275.1_ASM1634227v1_genomic.fna/target_genomes.txt
[2024-01-24 12:36:35,906] [INFO] Task started: fastANI
[2024-01-24 12:36:35,907] [INFO] Running command: fastANI --query /var/lib/cwl/stg563d9405-5d6b-4aa2-8069-c520f4c76c7f/GCF_016342275.1_ASM1634227v1_genomic.fna.gz --refList GCF_016342275.1_ASM1634227v1_genomic.fna/target_genomes.txt --output GCF_016342275.1_ASM1634227v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:36:45,743] [INFO] Task succeeded: fastANI
[2024-01-24 12:36:45,744] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg288a1050-8d99-4006-ab96-48c282e59a97/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:36:45,744] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg288a1050-8d99-4006-ab96-48c282e59a97/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:36:45,763] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:36:45,763] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:36:45,764] [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 halotolerans	strain=DSM 44683	GCA_000688435.1	225326	225326	type	True	78.6494	261	933	95	below_threshold
Corynebacterium halotolerans	strain=YIM 70093 = DSM 44683	GCA_000341345.1	225326	225326	type	True	78.6006	271	933	95	below_threshold
Corynebacterium aquilae	strain=S-613	GCA_001941445.1	203263	203263	type	True	78.5862	196	933	95	below_threshold
Corynebacterium humireducens	strain=NBRC 106098	GCA_001571025.1	1223514	1223514	type	True	78.5317	271	933	95	below_threshold
Corynebacterium humireducens	strain=DSM 45392	GCA_000819445.1	1223514	1223514	type	True	78.4417	273	933	95	below_threshold
Corynebacterium marinum	strain=CGMCC 1.6998	GCA_014645275.1	349751	349751	type	True	78.4089	250	933	95	below_threshold
Corynebacterium pollutisoli	strain=VDS11	GCA_900177745.1	1610489	1610489	type	True	78.3699	273	933	95	below_threshold
Corynebacterium marinum	strain=DSM 44953	GCA_000835165.1	349751	349751	type	True	78.3486	255	933	95	below_threshold
Corynebacterium vitaeruminis	strain=DSM 20294	GCA_000550805.1	38305	38305	type	True	78.2871	245	933	95	below_threshold
Corynebacterium bovis	strain=DSM 20582	GCA_000183325.2	36808	36808	type	True	78.0451	163	933	95	below_threshold
Corynebacterium frankenforstense	strain=ST18	GCA_001941485.1	1230998	1230998	type	True	77.9429	248	933	95	below_threshold
Corynebacterium efficiens	strain=YS-314	GCA_000160795.1	152794	152794	type	True	77.8912	224	933	95	below_threshold
Corynebacterium bovis	strain=DSM 20582	GCA_014191555.1	36808	36808	type	True	77.881	189	933	95	below_threshold
Corynebacterium bovis	strain=FDAARGOS_1052	GCA_016128075.1	36808	36808	type	True	77.8494	187	933	95	below_threshold
Corynebacterium gallinarum	strain=Sa1YVA5	GCA_014837045.1	2762214	2762214	type	True	77.8476	222	933	95	below_threshold
Corynebacterium efficiens	strain=YS-314	GCA_000011305.1	152794	152794	type	True	77.8475	220	933	95	below_threshold
Corynebacterium yudongzhengii	strain=2183	GCA_003065405.1	2080740	2080740	type	True	77.6899	176	933	95	below_threshold
Corynebacterium terpenotabidum	strain=Y-11	GCA_000418365.1	89154	89154	type	True	77.6327	167	933	95	below_threshold
Corynebacterium mastitidis	strain=DSM 44356	GCA_000375365.1	161890	161890	type	True	77.3114	176	933	95	below_threshold
Streptoalloteichus tenebrarius	strain=DSM 40477	GCA_024171885.1	1933	1933	type	True	76.3799	97	933	95	below_threshold
Curtobacterium luteum	strain=JCM 1480	GCA_014646995.1	33881	33881	type	True	75.9931	65	933	95	below_threshold
Agromyces archimandritae	strain=G127AT	GCA_018024495.1	2781962	2781962	type	True	75.9623	81	933	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:36:45,765] [INFO] DFAST Taxonomy check result was written to GCF_016342275.1_ASM1634227v1_genomic.fna/tc_result.tsv
[2024-01-24 12:36:45,766] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:36:45,766] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:36:45,766] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg288a1050-8d99-4006-ab96-48c282e59a97/dqc_reference/checkm_data
[2024-01-24 12:36:45,767] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:36:45,795] [INFO] Task started: CheckM
[2024-01-24 12:36:45,795] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016342275.1_ASM1634227v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016342275.1_ASM1634227v1_genomic.fna/checkm_input GCF_016342275.1_ASM1634227v1_genomic.fna/checkm_result
[2024-01-24 12:37:14,531] [INFO] Task succeeded: CheckM
[2024-01-24 12:37:14,532] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:37:14,555] [INFO] ===== Completeness check finished =====
[2024-01-24 12:37:14,555] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:37:14,556] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016342275.1_ASM1634227v1_genomic.fna/markers.fasta)
[2024-01-24 12:37:14,556] [INFO] Task started: Blastn
[2024-01-24 12:37:14,556] [INFO] Running command: blastn -query GCF_016342275.1_ASM1634227v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg288a1050-8d99-4006-ab96-48c282e59a97/dqc_reference/reference_markers_gtdb.fasta -out GCF_016342275.1_ASM1634227v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:15,879] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:15,885] [INFO] Selected 10 target genomes.
[2024-01-24 12:37:15,885] [INFO] Target genome list was writen to GCF_016342275.1_ASM1634227v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:37:15,899] [INFO] Task started: fastANI
[2024-01-24 12:37:15,900] [INFO] Running command: fastANI --query /var/lib/cwl/stg563d9405-5d6b-4aa2-8069-c520f4c76c7f/GCF_016342275.1_ASM1634227v1_genomic.fna.gz --refList GCF_016342275.1_ASM1634227v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016342275.1_ASM1634227v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:37:21,602] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:21,615] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:37:21,616] [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_016342275.1	s__Corynebacterium sp016342275	100.0	933	933	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016342265.1	s__Corynebacterium sp016342265	87.5656	794	933	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019209935.1	s__Corynebacterium sp019209935	87.5632	757	933	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	95.84	95.84	0.96	0.96	2	-
GCF_016595275.1	s__Corynebacterium sp016595275	85.2076	728	933	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002994655.1	s__Corynebacterium sp002994655	78.6179	225	933	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000819445.1	s__Corynebacterium humireducens	78.4417	273	933	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.80	97.60	0.97	0.93	3	-
GCF_900177745.1	s__Corynebacterium pollutisoli	78.3841	272	933	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.83	98.83	0.98	0.98	2	-
GCF_000011305.1	s__Corynebacterium efficiens	77.8475	220	933	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.90	99.90	0.99	0.99	2	-
GCF_000418365.1	s__Corynebacterium terpenotabidum	77.6327	167	933	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873635.1	s__Nocardioides sp014873635	76.2503	80	933	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:37:21,617] [INFO] GTDB search result was written to GCF_016342275.1_ASM1634227v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:37:21,618] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:37:21,621] [INFO] DFAST_QC result json was written to GCF_016342275.1_ASM1634227v1_genomic.fna/dqc_result.json
[2024-01-24 12:37:21,621] [INFO] DFAST_QC completed!
[2024-01-24 12:37:21,621] [INFO] Total running time: 0h0m57s