[2024-01-24 15:03:15,157] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:03:15,170] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:03:15,170] [INFO] DQC Reference Directory: /var/lib/cwl/stgbbe8055c-64b2-4c30-b4f3-6d734d010af2/dqc_reference
[2024-01-24 15:03:16,717] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:03:16,718] [INFO] Task started: Prodigal
[2024-01-24 15:03:16,718] [INFO] Running command: gunzip -c /var/lib/cwl/stgeaab5a30-0a66-4aef-b5cf-df017a448d83/GCF_016592575.1_ASM1659257v1_genomic.fna.gz | prodigal -d GCF_016592575.1_ASM1659257v1_genomic.fna/cds.fna -a GCF_016592575.1_ASM1659257v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:03:21,684] [INFO] Task succeeded: Prodigal
[2024-01-24 15:03:21,685] [INFO] Task started: HMMsearch
[2024-01-24 15:03:21,685] [INFO] Running command: hmmsearch --tblout GCF_016592575.1_ASM1659257v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbbe8055c-64b2-4c30-b4f3-6d734d010af2/dqc_reference/reference_markers.hmm GCF_016592575.1_ASM1659257v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:03:21,986] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:03:21,988] [INFO] Found 6/6 markers.
[2024-01-24 15:03:22,013] [INFO] Query marker FASTA was written to GCF_016592575.1_ASM1659257v1_genomic.fna/markers.fasta
[2024-01-24 15:03:22,013] [INFO] Task started: Blastn
[2024-01-24 15:03:22,013] [INFO] Running command: blastn -query GCF_016592575.1_ASM1659257v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbbe8055c-64b2-4c30-b4f3-6d734d010af2/dqc_reference/reference_markers.fasta -out GCF_016592575.1_ASM1659257v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:22,667] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:22,670] [INFO] Selected 14 target genomes.
[2024-01-24 15:03:22,671] [INFO] Target genome list was writen to GCF_016592575.1_ASM1659257v1_genomic.fna/target_genomes.txt
[2024-01-24 15:03:22,677] [INFO] Task started: fastANI
[2024-01-24 15:03:22,677] [INFO] Running command: fastANI --query /var/lib/cwl/stgeaab5a30-0a66-4aef-b5cf-df017a448d83/GCF_016592575.1_ASM1659257v1_genomic.fna.gz --refList GCF_016592575.1_ASM1659257v1_genomic.fna/target_genomes.txt --output GCF_016592575.1_ASM1659257v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:03:29,693] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:29,693] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbbe8055c-64b2-4c30-b4f3-6d734d010af2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:03:29,693] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbbe8055c-64b2-4c30-b4f3-6d734d010af2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:03:29,697] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:03:29,697] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:03:29,697] [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
Thermotomaculum hydrothermale	strain=AC55	GCA_016592575.1	981385	981385	type	True	100.0	772	772	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 15:03:29,699] [INFO] DFAST Taxonomy check result was written to GCF_016592575.1_ASM1659257v1_genomic.fna/tc_result.tsv
[2024-01-24 15:03:29,700] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:03:29,700] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:03:29,700] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbbe8055c-64b2-4c30-b4f3-6d734d010af2/dqc_reference/checkm_data
[2024-01-24 15:03:29,701] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:03:29,730] [INFO] Task started: CheckM
[2024-01-24 15:03:29,731] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016592575.1_ASM1659257v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016592575.1_ASM1659257v1_genomic.fna/checkm_input GCF_016592575.1_ASM1659257v1_genomic.fna/checkm_result
[2024-01-24 15:03:51,370] [INFO] Task succeeded: CheckM
[2024-01-24 15:03:51,372] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:03:51,391] [INFO] ===== Completeness check finished =====
[2024-01-24 15:03:51,391] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:03:51,391] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016592575.1_ASM1659257v1_genomic.fna/markers.fasta)
[2024-01-24 15:03:51,392] [INFO] Task started: Blastn
[2024-01-24 15:03:51,392] [INFO] Running command: blastn -query GCF_016592575.1_ASM1659257v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbbe8055c-64b2-4c30-b4f3-6d734d010af2/dqc_reference/reference_markers_gtdb.fasta -out GCF_016592575.1_ASM1659257v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:52,240] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:52,244] [INFO] Selected 18 target genomes.
[2024-01-24 15:03:52,244] [INFO] Target genome list was writen to GCF_016592575.1_ASM1659257v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:03:52,273] [INFO] Task started: fastANI
[2024-01-24 15:03:52,274] [INFO] Running command: fastANI --query /var/lib/cwl/stgeaab5a30-0a66-4aef-b5cf-df017a448d83/GCF_016592575.1_ASM1659257v1_genomic.fna.gz --refList GCF_016592575.1_ASM1659257v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016592575.1_ASM1659257v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:04:00,104] [INFO] Task succeeded: fastANI
[2024-01-24 15:04:00,108] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:04:00,108] [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_016592575.1	s__Thermotomaculum hydrothermale	100.0	772	772	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Thermotomaculales;f__Thermotomaculaceae;g__Thermotomaculum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_015487755.1	s__Thermotomaculum sp015487755	80.3549	281	772	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Thermotomaculales;f__Thermotomaculaceae;g__Thermotomaculum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:04:00,110] [INFO] GTDB search result was written to GCF_016592575.1_ASM1659257v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:04:00,110] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:04:00,112] [INFO] DFAST_QC result json was written to GCF_016592575.1_ASM1659257v1_genomic.fna/dqc_result.json
[2024-01-24 15:04:00,113] [INFO] DFAST_QC completed!
[2024-01-24 15:04:00,113] [INFO] Total running time: 0h0m45s