[2024-01-24 13:25:47,360] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:25:47,362] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:25:47,364] [INFO] DQC Reference Directory: /var/lib/cwl/stgabfbe2c6-57ba-43f7-b8aa-c2ce0e1eb079/dqc_reference
[2024-01-24 13:25:48,763] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:25:48,764] [INFO] Task started: Prodigal
[2024-01-24 13:25:48,764] [INFO] Running command: gunzip -c /var/lib/cwl/stg4f3c0442-7392-4a0a-acfc-0d60f90746f5/GCF_014384795.1_ASM1438479v1_genomic.fna.gz | prodigal -d GCF_014384795.1_ASM1438479v1_genomic.fna/cds.fna -a GCF_014384795.1_ASM1438479v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:25:55,872] [INFO] Task succeeded: Prodigal
[2024-01-24 13:25:55,872] [INFO] Task started: HMMsearch
[2024-01-24 13:25:55,872] [INFO] Running command: hmmsearch --tblout GCF_014384795.1_ASM1438479v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgabfbe2c6-57ba-43f7-b8aa-c2ce0e1eb079/dqc_reference/reference_markers.hmm GCF_014384795.1_ASM1438479v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:25:56,137] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:25:56,138] [INFO] Found 6/6 markers.
[2024-01-24 13:25:56,161] [INFO] Query marker FASTA was written to GCF_014384795.1_ASM1438479v1_genomic.fna/markers.fasta
[2024-01-24 13:25:56,162] [INFO] Task started: Blastn
[2024-01-24 13:25:56,162] [INFO] Running command: blastn -query GCF_014384795.1_ASM1438479v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgabfbe2c6-57ba-43f7-b8aa-c2ce0e1eb079/dqc_reference/reference_markers.fasta -out GCF_014384795.1_ASM1438479v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:56,782] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:56,785] [INFO] Selected 22 target genomes.
[2024-01-24 13:25:56,786] [INFO] Target genome list was writen to GCF_014384795.1_ASM1438479v1_genomic.fna/target_genomes.txt
[2024-01-24 13:25:56,794] [INFO] Task started: fastANI
[2024-01-24 13:25:56,794] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f3c0442-7392-4a0a-acfc-0d60f90746f5/GCF_014384795.1_ASM1438479v1_genomic.fna.gz --refList GCF_014384795.1_ASM1438479v1_genomic.fna/target_genomes.txt --output GCF_014384795.1_ASM1438479v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:26:12,237] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:12,237] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgabfbe2c6-57ba-43f7-b8aa-c2ce0e1eb079/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:26:12,238] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgabfbe2c6-57ba-43f7-b8aa-c2ce0e1eb079/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:26:12,242] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:26:12,242] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:26:12,242] [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
Gehongia tenuis	strain=NSJ-53	GCA_014384795.1	2763655	2763655	type	True	100.0	734	734	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 13:26:12,244] [INFO] DFAST Taxonomy check result was written to GCF_014384795.1_ASM1438479v1_genomic.fna/tc_result.tsv
[2024-01-24 13:26:12,244] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:26:12,244] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:26:12,245] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgabfbe2c6-57ba-43f7-b8aa-c2ce0e1eb079/dqc_reference/checkm_data
[2024-01-24 13:26:12,246] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:26:12,270] [INFO] Task started: CheckM
[2024-01-24 13:26:12,271] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014384795.1_ASM1438479v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014384795.1_ASM1438479v1_genomic.fna/checkm_input GCF_014384795.1_ASM1438479v1_genomic.fna/checkm_result
[2024-01-24 13:26:38,387] [INFO] Task succeeded: CheckM
[2024-01-24 13:26:38,388] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:26:38,404] [INFO] ===== Completeness check finished =====
[2024-01-24 13:26:38,404] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:26:38,405] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014384795.1_ASM1438479v1_genomic.fna/markers.fasta)
[2024-01-24 13:26:38,405] [INFO] Task started: Blastn
[2024-01-24 13:26:38,405] [INFO] Running command: blastn -query GCF_014384795.1_ASM1438479v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgabfbe2c6-57ba-43f7-b8aa-c2ce0e1eb079/dqc_reference/reference_markers_gtdb.fasta -out GCF_014384795.1_ASM1438479v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:39,342] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:39,347] [INFO] Selected 30 target genomes.
[2024-01-24 13:26:39,347] [INFO] Target genome list was writen to GCF_014384795.1_ASM1438479v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:26:39,418] [INFO] Task started: fastANI
[2024-01-24 13:26:39,419] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f3c0442-7392-4a0a-acfc-0d60f90746f5/GCF_014384795.1_ASM1438479v1_genomic.fna.gz --refList GCF_014384795.1_ASM1438479v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014384795.1_ASM1438479v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:26:52,864] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:52,870] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:26:52,870] [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
GCA_014384795.1	s__NSJ-53 sp014384795	100.0	734	734	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__NSJ-53;g__NSJ-53	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017512905.1	s__UBA2862 sp017512905	76.5575	53	734	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA2862	95.0	98.42	98.42	0.84	0.84	2	-
GCA_904393115.1	s__Spyradocola merdavium	76.5515	65	734	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__UBA1750;g__Spyradocola	95.0	98.74	98.61	0.95	0.94	8	-
--------------------------------------------------------------------------------
[2024-01-24 13:26:52,872] [INFO] GTDB search result was written to GCF_014384795.1_ASM1438479v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:26:52,872] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:26:52,874] [INFO] DFAST_QC result json was written to GCF_014384795.1_ASM1438479v1_genomic.fna/dqc_result.json
[2024-01-24 13:26:52,874] [INFO] DFAST_QC completed!
[2024-01-24 13:26:52,874] [INFO] Total running time: 0h1m6s