[2023-06-29 17:18:49,184] [INFO] DFAST_QC pipeline started.
[2023-06-29 17:18:49,187] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 17:18:49,187] [INFO] DQC Reference Directory: /var/lib/cwl/stga7769aee-00d1-4bd6-8810-c5b18b374b88/dqc_reference
[2023-06-29 17:18:50,469] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 17:18:50,470] [INFO] Task started: Prodigal
[2023-06-29 17:18:50,470] [INFO] Running command: gunzip -c /var/lib/cwl/stg915bb25d-eff1-4f62-a9f2-81d1552890dd/GCA_021806295.1_ASM2180629v1_genomic.fna.gz | prodigal -d GCA_021806295.1_ASM2180629v1_genomic.fna/cds.fna -a GCA_021806295.1_ASM2180629v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 17:18:56,443] [INFO] Task succeeded: Prodigal
[2023-06-29 17:18:56,444] [INFO] Task started: HMMsearch
[2023-06-29 17:18:56,444] [INFO] Running command: hmmsearch --tblout GCA_021806295.1_ASM2180629v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga7769aee-00d1-4bd6-8810-c5b18b374b88/dqc_reference/reference_markers.hmm GCA_021806295.1_ASM2180629v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 17:18:56,636] [INFO] Task succeeded: HMMsearch
[2023-06-29 17:18:56,637] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg915bb25d-eff1-4f62-a9f2-81d1552890dd/GCA_021806295.1_ASM2180629v1_genomic.fna.gz]
[2023-06-29 17:18:56,659] [INFO] Query marker FASTA was written to GCA_021806295.1_ASM2180629v1_genomic.fna/markers.fasta
[2023-06-29 17:18:56,660] [INFO] Task started: Blastn
[2023-06-29 17:18:56,660] [INFO] Running command: blastn -query GCA_021806295.1_ASM2180629v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga7769aee-00d1-4bd6-8810-c5b18b374b88/dqc_reference/reference_markers.fasta -out GCA_021806295.1_ASM2180629v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 17:18:57,140] [INFO] Task succeeded: Blastn
[2023-06-29 17:18:57,143] [INFO] Selected 4 target genomes.
[2023-06-29 17:18:57,144] [INFO] Target genome list was writen to GCA_021806295.1_ASM2180629v1_genomic.fna/target_genomes.txt
[2023-06-29 17:18:57,149] [INFO] Task started: fastANI
[2023-06-29 17:18:57,149] [INFO] Running command: fastANI --query /var/lib/cwl/stg915bb25d-eff1-4f62-a9f2-81d1552890dd/GCA_021806295.1_ASM2180629v1_genomic.fna.gz --refList GCA_021806295.1_ASM2180629v1_genomic.fna/target_genomes.txt --output GCA_021806295.1_ASM2180629v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 17:18:59,132] [INFO] Task succeeded: fastANI
[2023-06-29 17:18:59,133] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga7769aee-00d1-4bd6-8810-c5b18b374b88/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 17:18:59,133] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga7769aee-00d1-4bd6-8810-c5b18b374b88/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 17:18:59,138] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 17:18:59,138] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 17:18:59,138] [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
Ferroplasma acidarmanus	strain=Fer1	GCA_000152265.2	97393	97393	type	True	77.8736	179	468	95	below_threshold
Ferroplasma acidiphilum	strain=Y	GCA_002078355.1	74969	74969	type	True	77.6898	177	468	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 17:18:59,140] [INFO] DFAST Taxonomy check result was written to GCA_021806295.1_ASM2180629v1_genomic.fna/tc_result.tsv
[2023-06-29 17:18:59,140] [INFO] ===== Taxonomy check completed =====
[2023-06-29 17:18:59,140] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 17:18:59,141] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga7769aee-00d1-4bd6-8810-c5b18b374b88/dqc_reference/checkm_data
[2023-06-29 17:18:59,142] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 17:18:59,164] [INFO] Task started: CheckM
[2023-06-29 17:18:59,164] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021806295.1_ASM2180629v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021806295.1_ASM2180629v1_genomic.fna/checkm_input GCA_021806295.1_ASM2180629v1_genomic.fna/checkm_result
[2023-06-29 17:19:23,737] [INFO] Task succeeded: CheckM
[2023-06-29 17:19:23,739] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 17:19:23,773] [INFO] ===== Completeness check finished =====
[2023-06-29 17:19:23,774] [INFO] ===== Start GTDB Search =====
[2023-06-29 17:19:23,774] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021806295.1_ASM2180629v1_genomic.fna/markers.fasta)
[2023-06-29 17:19:23,775] [INFO] Task started: Blastn
[2023-06-29 17:19:23,775] [INFO] Running command: blastn -query GCA_021806295.1_ASM2180629v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga7769aee-00d1-4bd6-8810-c5b18b374b88/dqc_reference/reference_markers_gtdb.fasta -out GCA_021806295.1_ASM2180629v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 17:19:24,211] [INFO] Task succeeded: Blastn
[2023-06-29 17:19:24,215] [INFO] Selected 5 target genomes.
[2023-06-29 17:19:24,215] [INFO] Target genome list was writen to GCA_021806295.1_ASM2180629v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 17:19:24,221] [INFO] Task started: fastANI
[2023-06-29 17:19:24,221] [INFO] Running command: fastANI --query /var/lib/cwl/stg915bb25d-eff1-4f62-a9f2-81d1552890dd/GCA_021806295.1_ASM2180629v1_genomic.fna.gz --refList GCA_021806295.1_ASM2180629v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021806295.1_ASM2180629v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 17:19:25,503] [INFO] Task succeeded: fastANI
[2023-06-29 17:19:25,512] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 17:19:25,512] [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_000152265.2	s__Ferroplasma acidarmanus	77.8736	179	468	d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__Thermoplasmatales;f__Thermoplasmataceae;g__Ferroplasma	96.9486	N/A	N/A	N/A	N/A	1	-
GCF_002078355.1	s__Ferroplasma acidiphilum	77.6898	177	468	d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__Thermoplasmatales;f__Thermoplasmataceae;g__Ferroplasma	96.9486	97.96	97.96	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2023-06-29 17:19:25,519] [INFO] GTDB search result was written to GCA_021806295.1_ASM2180629v1_genomic.fna/result_gtdb.tsv
[2023-06-29 17:19:25,524] [INFO] ===== GTDB Search completed =====
[2023-06-29 17:19:25,528] [INFO] DFAST_QC result json was written to GCA_021806295.1_ASM2180629v1_genomic.fna/dqc_result.json
[2023-06-29 17:19:25,528] [INFO] DFAST_QC completed!
[2023-06-29 17:19:25,529] [INFO] Total running time: 0h0m36s