[2024-01-24 13:40:34,096] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:34,099] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:34,099] [INFO] DQC Reference Directory: /var/lib/cwl/stg7025eee0-844d-457a-a7a4-8d47edcbbfc1/dqc_reference
[2024-01-24 13:40:35,485] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:35,486] [INFO] Task started: Prodigal
[2024-01-24 13:40:35,486] [INFO] Running command: gunzip -c /var/lib/cwl/stgef4d9ebd-382b-4e58-9276-0365a280ea26/GCF_003967175.1_Sacidi_1.0_genomic.fna.gz | prodigal -d GCF_003967175.1_Sacidi_1.0_genomic.fna/cds.fna -a GCF_003967175.1_Sacidi_1.0_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:46,150] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:46,151] [INFO] Task started: HMMsearch
[2024-01-24 13:40:46,151] [INFO] Running command: hmmsearch --tblout GCF_003967175.1_Sacidi_1.0_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7025eee0-844d-457a-a7a4-8d47edcbbfc1/dqc_reference/reference_markers.hmm GCF_003967175.1_Sacidi_1.0_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:46,417] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:46,418] [WARNING] Found 1/6 markers. [/var/lib/cwl/stgef4d9ebd-382b-4e58-9276-0365a280ea26/GCF_003967175.1_Sacidi_1.0_genomic.fna.gz]
[2024-01-24 13:40:46,440] [INFO] Query marker FASTA was written to GCF_003967175.1_Sacidi_1.0_genomic.fna/markers.fasta
[2024-01-24 13:40:46,440] [INFO] Task started: Blastn
[2024-01-24 13:40:46,440] [INFO] Running command: blastn -query GCF_003967175.1_Sacidi_1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stg7025eee0-844d-457a-a7a4-8d47edcbbfc1/dqc_reference/reference_markers.fasta -out GCF_003967175.1_Sacidi_1.0_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:46,929] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:46,932] [INFO] Selected 2 target genomes.
[2024-01-24 13:40:46,933] [INFO] Target genome list was writen to GCF_003967175.1_Sacidi_1.0_genomic.fna/target_genomes.txt
[2024-01-24 13:40:46,934] [INFO] Task started: fastANI
[2024-01-24 13:40:46,934] [INFO] Running command: fastANI --query /var/lib/cwl/stgef4d9ebd-382b-4e58-9276-0365a280ea26/GCF_003967175.1_Sacidi_1.0_genomic.fna.gz --refList GCF_003967175.1_Sacidi_1.0_genomic.fna/target_genomes.txt --output GCF_003967175.1_Sacidi_1.0_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:40:49,526] [INFO] Task succeeded: fastANI
[2024-01-24 13:40:49,527] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7025eee0-844d-457a-a7a4-8d47edcbbfc1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:40:49,527] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7025eee0-844d-457a-a7a4-8d47edcbbfc1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:40:49,531] [INFO] Found 2 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:40:49,531] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:40:49,531] [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
Sulfodiicoccus acidiphilus	strain=HS-1	GCA_003967175.1	1670455	1670455	type	True	100.0	784	784	95	conclusive
Sulfodiicoccus acidiphilus	strain=JCM 31740	GCA_014648235.1	1670455	1670455	type	True	99.9557	756	784	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 13:40:49,532] [INFO] DFAST Taxonomy check result was written to GCF_003967175.1_Sacidi_1.0_genomic.fna/tc_result.tsv
[2024-01-24 13:40:49,533] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:40:49,533] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:40:49,533] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7025eee0-844d-457a-a7a4-8d47edcbbfc1/dqc_reference/checkm_data
[2024-01-24 13:40:49,534] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:40:49,560] [INFO] Task started: CheckM
[2024-01-24 13:40:49,560] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003967175.1_Sacidi_1.0_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003967175.1_Sacidi_1.0_genomic.fna/checkm_input GCF_003967175.1_Sacidi_1.0_genomic.fna/checkm_result
[2024-01-24 13:41:24,742] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:24,744] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:24,776] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:24,776] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:24,777] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003967175.1_Sacidi_1.0_genomic.fna/markers.fasta)
[2024-01-24 13:41:24,777] [INFO] Task started: Blastn
[2024-01-24 13:41:24,777] [INFO] Running command: blastn -query GCF_003967175.1_Sacidi_1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stg7025eee0-844d-457a-a7a4-8d47edcbbfc1/dqc_reference/reference_markers_gtdb.fasta -out GCF_003967175.1_Sacidi_1.0_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:25,246] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:25,249] [INFO] Selected 1 target genomes.
[2024-01-24 13:41:25,250] [INFO] Target genome list was writen to GCF_003967175.1_Sacidi_1.0_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:25,251] [INFO] Task started: fastANI
[2024-01-24 13:41:25,251] [INFO] Running command: fastANI --query /var/lib/cwl/stgef4d9ebd-382b-4e58-9276-0365a280ea26/GCF_003967175.1_Sacidi_1.0_genomic.fna.gz --refList GCF_003967175.1_Sacidi_1.0_genomic.fna/target_genomes_gtdb.txt --output GCF_003967175.1_Sacidi_1.0_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:26,861] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:26,863] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:41:26,863] [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_003967175.1	s__Sulfodiicoccus acidiphilus	100.0	784	784	d__Archaea;p__Thermoproteota;c__Thermoproteia;o__Sulfolobales;f__Sulfolobaceae;g__Sulfodiicoccus	95.0	99.99	99.99	1.00	1.00	2	conclusive
--------------------------------------------------------------------------------
[2024-01-24 13:41:26,865] [INFO] GTDB search result was written to GCF_003967175.1_Sacidi_1.0_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:26,866] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:26,868] [INFO] DFAST_QC result json was written to GCF_003967175.1_Sacidi_1.0_genomic.fna/dqc_result.json
[2024-01-24 13:41:26,868] [INFO] DFAST_QC completed!
[2024-01-24 13:41:26,868] [INFO] Total running time: 0h0m53s