[2023-06-28 11:38:31,537] [INFO] DFAST_QC pipeline started.
[2023-06-28 11:38:31,539] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 11:38:31,540] [INFO] DQC Reference Directory: /var/lib/cwl/stg84de50b2-6c4d-45e3-917b-6899661ad894/dqc_reference
[2023-06-28 11:38:32,781] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 11:38:32,782] [INFO] Task started: Prodigal
[2023-06-28 11:38:32,782] [INFO] Running command: gunzip -c /var/lib/cwl/stg3b6d23bc-c214-4e84-a1ac-3c95297b39db/GCA_019689735.1_ASM1968973v1_genomic.fna.gz | prodigal -d GCA_019689735.1_ASM1968973v1_genomic.fna/cds.fna -a GCA_019689735.1_ASM1968973v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 11:38:48,314] [INFO] Task succeeded: Prodigal
[2023-06-28 11:38:48,315] [INFO] Task started: HMMsearch
[2023-06-28 11:38:48,315] [INFO] Running command: hmmsearch --tblout GCA_019689735.1_ASM1968973v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg84de50b2-6c4d-45e3-917b-6899661ad894/dqc_reference/reference_markers.hmm GCA_019689735.1_ASM1968973v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 11:38:48,559] [INFO] Task succeeded: HMMsearch
[2023-06-28 11:38:48,560] [INFO] Found 6/6 markers.
[2023-06-28 11:38:48,588] [INFO] Query marker FASTA was written to GCA_019689735.1_ASM1968973v1_genomic.fna/markers.fasta
[2023-06-28 11:38:48,589] [INFO] Task started: Blastn
[2023-06-28 11:38:48,589] [INFO] Running command: blastn -query GCA_019689735.1_ASM1968973v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg84de50b2-6c4d-45e3-917b-6899661ad894/dqc_reference/reference_markers.fasta -out GCA_019689735.1_ASM1968973v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 11:38:49,167] [INFO] Task succeeded: Blastn
[2023-06-28 11:38:49,171] [INFO] Selected 17 target genomes.
[2023-06-28 11:38:49,172] [INFO] Target genome list was writen to GCA_019689735.1_ASM1968973v1_genomic.fna/target_genomes.txt
[2023-06-28 11:38:49,178] [INFO] Task started: fastANI
[2023-06-28 11:38:49,178] [INFO] Running command: fastANI --query /var/lib/cwl/stg3b6d23bc-c214-4e84-a1ac-3c95297b39db/GCA_019689735.1_ASM1968973v1_genomic.fna.gz --refList GCA_019689735.1_ASM1968973v1_genomic.fna/target_genomes.txt --output GCA_019689735.1_ASM1968973v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 11:39:07,502] [INFO] Task succeeded: fastANI
[2023-06-28 11:39:07,503] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg84de50b2-6c4d-45e3-917b-6899661ad894/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 11:39:07,503] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg84de50b2-6c4d-45e3-917b-6899661ad894/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 11:39:07,508] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2023-06-28 11:39:07,508] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-28 11:39:07,508] [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
Thermoflavifilum aggregans	strain=DSM 27268	GCA_002797735.1	454188	454188	type	True	98.3386	809	857	95	conclusive
Thermoflavifilum thermophilum	strain=DSM 14807	GCA_900116565.1	1393122	1393122	type	True	90.2016	752	857	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 11:39:07,510] [INFO] DFAST Taxonomy check result was written to GCA_019689735.1_ASM1968973v1_genomic.fna/tc_result.tsv
[2023-06-28 11:39:07,511] [INFO] ===== Taxonomy check completed =====
[2023-06-28 11:39:07,511] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 11:39:07,512] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg84de50b2-6c4d-45e3-917b-6899661ad894/dqc_reference/checkm_data
[2023-06-28 11:39:07,514] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 11:39:07,549] [INFO] Task started: CheckM
[2023-06-28 11:39:07,550] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_019689735.1_ASM1968973v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_019689735.1_ASM1968973v1_genomic.fna/checkm_input GCA_019689735.1_ASM1968973v1_genomic.fna/checkm_result
[2023-06-28 11:39:55,400] [INFO] Task succeeded: CheckM
[2023-06-28 11:39:55,402] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 11:39:55,423] [INFO] ===== Completeness check finished =====
[2023-06-28 11:39:55,423] [INFO] ===== Start GTDB Search =====
[2023-06-28 11:39:55,424] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_019689735.1_ASM1968973v1_genomic.fna/markers.fasta)
[2023-06-28 11:39:55,424] [INFO] Task started: Blastn
[2023-06-28 11:39:55,424] [INFO] Running command: blastn -query GCA_019689735.1_ASM1968973v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg84de50b2-6c4d-45e3-917b-6899661ad894/dqc_reference/reference_markers_gtdb.fasta -out GCA_019689735.1_ASM1968973v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 11:39:56,238] [INFO] Task succeeded: Blastn
[2023-06-28 11:39:56,243] [INFO] Selected 16 target genomes.
[2023-06-28 11:39:56,243] [INFO] Target genome list was writen to GCA_019689735.1_ASM1968973v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 11:39:56,260] [INFO] Task started: fastANI
[2023-06-28 11:39:56,260] [INFO] Running command: fastANI --query /var/lib/cwl/stg3b6d23bc-c214-4e84-a1ac-3c95297b39db/GCA_019689735.1_ASM1968973v1_genomic.fna.gz --refList GCA_019689735.1_ASM1968973v1_genomic.fna/target_genomes_gtdb.txt --output GCA_019689735.1_ASM1968973v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 11:40:07,004] [INFO] Task succeeded: fastANI
[2023-06-28 11:40:07,012] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 11:40:07,012] [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_002797735.1	s__Thermoflavifilum aggregans	98.3386	809	857	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Thermoflavifilum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900116565.1	s__Thermoflavifilum thermophilum	90.2016	752	857	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Thermoflavifilum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014961315.1	s__Thermoflavifilum sp014961315	79.6337	552	857	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Thermoflavifilum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 11:40:07,015] [INFO] GTDB search result was written to GCA_019689735.1_ASM1968973v1_genomic.fna/result_gtdb.tsv
[2023-06-28 11:40:07,015] [INFO] ===== GTDB Search completed =====
[2023-06-28 11:40:07,018] [INFO] DFAST_QC result json was written to GCA_019689735.1_ASM1968973v1_genomic.fna/dqc_result.json
[2023-06-28 11:40:07,019] [INFO] DFAST_QC completed!
[2023-06-28 11:40:07,019] [INFO] Total running time: 0h1m35s