[2024-01-24 14:06:07,198] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:07,200] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:07,201] [INFO] DQC Reference Directory: /var/lib/cwl/stg5982e808-d9f6-45e1-b507-089d6e2ea68e/dqc_reference
[2024-01-24 14:06:08,615] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:08,616] [INFO] Task started: Prodigal
[2024-01-24 14:06:08,616] [INFO] Running command: gunzip -c /var/lib/cwl/stgf59f9768-dde2-42eb-9aae-a7f5ff0f9cea/GCF_032304395.1_ASM3230439v1_genomic.fna.gz | prodigal -d GCF_032304395.1_ASM3230439v1_genomic.fna/cds.fna -a GCF_032304395.1_ASM3230439v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:13,103] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:13,103] [INFO] Task started: HMMsearch
[2024-01-24 14:06:13,103] [INFO] Running command: hmmsearch --tblout GCF_032304395.1_ASM3230439v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5982e808-d9f6-45e1-b507-089d6e2ea68e/dqc_reference/reference_markers.hmm GCF_032304395.1_ASM3230439v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:13,329] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:13,331] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgf59f9768-dde2-42eb-9aae-a7f5ff0f9cea/GCF_032304395.1_ASM3230439v1_genomic.fna.gz]
[2024-01-24 14:06:13,360] [INFO] Query marker FASTA was written to GCF_032304395.1_ASM3230439v1_genomic.fna/markers.fasta
[2024-01-24 14:06:13,361] [INFO] Task started: Blastn
[2024-01-24 14:06:13,361] [INFO] Running command: blastn -query GCF_032304395.1_ASM3230439v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5982e808-d9f6-45e1-b507-089d6e2ea68e/dqc_reference/reference_markers.fasta -out GCF_032304395.1_ASM3230439v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:13,924] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:13,927] [INFO] Selected 6 target genomes.
[2024-01-24 14:06:13,928] [INFO] Target genome list was writen to GCF_032304395.1_ASM3230439v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:13,933] [INFO] Task started: fastANI
[2024-01-24 14:06:13,934] [INFO] Running command: fastANI --query /var/lib/cwl/stgf59f9768-dde2-42eb-9aae-a7f5ff0f9cea/GCF_032304395.1_ASM3230439v1_genomic.fna.gz --refList GCF_032304395.1_ASM3230439v1_genomic.fna/target_genomes.txt --output GCF_032304395.1_ASM3230439v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:16,969] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:16,970] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5982e808-d9f6-45e1-b507-089d6e2ea68e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:16,970] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5982e808-d9f6-45e1-b507-089d6e2ea68e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:16,977] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:06:16,978] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:16,978] [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
Thermococcus zilligii	strain=AN1	GCA_000258515.1	54076	54076	type	True	95.678	528	597	95	conclusive
Thermococcus gorgonarius	strain=W-12	GCA_002214385.1	71997	71997	type	True	86.5616	456	597	95	below_threshold
Thermococcus pacificus	strain=P-4	GCA_002214485.1	71998	71998	type	True	83.5014	370	597	95	below_threshold
Thermococcus stetteri	strain=DSM 5262	GCA_017873335.1	49900	49900	type	True	79.407	286	597	95	below_threshold
Thermococcus cleftensis	strain=CL1	GCA_000265525.1	163003	163003	type	True	79.2611	282	597	95	below_threshold
Thermococcus siculi	strain=RG-20	GCA_002214505.1	72803	72803	type	True	79.2565	291	597	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:16,982] [INFO] DFAST Taxonomy check result was written to GCF_032304395.1_ASM3230439v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:16,984] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:16,984] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:16,984] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5982e808-d9f6-45e1-b507-089d6e2ea68e/dqc_reference/checkm_data
[2024-01-24 14:06:16,986] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:17,008] [INFO] Task started: CheckM
[2024-01-24 14:06:17,009] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_032304395.1_ASM3230439v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_032304395.1_ASM3230439v1_genomic.fna/checkm_input GCF_032304395.1_ASM3230439v1_genomic.fna/checkm_result
[2024-01-24 14:06:38,264] [INFO] Task succeeded: CheckM
[2024-01-24 14:06:38,265] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:06:38,285] [INFO] ===== Completeness check finished =====
[2024-01-24 14:06:38,285] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:06:38,286] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_032304395.1_ASM3230439v1_genomic.fna/markers.fasta)
[2024-01-24 14:06:38,286] [INFO] Task started: Blastn
[2024-01-24 14:06:38,286] [INFO] Running command: blastn -query GCF_032304395.1_ASM3230439v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5982e808-d9f6-45e1-b507-089d6e2ea68e/dqc_reference/reference_markers_gtdb.fasta -out GCF_032304395.1_ASM3230439v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:38,883] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:38,887] [INFO] Selected 6 target genomes.
[2024-01-24 14:06:38,887] [INFO] Target genome list was writen to GCF_032304395.1_ASM3230439v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:06:38,896] [INFO] Task started: fastANI
[2024-01-24 14:06:38,896] [INFO] Running command: fastANI --query /var/lib/cwl/stgf59f9768-dde2-42eb-9aae-a7f5ff0f9cea/GCF_032304395.1_ASM3230439v1_genomic.fna.gz --refList GCF_032304395.1_ASM3230439v1_genomic.fna/target_genomes_gtdb.txt --output GCF_032304395.1_ASM3230439v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:06:42,085] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:42,092] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:06:42,093] [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_000258515.1	s__Thermococcus zilligii	95.678	528	597	d__Archaea;p__Methanobacteriota_B;c__Thermococci;o__Thermococcales;f__Thermococcaceae;g__Thermococcus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002214385.1	s__Thermococcus gorgonarius	86.5521	457	597	d__Archaea;p__Methanobacteriota_B;c__Thermococci;o__Thermococcales;f__Thermococcaceae;g__Thermococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002214485.1	s__Thermococcus pacificus	83.45	373	597	d__Archaea;p__Methanobacteriota_B;c__Thermococci;o__Thermococcales;f__Thermococcaceae;g__Thermococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015523195.1	s__Thermococcus sp015523195	79.5102	262	597	d__Archaea;p__Methanobacteriota_B;c__Thermococci;o__Thermococcales;f__Thermococcaceae;g__Thermococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017873335.1	s__Thermococcus stetteri	79.3806	287	597	d__Archaea;p__Methanobacteriota_B;c__Thermococci;o__Thermococcales;f__Thermococcaceae;g__Thermococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002214505.1	s__Thermococcus siculi	79.2253	293	597	d__Archaea;p__Methanobacteriota_B;c__Thermococci;o__Thermococcales;f__Thermococcaceae;g__Thermococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:06:42,098] [INFO] GTDB search result was written to GCF_032304395.1_ASM3230439v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:06:42,099] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:06:42,102] [INFO] DFAST_QC result json was written to GCF_032304395.1_ASM3230439v1_genomic.fna/dqc_result.json
[2024-01-24 14:06:42,103] [INFO] DFAST_QC completed!
[2024-01-24 14:06:42,103] [INFO] Total running time: 0h0m35s