[2024-01-24 13:40:40,247] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:40,250] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:40,250] [INFO] DQC Reference Directory: /var/lib/cwl/stg55ad27bc-c5b2-427d-aa60-57afc407f214/dqc_reference
[2024-01-24 13:40:41,468] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:41,469] [INFO] Task started: Prodigal
[2024-01-24 13:40:41,469] [INFO] Running command: gunzip -c /var/lib/cwl/stgdba0c1d7-238b-47e9-9e14-bfc598e00c64/GCF_002214385.1_ASM221438v1_genomic.fna.gz | prodigal -d GCF_002214385.1_ASM221438v1_genomic.fna/cds.fna -a GCF_002214385.1_ASM221438v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:45,624] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:45,624] [INFO] Task started: HMMsearch
[2024-01-24 13:40:45,624] [INFO] Running command: hmmsearch --tblout GCF_002214385.1_ASM221438v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg55ad27bc-c5b2-427d-aa60-57afc407f214/dqc_reference/reference_markers.hmm GCF_002214385.1_ASM221438v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:45,814] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:45,816] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgdba0c1d7-238b-47e9-9e14-bfc598e00c64/GCF_002214385.1_ASM221438v1_genomic.fna.gz]
[2024-01-24 13:40:45,834] [INFO] Query marker FASTA was written to GCF_002214385.1_ASM221438v1_genomic.fna/markers.fasta
[2024-01-24 13:40:45,834] [INFO] Task started: Blastn
[2024-01-24 13:40:45,834] [INFO] Running command: blastn -query GCF_002214385.1_ASM221438v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg55ad27bc-c5b2-427d-aa60-57afc407f214/dqc_reference/reference_markers.fasta -out GCF_002214385.1_ASM221438v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:46,338] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:46,341] [INFO] Selected 5 target genomes.
[2024-01-24 13:40:46,341] [INFO] Target genome list was writen to GCF_002214385.1_ASM221438v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:46,344] [INFO] Task started: fastANI
[2024-01-24 13:40:46,344] [INFO] Running command: fastANI --query /var/lib/cwl/stgdba0c1d7-238b-47e9-9e14-bfc598e00c64/GCF_002214385.1_ASM221438v1_genomic.fna.gz --refList GCF_002214385.1_ASM221438v1_genomic.fna/target_genomes.txt --output GCF_002214385.1_ASM221438v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:40:48,469] [INFO] Task succeeded: fastANI
[2024-01-24 13:40:48,470] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg55ad27bc-c5b2-427d-aa60-57afc407f214/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:40:48,470] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg55ad27bc-c5b2-427d-aa60-57afc407f214/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:40:48,476] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:40:48,476] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:40:48,476] [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 gorgonarius	strain=W-12	GCA_002214385.1	71997	71997	type	True	100.0	558	558	95	conclusive
Thermococcus zilligii	strain=AN1	GCA_000258515.1	54076	54076	type	True	86.7119	442	558	95	below_threshold
Thermococcus pacificus	strain=P-4	GCA_002214485.1	71998	71998	type	True	86.2908	373	558	95	below_threshold
Thermococcus gammatolerans	strain=EJ3; DSM 15229	GCA_000022365.1	187878	187878	type	True	80.1398	299	558	95	below_threshold
Thermococcus cleftensis	strain=CL1	GCA_000265525.1	163003	163003	type	True	79.9392	280	558	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:40:48,478] [INFO] DFAST Taxonomy check result was written to GCF_002214385.1_ASM221438v1_genomic.fna/tc_result.tsv
[2024-01-24 13:40:48,478] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:40:48,478] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:40:48,479] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg55ad27bc-c5b2-427d-aa60-57afc407f214/dqc_reference/checkm_data
[2024-01-24 13:40:48,480] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:40:48,499] [INFO] Task started: CheckM
[2024-01-24 13:40:48,499] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002214385.1_ASM221438v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002214385.1_ASM221438v1_genomic.fna/checkm_input GCF_002214385.1_ASM221438v1_genomic.fna/checkm_result
[2024-01-24 13:41:06,875] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:06,876] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:06,891] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:06,891] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:06,892] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002214385.1_ASM221438v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:06,892] [INFO] Task started: Blastn
[2024-01-24 13:41:06,892] [INFO] Running command: blastn -query GCF_002214385.1_ASM221438v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg55ad27bc-c5b2-427d-aa60-57afc407f214/dqc_reference/reference_markers_gtdb.fasta -out GCF_002214385.1_ASM221438v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:07,422] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:07,425] [INFO] Selected 5 target genomes.
[2024-01-24 13:41:07,425] [INFO] Target genome list was writen to GCF_002214385.1_ASM221438v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:07,429] [INFO] Task started: fastANI
[2024-01-24 13:41:07,430] [INFO] Running command: fastANI --query /var/lib/cwl/stgdba0c1d7-238b-47e9-9e14-bfc598e00c64/GCF_002214385.1_ASM221438v1_genomic.fna.gz --refList GCF_002214385.1_ASM221438v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002214385.1_ASM221438v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:09,639] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:09,645] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:41:09,645] [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_002214385.1	s__Thermococcus gorgonarius	100.0	558	558	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_000258515.1	s__Thermococcus zilligii	86.7119	442	558	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	80.2064	258	558	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_000022365.1	s__Thermococcus gammatolerans	80.1398	299	558	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_000265525.1	s__Thermococcus cleftensis	79.9976	277	558	d__Archaea;p__Methanobacteriota_B;c__Thermococci;o__Thermococcales;f__Thermococcaceae;g__Thermococcus	95.0	97.89	97.89	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:41:09,647] [INFO] GTDB search result was written to GCF_002214385.1_ASM221438v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:09,647] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:09,655] [INFO] DFAST_QC result json was written to GCF_002214385.1_ASM221438v1_genomic.fna/dqc_result.json
[2024-01-24 13:41:09,656] [INFO] DFAST_QC completed!
[2024-01-24 13:41:09,656] [INFO] Total running time: 0h0m29s