[2024-01-24 12:28:34,525] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:28:34,527] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:28:34,527] [INFO] DQC Reference Directory: /var/lib/cwl/stg2cc1fad3-1a69-4016-946d-440c4e9a32d3/dqc_reference
[2024-01-24 12:28:35,700] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:28:35,701] [INFO] Task started: Prodigal
[2024-01-24 12:28:35,701] [INFO] Running command: gunzip -c /var/lib/cwl/stg5f92fe37-bc39-4437-bb45-50d5be9a6b88/GCF_000819445.1_ASM81944v1_genomic.fna.gz | prodigal -d GCF_000819445.1_ASM81944v1_genomic.fna/cds.fna -a GCF_000819445.1_ASM81944v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:28:43,725] [INFO] Task succeeded: Prodigal
[2024-01-24 12:28:43,726] [INFO] Task started: HMMsearch
[2024-01-24 12:28:43,726] [INFO] Running command: hmmsearch --tblout GCF_000819445.1_ASM81944v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2cc1fad3-1a69-4016-946d-440c4e9a32d3/dqc_reference/reference_markers.hmm GCF_000819445.1_ASM81944v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:28:43,941] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:28:43,943] [INFO] Found 6/6 markers.
[2024-01-24 12:28:43,971] [INFO] Query marker FASTA was written to GCF_000819445.1_ASM81944v1_genomic.fna/markers.fasta
[2024-01-24 12:28:43,972] [INFO] Task started: Blastn
[2024-01-24 12:28:43,972] [INFO] Running command: blastn -query GCF_000819445.1_ASM81944v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2cc1fad3-1a69-4016-946d-440c4e9a32d3/dqc_reference/reference_markers.fasta -out GCF_000819445.1_ASM81944v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:28:45,120] [INFO] Task succeeded: Blastn
[2024-01-24 12:28:45,125] [INFO] Selected 8 target genomes.
[2024-01-24 12:28:45,126] [INFO] Target genome list was writen to GCF_000819445.1_ASM81944v1_genomic.fna/target_genomes.txt
[2024-01-24 12:28:45,169] [INFO] Task started: fastANI
[2024-01-24 12:28:45,169] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f92fe37-bc39-4437-bb45-50d5be9a6b88/GCF_000819445.1_ASM81944v1_genomic.fna.gz --refList GCF_000819445.1_ASM81944v1_genomic.fna/target_genomes.txt --output GCF_000819445.1_ASM81944v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:28:50,322] [INFO] Task succeeded: fastANI
[2024-01-24 12:28:50,323] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2cc1fad3-1a69-4016-946d-440c4e9a32d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:28:50,323] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2cc1fad3-1a69-4016-946d-440c4e9a32d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:28:50,334] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:28:50,334] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:28:50,334] [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 humireducens	strain=DSM 45392	GCA_000819445.1	1223514	1223514	type	True	100.0	893	893	95	conclusive
Corynebacterium humireducens	strain=NBRC 106098	GCA_001571025.1	1223514	1223514	type	True	99.9791	845	893	95	conclusive
Corynebacterium pollutisoli	strain=VDS11	GCA_900177745.1	1610489	1610489	type	True	87.9181	699	893	95	below_threshold
Corynebacterium marinum	strain=DSM 44953	GCA_000835165.1	349751	349751	type	True	84.3635	656	893	95	below_threshold
Corynebacterium marinum	strain=CGMCC 1.6998	GCA_014645275.1	349751	349751	type	True	84.3132	652	893	95	below_threshold
Corynebacterium comes	strain=2019	GCA_009734405.1	2675218	2675218	type	True	83.9049	634	893	95	below_threshold
Corynebacterium halotolerans	strain=YIM 70093 = DSM 44683	GCA_000341345.1	225326	225326	type	True	82.5051	578	893	95	below_threshold
Corynebacterium halotolerans	strain=DSM 44683	GCA_000688435.1	225326	225326	type	True	82.2983	587	893	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:28:50,336] [INFO] DFAST Taxonomy check result was written to GCF_000819445.1_ASM81944v1_genomic.fna/tc_result.tsv
[2024-01-24 12:28:50,336] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:28:50,336] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:28:50,336] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2cc1fad3-1a69-4016-946d-440c4e9a32d3/dqc_reference/checkm_data
[2024-01-24 12:28:50,337] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:28:50,363] [INFO] Task started: CheckM
[2024-01-24 12:28:50,363] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000819445.1_ASM81944v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000819445.1_ASM81944v1_genomic.fna/checkm_input GCF_000819445.1_ASM81944v1_genomic.fna/checkm_result
[2024-01-24 12:29:18,505] [INFO] Task succeeded: CheckM
[2024-01-24 12:29:18,507] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:29:18,528] [INFO] ===== Completeness check finished =====
[2024-01-24 12:29:18,528] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:29:18,528] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000819445.1_ASM81944v1_genomic.fna/markers.fasta)
[2024-01-24 12:29:18,529] [INFO] Task started: Blastn
[2024-01-24 12:29:18,529] [INFO] Running command: blastn -query GCF_000819445.1_ASM81944v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2cc1fad3-1a69-4016-946d-440c4e9a32d3/dqc_reference/reference_markers_gtdb.fasta -out GCF_000819445.1_ASM81944v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:29:20,228] [INFO] Task succeeded: Blastn
[2024-01-24 12:29:20,234] [INFO] Selected 8 target genomes.
[2024-01-24 12:29:20,234] [INFO] Target genome list was writen to GCF_000819445.1_ASM81944v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:29:20,262] [INFO] Task started: fastANI
[2024-01-24 12:29:20,262] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f92fe37-bc39-4437-bb45-50d5be9a6b88/GCF_000819445.1_ASM81944v1_genomic.fna.gz --refList GCF_000819445.1_ASM81944v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000819445.1_ASM81944v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:29:25,585] [INFO] Task succeeded: fastANI
[2024-01-24 12:29:25,595] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:29:25,595] [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_000819445.1	s__Corynebacterium humireducens	100.0	893	893	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.80	97.60	0.97	0.93	3	conclusive
GCA_012838985.1	s__Corynebacterium sp012838985	92.5099	624	893	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177745.1	s__Corynebacterium pollutisoli	87.9132	700	893	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.83	98.83	0.98	0.98	2	-
GCF_000835165.1	s__Corynebacterium marinum	84.3499	657	893	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.21	98.42	0.97	0.94	3	-
GCF_003955685.1	s__Corynebacterium sp003955685	84.1923	634	893	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009734405.1	s__Corynebacterium sp009734405	83.8507	629	893	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000341345.1	s__Corynebacterium halotolerans	82.5484	574	893	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001021045.1	s__Corynebacterium testudinoris	80.2817	499	893	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 12:29:25,597] [INFO] GTDB search result was written to GCF_000819445.1_ASM81944v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:29:25,598] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:29:25,601] [INFO] DFAST_QC result json was written to GCF_000819445.1_ASM81944v1_genomic.fna/dqc_result.json
[2024-01-24 12:29:25,601] [INFO] DFAST_QC completed!
[2024-01-24 12:29:25,601] [INFO] Total running time: 0h0m51s