[2024-01-24 12:54:05,549] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:54:05,551] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:54:05,551] [INFO] DQC Reference Directory: /var/lib/cwl/stg39d0b9a9-19ac-4d8b-833e-c1da197de649/dqc_reference
[2024-01-24 12:54:06,900] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:54:06,901] [INFO] Task started: Prodigal
[2024-01-24 12:54:06,901] [INFO] Running command: gunzip -c /var/lib/cwl/stgdc7b2b25-852e-42b6-9ea1-9ef69e302bbf/GCF_018704065.1_ASM1870406v1_genomic.fna.gz | prodigal -d GCF_018704065.1_ASM1870406v1_genomic.fna/cds.fna -a GCF_018704065.1_ASM1870406v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:54:12,577] [INFO] Task succeeded: Prodigal
[2024-01-24 12:54:12,577] [INFO] Task started: HMMsearch
[2024-01-24 12:54:12,578] [INFO] Running command: hmmsearch --tblout GCF_018704065.1_ASM1870406v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg39d0b9a9-19ac-4d8b-833e-c1da197de649/dqc_reference/reference_markers.hmm GCF_018704065.1_ASM1870406v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:54:12,867] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:54:12,868] [INFO] Found 6/6 markers.
[2024-01-24 12:54:12,896] [INFO] Query marker FASTA was written to GCF_018704065.1_ASM1870406v1_genomic.fna/markers.fasta
[2024-01-24 12:54:12,897] [INFO] Task started: Blastn
[2024-01-24 12:54:12,897] [INFO] Running command: blastn -query GCF_018704065.1_ASM1870406v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg39d0b9a9-19ac-4d8b-833e-c1da197de649/dqc_reference/reference_markers.fasta -out GCF_018704065.1_ASM1870406v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:13,482] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:13,489] [INFO] Selected 15 target genomes.
[2024-01-24 12:54:13,490] [INFO] Target genome list was writen to GCF_018704065.1_ASM1870406v1_genomic.fna/target_genomes.txt
[2024-01-24 12:54:13,630] [INFO] Task started: fastANI
[2024-01-24 12:54:13,630] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc7b2b25-852e-42b6-9ea1-9ef69e302bbf/GCF_018704065.1_ASM1870406v1_genomic.fna.gz --refList GCF_018704065.1_ASM1870406v1_genomic.fna/target_genomes.txt --output GCF_018704065.1_ASM1870406v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:54:23,561] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:23,561] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg39d0b9a9-19ac-4d8b-833e-c1da197de649/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:54:23,562] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg39d0b9a9-19ac-4d8b-833e-c1da197de649/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:54:23,566] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:54:23,567] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:54:23,567] [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
Desulfovulcanus ferrireducens	strain=Ax17	GCA_018704065.1	2831190	2831190	type	True	99.9799	829	830	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 12:54:23,569] [INFO] DFAST Taxonomy check result was written to GCF_018704065.1_ASM1870406v1_genomic.fna/tc_result.tsv
[2024-01-24 12:54:23,570] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:54:23,570] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:54:23,570] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg39d0b9a9-19ac-4d8b-833e-c1da197de649/dqc_reference/checkm_data
[2024-01-24 12:54:23,571] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:54:23,611] [INFO] Task started: CheckM
[2024-01-24 12:54:23,612] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018704065.1_ASM1870406v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018704065.1_ASM1870406v1_genomic.fna/checkm_input GCF_018704065.1_ASM1870406v1_genomic.fna/checkm_result
[2024-01-24 12:54:47,792] [INFO] Task succeeded: CheckM
[2024-01-24 12:54:47,793] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:54:47,809] [INFO] ===== Completeness check finished =====
[2024-01-24 12:54:47,809] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:54:47,810] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018704065.1_ASM1870406v1_genomic.fna/markers.fasta)
[2024-01-24 12:54:47,810] [INFO] Task started: Blastn
[2024-01-24 12:54:47,810] [INFO] Running command: blastn -query GCF_018704065.1_ASM1870406v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg39d0b9a9-19ac-4d8b-833e-c1da197de649/dqc_reference/reference_markers_gtdb.fasta -out GCF_018704065.1_ASM1870406v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:48,632] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:48,636] [INFO] Selected 21 target genomes.
[2024-01-24 12:54:48,636] [INFO] Target genome list was writen to GCF_018704065.1_ASM1870406v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:54:48,685] [INFO] Task started: fastANI
[2024-01-24 12:54:48,685] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc7b2b25-852e-42b6-9ea1-9ef69e302bbf/GCF_018704065.1_ASM1870406v1_genomic.fna.gz --refList GCF_018704065.1_ASM1870406v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018704065.1_ASM1870406v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:55:02,475] [INFO] Task succeeded: fastANI
[2024-01-24 12:55:02,480] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:55:02,480] [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_018704065.1	s__Ax17 sp018704065	99.9799	829	830	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfonauticaceae;g__Ax17	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_001507915.1	s__Desulfonauticus sp001507915	78.7832	55	830	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfonauticaceae;g__Desulfonauticus	95.0	98.09	98.09	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:55:02,482] [INFO] GTDB search result was written to GCF_018704065.1_ASM1870406v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:55:02,484] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:55:02,487] [INFO] DFAST_QC result json was written to GCF_018704065.1_ASM1870406v1_genomic.fna/dqc_result.json
[2024-01-24 12:55:02,487] [INFO] DFAST_QC completed!
[2024-01-24 12:55:02,487] [INFO] Total running time: 0h0m57s