[2024-01-24 12:42:07,805] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:42:07,807] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:42:07,807] [INFO] DQC Reference Directory: /var/lib/cwl/stga1237cce-99a4-441b-ac93-544682ebe5a1/dqc_reference
[2024-01-24 12:42:09,094] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:42:09,095] [INFO] Task started: Prodigal
[2024-01-24 12:42:09,096] [INFO] Running command: gunzip -c /var/lib/cwl/stg11041442-b5ec-4d49-896d-2bd1317496f7/GCF_000421585.1_ASM42158v1_genomic.fna.gz | prodigal -d GCF_000421585.1_ASM42158v1_genomic.fna/cds.fna -a GCF_000421585.1_ASM42158v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:42:14,282] [INFO] Task succeeded: Prodigal
[2024-01-24 12:42:14,282] [INFO] Task started: HMMsearch
[2024-01-24 12:42:14,283] [INFO] Running command: hmmsearch --tblout GCF_000421585.1_ASM42158v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga1237cce-99a4-441b-ac93-544682ebe5a1/dqc_reference/reference_markers.hmm GCF_000421585.1_ASM42158v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:42:14,550] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:42:14,551] [INFO] Found 6/6 markers.
[2024-01-24 12:42:14,575] [INFO] Query marker FASTA was written to GCF_000421585.1_ASM42158v1_genomic.fna/markers.fasta
[2024-01-24 12:42:14,576] [INFO] Task started: Blastn
[2024-01-24 12:42:14,576] [INFO] Running command: blastn -query GCF_000421585.1_ASM42158v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga1237cce-99a4-441b-ac93-544682ebe5a1/dqc_reference/reference_markers.fasta -out GCF_000421585.1_ASM42158v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:42:15,163] [INFO] Task succeeded: Blastn
[2024-01-24 12:42:15,166] [INFO] Selected 15 target genomes.
[2024-01-24 12:42:15,167] [INFO] Target genome list was writen to GCF_000421585.1_ASM42158v1_genomic.fna/target_genomes.txt
[2024-01-24 12:42:15,187] [INFO] Task started: fastANI
[2024-01-24 12:42:15,187] [INFO] Running command: fastANI --query /var/lib/cwl/stg11041442-b5ec-4d49-896d-2bd1317496f7/GCF_000421585.1_ASM42158v1_genomic.fna.gz --refList GCF_000421585.1_ASM42158v1_genomic.fna/target_genomes.txt --output GCF_000421585.1_ASM42158v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:42:23,395] [INFO] Task succeeded: fastANI
[2024-01-24 12:42:23,395] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga1237cce-99a4-441b-ac93-544682ebe5a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:42:23,395] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga1237cce-99a4-441b-ac93-544682ebe5a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:42:23,400] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:42:23,400] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:42:23,400] [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
Thermodesulfatator atlanticus	strain=DSM 21156	GCA_000421585.1	501497	501497	type	True	100.0	735	739	95	conclusive
Thermodesulfatator autotrophicus	strain=S606	GCA_001642325.1	1795632	1795632	type	True	77.2949	184	739	95	below_threshold
Thermodesulfatator indicus	strain=DSM 15286	GCA_000217795.1	171695	171695	type	True	77.2502	173	739	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:42:23,402] [INFO] DFAST Taxonomy check result was written to GCF_000421585.1_ASM42158v1_genomic.fna/tc_result.tsv
[2024-01-24 12:42:23,402] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:42:23,403] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:42:23,403] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga1237cce-99a4-441b-ac93-544682ebe5a1/dqc_reference/checkm_data
[2024-01-24 12:42:23,404] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:42:23,433] [INFO] Task started: CheckM
[2024-01-24 12:42:23,434] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000421585.1_ASM42158v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000421585.1_ASM42158v1_genomic.fna/checkm_input GCF_000421585.1_ASM42158v1_genomic.fna/checkm_result
[2024-01-24 12:42:45,509] [INFO] Task succeeded: CheckM
[2024-01-24 12:42:45,511] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:42:45,532] [INFO] ===== Completeness check finished =====
[2024-01-24 12:42:45,532] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:42:45,533] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000421585.1_ASM42158v1_genomic.fna/markers.fasta)
[2024-01-24 12:42:45,533] [INFO] Task started: Blastn
[2024-01-24 12:42:45,533] [INFO] Running command: blastn -query GCF_000421585.1_ASM42158v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga1237cce-99a4-441b-ac93-544682ebe5a1/dqc_reference/reference_markers_gtdb.fasta -out GCF_000421585.1_ASM42158v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:42:46,360] [INFO] Task succeeded: Blastn
[2024-01-24 12:42:46,363] [INFO] Selected 18 target genomes.
[2024-01-24 12:42:46,364] [INFO] Target genome list was writen to GCF_000421585.1_ASM42158v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:42:46,400] [INFO] Task started: fastANI
[2024-01-24 12:42:46,400] [INFO] Running command: fastANI --query /var/lib/cwl/stg11041442-b5ec-4d49-896d-2bd1317496f7/GCF_000421585.1_ASM42158v1_genomic.fna.gz --refList GCF_000421585.1_ASM42158v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000421585.1_ASM42158v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:42:56,877] [INFO] Task succeeded: fastANI
[2024-01-24 12:42:56,883] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:42:56,883] [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_000421585.1	s__Thermodesulfatator atlanticus	100.0	735	739	d__Bacteria;p__Desulfobacterota;c__Thermodesulfobacteria;o__Thermodesulfobacteriales;f__Thermodesulfatatoraceae;g__Thermodesulfatator	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001642325.1	s__Thermodesulfatator autotrophicus	77.2949	184	739	d__Bacteria;p__Desulfobacterota;c__Thermodesulfobacteria;o__Thermodesulfobacteriales;f__Thermodesulfatatoraceae;g__Thermodesulfatator	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000217795.1	s__Thermodesulfatator indicus	77.2509	173	739	d__Bacteria;p__Desulfobacterota;c__Thermodesulfobacteria;o__Thermodesulfobacteriales;f__Thermodesulfatatoraceae;g__Thermodesulfatator	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013153725.1	s__Thermodesulfatator_A sp013153725	76.6108	64	739	d__Bacteria;p__Desulfobacterota;c__Thermodesulfobacteria;o__Thermodesulfobacteriales;f__Thermodesulfatatoraceae;g__Thermodesulfatator_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:42:56,885] [INFO] GTDB search result was written to GCF_000421585.1_ASM42158v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:42:56,885] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:42:56,888] [INFO] DFAST_QC result json was written to GCF_000421585.1_ASM42158v1_genomic.fna/dqc_result.json
[2024-01-24 12:42:56,888] [INFO] DFAST_QC completed!
[2024-01-24 12:42:56,888] [INFO] Total running time: 0h0m49s