[2024-01-24 13:39:59,015] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:39:59,017] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:39:59,017] [INFO] DQC Reference Directory: /var/lib/cwl/stgfb5d44f4-ea8f-4d22-a386-fa290ac8d55f/dqc_reference
[2024-01-24 13:40:00,274] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:00,275] [INFO] Task started: Prodigal
[2024-01-24 13:40:00,275] [INFO] Running command: gunzip -c /var/lib/cwl/stg6f8a1e80-941e-469d-8b51-c8403ae93c17/GCF_000009965.1_ASM996v1_genomic.fna.gz | prodigal -d GCF_000009965.1_ASM996v1_genomic.fna/cds.fna -a GCF_000009965.1_ASM996v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:05,187] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:05,188] [INFO] Task started: HMMsearch
[2024-01-24 13:40:05,188] [INFO] Running command: hmmsearch --tblout GCF_000009965.1_ASM996v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfb5d44f4-ea8f-4d22-a386-fa290ac8d55f/dqc_reference/reference_markers.hmm GCF_000009965.1_ASM996v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:05,410] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:05,412] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg6f8a1e80-941e-469d-8b51-c8403ae93c17/GCF_000009965.1_ASM996v1_genomic.fna.gz]
[2024-01-24 13:40:05,434] [INFO] Query marker FASTA was written to GCF_000009965.1_ASM996v1_genomic.fna/markers.fasta
[2024-01-24 13:40:05,435] [INFO] Task started: Blastn
[2024-01-24 13:40:05,435] [INFO] Running command: blastn -query GCF_000009965.1_ASM996v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfb5d44f4-ea8f-4d22-a386-fa290ac8d55f/dqc_reference/reference_markers.fasta -out GCF_000009965.1_ASM996v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:05,965] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:05,972] [INFO] Selected 5 target genomes.
[2024-01-24 13:40:05,972] [INFO] Target genome list was writen to GCF_000009965.1_ASM996v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:05,987] [INFO] Task started: fastANI
[2024-01-24 13:40:05,988] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f8a1e80-941e-469d-8b51-c8403ae93c17/GCF_000009965.1_ASM996v1_genomic.fna.gz --refList GCF_000009965.1_ASM996v1_genomic.fna/target_genomes.txt --output GCF_000009965.1_ASM996v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:40:08,854] [INFO] Task succeeded: fastANI
[2024-01-24 13:40:08,854] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfb5d44f4-ea8f-4d22-a386-fa290ac8d55f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:40:08,855] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfb5d44f4-ea8f-4d22-a386-fa290ac8d55f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:40:08,864] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:40:08,864] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:40:08,864] [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 kodakarensis	strain=KOD1	GCA_000009965.1	311400	311400	type	True	100.0	696	696	95	conclusive
Thermococcus peptonophilus	strain=OG-1	GCA_001592435.1	53952	53952	type	True	89.0693	507	696	95	below_threshold
Thermococcus stetteri	strain=DSM 5262	GCA_017873335.1	49900	49900	type	True	85.7411	506	696	95	below_threshold
Thermococcus profundus	strain=DT 5432	GCA_002214585.1	49899	49899	type	True	81.2027	380	696	95	below_threshold
Thermococcus eurythermalis	strain=A501	GCA_000769655.1	1505907	1505907	type	True	80.1798	371	696	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:40:08,867] [INFO] DFAST Taxonomy check result was written to GCF_000009965.1_ASM996v1_genomic.fna/tc_result.tsv
[2024-01-24 13:40:08,867] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:40:08,868] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:40:08,868] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfb5d44f4-ea8f-4d22-a386-fa290ac8d55f/dqc_reference/checkm_data
[2024-01-24 13:40:08,869] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:40:08,891] [INFO] Task started: CheckM
[2024-01-24 13:40:08,891] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000009965.1_ASM996v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000009965.1_ASM996v1_genomic.fna/checkm_input GCF_000009965.1_ASM996v1_genomic.fna/checkm_result
[2024-01-24 13:40:30,496] [INFO] Task succeeded: CheckM
[2024-01-24 13:40:30,498] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:40:30,518] [INFO] ===== Completeness check finished =====
[2024-01-24 13:40:30,518] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:40:30,519] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000009965.1_ASM996v1_genomic.fna/markers.fasta)
[2024-01-24 13:40:30,519] [INFO] Task started: Blastn
[2024-01-24 13:40:30,519] [INFO] Running command: blastn -query GCF_000009965.1_ASM996v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfb5d44f4-ea8f-4d22-a386-fa290ac8d55f/dqc_reference/reference_markers_gtdb.fasta -out GCF_000009965.1_ASM996v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:31,029] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:31,033] [INFO] Selected 6 target genomes.
[2024-01-24 13:40:31,033] [INFO] Target genome list was writen to GCF_000009965.1_ASM996v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:40:31,038] [INFO] Task started: fastANI
[2024-01-24 13:40:31,038] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f8a1e80-941e-469d-8b51-c8403ae93c17/GCF_000009965.1_ASM996v1_genomic.fna.gz --refList GCF_000009965.1_ASM996v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000009965.1_ASM996v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:40:34,013] [INFO] Task succeeded: fastANI
[2024-01-24 13:40:34,026] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:40:34,027] [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_000009965.1	s__Thermococcus kodakarensis	100.0	696	696	d__Archaea;p__Methanobacteriota_B;c__Thermococci;o__Thermococcales;f__Thermococcaceae;g__Thermococcus	95.0	97.75	97.75	0.93	0.93	2	conclusive
GCF_001592435.1	s__Thermococcus peptonophilus	89.0693	507	696	d__Archaea;p__Methanobacteriota_B;c__Thermococci;o__Thermococcales;f__Thermococcaceae;g__Thermococcus	95.0	99.53	99.53	0.99	0.99	2	-
GCF_017873335.1	s__Thermococcus stetteri	85.7411	506	696	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_002214585.1	s__Thermococcus profundus	81.2199	379	696	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_012027595.1	s__Thermococcus sp012027595	81.1405	353	696	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_015521605.1	s__Thermococcus sp015521605	79.4822	297	696	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 13:40:34,029] [INFO] GTDB search result was written to GCF_000009965.1_ASM996v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:40:34,030] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:40:34,034] [INFO] DFAST_QC result json was written to GCF_000009965.1_ASM996v1_genomic.fna/dqc_result.json
[2024-01-24 13:40:34,034] [INFO] DFAST_QC completed!
[2024-01-24 13:40:34,034] [INFO] Total running time: 0h0m35s