[2024-01-24 13:17:11,458] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:11,466] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:11,466] [INFO] DQC Reference Directory: /var/lib/cwl/stg2cebf744-27bd-4f57-a836-dc549bfc80a9/dqc_reference
[2024-01-24 13:17:12,632] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:12,633] [INFO] Task started: Prodigal
[2024-01-24 13:17:12,633] [INFO] Running command: gunzip -c /var/lib/cwl/stgf565528b-3a0e-41df-a1ff-c8bbf7dcffdb/GCF_001643015.1_ASM164301v1_genomic.fna.gz | prodigal -d GCF_001643015.1_ASM164301v1_genomic.fna/cds.fna -a GCF_001643015.1_ASM164301v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:22,711] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:22,711] [INFO] Task started: HMMsearch
[2024-01-24 13:17:22,711] [INFO] Running command: hmmsearch --tblout GCF_001643015.1_ASM164301v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2cebf744-27bd-4f57-a836-dc549bfc80a9/dqc_reference/reference_markers.hmm GCF_001643015.1_ASM164301v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:22,939] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:22,940] [INFO] Found 6/6 markers.
[2024-01-24 13:17:22,969] [INFO] Query marker FASTA was written to GCF_001643015.1_ASM164301v1_genomic.fna/markers.fasta
[2024-01-24 13:17:22,969] [INFO] Task started: Blastn
[2024-01-24 13:17:22,970] [INFO] Running command: blastn -query GCF_001643015.1_ASM164301v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2cebf744-27bd-4f57-a836-dc549bfc80a9/dqc_reference/reference_markers.fasta -out GCF_001643015.1_ASM164301v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:23,734] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:23,742] [INFO] Selected 6 target genomes.
[2024-01-24 13:17:23,742] [INFO] Target genome list was writen to GCF_001643015.1_ASM164301v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:23,749] [INFO] Task started: fastANI
[2024-01-24 13:17:23,749] [INFO] Running command: fastANI --query /var/lib/cwl/stgf565528b-3a0e-41df-a1ff-c8bbf7dcffdb/GCF_001643015.1_ASM164301v1_genomic.fna.gz --refList GCF_001643015.1_ASM164301v1_genomic.fna/target_genomes.txt --output GCF_001643015.1_ASM164301v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:28,198] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:28,199] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2cebf744-27bd-4f57-a836-dc549bfc80a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:28,200] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2cebf744-27bd-4f57-a836-dc549bfc80a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:28,211] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:17:28,211] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:17:28,211] [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 crudilactis	strain=JZ16	GCA_001643015.1	1652495	1652495	type	True	100.0	1067	1071	95	conclusive
Corynebacterium glutamicum	strain=ATCC 13032	GCA_011761195.1	1718	1718	type	True	84.1115	750	1071	95	below_threshold
Corynebacterium glutamicum	strain=ATCC 13032	GCA_000011325.1	1718	1718	type	True	84.0823	753	1071	95	below_threshold
Corynebacterium glutamicum	strain=ATCC 13032	GCA_002847405.1	1718	1718	type	True	84.068	751	1071	95	below_threshold
Corynebacterium glutamicum	strain=ATCC 13032 substr. K051	GCA_000382905.1	1718	1718	type	True	84.0445	753	1071	95	below_threshold
Corynebacterium suranareeae	strain=N24	GCA_002355155.1	2506452	2506452	type	True	82.6692	735	1071	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:17:28,214] [INFO] DFAST Taxonomy check result was written to GCF_001643015.1_ASM164301v1_genomic.fna/tc_result.tsv
[2024-01-24 13:17:28,214] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:28,214] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:28,215] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2cebf744-27bd-4f57-a836-dc549bfc80a9/dqc_reference/checkm_data
[2024-01-24 13:17:28,215] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:28,250] [INFO] Task started: CheckM
[2024-01-24 13:17:28,250] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001643015.1_ASM164301v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001643015.1_ASM164301v1_genomic.fna/checkm_input GCF_001643015.1_ASM164301v1_genomic.fna/checkm_result
[2024-01-24 13:18:02,452] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:02,454] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:02,474] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:02,474] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:02,475] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001643015.1_ASM164301v1_genomic.fna/markers.fasta)
[2024-01-24 13:18:02,475] [INFO] Task started: Blastn
[2024-01-24 13:18:02,476] [INFO] Running command: blastn -query GCF_001643015.1_ASM164301v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2cebf744-27bd-4f57-a836-dc549bfc80a9/dqc_reference/reference_markers_gtdb.fasta -out GCF_001643015.1_ASM164301v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:03,519] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:03,525] [INFO] Selected 8 target genomes.
[2024-01-24 13:18:03,525] [INFO] Target genome list was writen to GCF_001643015.1_ASM164301v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:03,552] [INFO] Task started: fastANI
[2024-01-24 13:18:03,552] [INFO] Running command: fastANI --query /var/lib/cwl/stgf565528b-3a0e-41df-a1ff-c8bbf7dcffdb/GCF_001643015.1_ASM164301v1_genomic.fna.gz --refList GCF_001643015.1_ASM164301v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001643015.1_ASM164301v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:18:08,745] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:08,761] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:18:08,761] [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_001643015.1	s__Corynebacterium crudilactis	100.0	1066	1071	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_000011325.1	s__Corynebacterium glutamicum	84.052	755	1071	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.67	97.34	0.92	0.85	76	-
GCF_002355155.1	s__Corynebacterium suranareeae	82.667	735	1071	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001277995.1	s__Corynebacterium deserti	81.1745	544	1071	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000344785.1	s__Corynebacterium callunae	80.0056	428	1071	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000011305.1	s__Corynebacterium efficiens	78.9404	275	1071	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.90	99.90	0.99	0.99	2	-
GCF_014837045.1	s__Corynebacterium sp014837045	78.9101	265	1071	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902702935.1	s__Corynebacterium rouxii	78.8214	96	1071	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 13:18:08,763] [INFO] GTDB search result was written to GCF_001643015.1_ASM164301v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:18:08,764] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:18:08,767] [INFO] DFAST_QC result json was written to GCF_001643015.1_ASM164301v1_genomic.fna/dqc_result.json
[2024-01-24 13:18:08,768] [INFO] DFAST_QC completed!
[2024-01-24 13:18:08,768] [INFO] Total running time: 0h0m57s