[2024-01-24 13:49:19,320] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:19,322] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:19,322] [INFO] DQC Reference Directory: /var/lib/cwl/stgebccc45d-41a8-45f7-8364-00c204b22863/dqc_reference
[2024-01-24 13:49:20,796] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:20,797] [INFO] Task started: Prodigal
[2024-01-24 13:49:20,797] [INFO] Running command: gunzip -c /var/lib/cwl/stgef4c1a60-6ef4-4ec9-bfb3-5ea179444904/GCF_001293545.1_ASM129354v1_genomic.fna.gz | prodigal -d GCF_001293545.1_ASM129354v1_genomic.fna/cds.fna -a GCF_001293545.1_ASM129354v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:33,963] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:33,963] [INFO] Task started: HMMsearch
[2024-01-24 13:49:33,963] [INFO] Running command: hmmsearch --tblout GCF_001293545.1_ASM129354v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgebccc45d-41a8-45f7-8364-00c204b22863/dqc_reference/reference_markers.hmm GCF_001293545.1_ASM129354v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:34,296] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:34,297] [INFO] Found 6/6 markers.
[2024-01-24 13:49:34,327] [INFO] Query marker FASTA was written to GCF_001293545.1_ASM129354v1_genomic.fna/markers.fasta
[2024-01-24 13:49:34,327] [INFO] Task started: Blastn
[2024-01-24 13:49:34,327] [INFO] Running command: blastn -query GCF_001293545.1_ASM129354v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgebccc45d-41a8-45f7-8364-00c204b22863/dqc_reference/reference_markers.fasta -out GCF_001293545.1_ASM129354v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:34,932] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:34,935] [INFO] Selected 19 target genomes.
[2024-01-24 13:49:34,936] [INFO] Target genome list was writen to GCF_001293545.1_ASM129354v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:34,942] [INFO] Task started: fastANI
[2024-01-24 13:49:34,943] [INFO] Running command: fastANI --query /var/lib/cwl/stgef4c1a60-6ef4-4ec9-bfb3-5ea179444904/GCF_001293545.1_ASM129354v1_genomic.fna.gz --refList GCF_001293545.1_ASM129354v1_genomic.fna/target_genomes.txt --output GCF_001293545.1_ASM129354v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:47,401] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:47,402] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgebccc45d-41a8-45f7-8364-00c204b22863/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:47,402] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgebccc45d-41a8-45f7-8364-00c204b22863/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:47,406] [INFO] Found 2 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:49:47,407] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:47,407] [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
Ardenticatena maritima	strain=110S	GCA_001293545.1	872965	872965	type	True	100.0	1046	1058	95	conclusive
Ardenticatena maritima	strain=110S	GCA_001306175.1	872965	872965	type	True	99.9841	1055	1058	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 13:49:47,408] [INFO] DFAST Taxonomy check result was written to GCF_001293545.1_ASM129354v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:47,409] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:47,409] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:47,409] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgebccc45d-41a8-45f7-8364-00c204b22863/dqc_reference/checkm_data
[2024-01-24 13:49:47,411] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:47,453] [INFO] Task started: CheckM
[2024-01-24 13:49:47,453] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001293545.1_ASM129354v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001293545.1_ASM129354v1_genomic.fna/checkm_input GCF_001293545.1_ASM129354v1_genomic.fna/checkm_result
[2024-01-24 13:50:31,798] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:31,799] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:31,817] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:31,817] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:31,818] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001293545.1_ASM129354v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:31,818] [INFO] Task started: Blastn
[2024-01-24 13:50:31,819] [INFO] Running command: blastn -query GCF_001293545.1_ASM129354v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgebccc45d-41a8-45f7-8364-00c204b22863/dqc_reference/reference_markers_gtdb.fasta -out GCF_001293545.1_ASM129354v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:32,667] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:32,671] [INFO] Selected 16 target genomes.
[2024-01-24 13:50:32,671] [INFO] Target genome list was writen to GCF_001293545.1_ASM129354v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:32,739] [INFO] Task started: fastANI
[2024-01-24 13:50:32,740] [INFO] Running command: fastANI --query /var/lib/cwl/stgef4c1a60-6ef4-4ec9-bfb3-5ea179444904/GCF_001293545.1_ASM129354v1_genomic.fna.gz --refList GCF_001293545.1_ASM129354v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001293545.1_ASM129354v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:42,253] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:42,261] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:42,261] [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_001306175.1	s__Ardenticatena maritima	99.9841	1055	1058	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Ardenticatenales;f__Ardenticatenaceae;g__Ardenticatena	95.0	98.28	96.57	0.97	0.94	3	conclusive
GCA_015487975.1	s__Ardenticatena sp015487975	80.407	664	1058	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Ardenticatenales;f__Ardenticatenaceae;g__Ardenticatena	95.0	99.35	99.35	0.98	0.98	2	-
GCA_015491235.1	s__WFWG01 sp015491235	76.6094	132	1058	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Ardenticatenales;f__Ardenticatenaceae;g__WFWG01	95.0	99.02	98.95	0.84	0.84	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:42,263] [INFO] GTDB search result was written to GCF_001293545.1_ASM129354v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:42,264] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:42,266] [INFO] DFAST_QC result json was written to GCF_001293545.1_ASM129354v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:42,266] [INFO] DFAST_QC completed!
[2024-01-24 13:50:42,266] [INFO] Total running time: 0h1m23s