[2024-01-25 19:45:35,495] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:45:35,497] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:45:35,497] [INFO] DQC Reference Directory: /var/lib/cwl/stg77f94cfd-c72a-4d41-872d-8c8f82d04b75/dqc_reference
[2024-01-25 19:45:36,620] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:45:36,621] [INFO] Task started: Prodigal
[2024-01-25 19:45:36,621] [INFO] Running command: gunzip -c /var/lib/cwl/stgeaa587bb-0a5a-44a0-bc71-a9ab6dde9f2e/GCF_001647085.1_ASM164708v1_genomic.fna.gz | prodigal -d GCF_001647085.1_ASM164708v1_genomic.fna/cds.fna -a GCF_001647085.1_ASM164708v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:45:40,780] [INFO] Task succeeded: Prodigal
[2024-01-25 19:45:40,781] [INFO] Task started: HMMsearch
[2024-01-25 19:45:40,781] [INFO] Running command: hmmsearch --tblout GCF_001647085.1_ASM164708v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg77f94cfd-c72a-4d41-872d-8c8f82d04b75/dqc_reference/reference_markers.hmm GCF_001647085.1_ASM164708v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:45:40,947] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:45:40,948] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgeaa587bb-0a5a-44a0-bc71-a9ab6dde9f2e/GCF_001647085.1_ASM164708v1_genomic.fna.gz]
[2024-01-25 19:45:40,967] [INFO] Query marker FASTA was written to GCF_001647085.1_ASM164708v1_genomic.fna/markers.fasta
[2024-01-25 19:45:40,967] [INFO] Task started: Blastn
[2024-01-25 19:45:40,967] [INFO] Running command: blastn -query GCF_001647085.1_ASM164708v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg77f94cfd-c72a-4d41-872d-8c8f82d04b75/dqc_reference/reference_markers.fasta -out GCF_001647085.1_ASM164708v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:45:41,418] [INFO] Task succeeded: Blastn
[2024-01-25 19:45:41,421] [INFO] Selected 5 target genomes.
[2024-01-25 19:45:41,421] [INFO] Target genome list was writen to GCF_001647085.1_ASM164708v1_genomic.fna/target_genomes.txt
[2024-01-25 19:45:41,443] [INFO] Task started: fastANI
[2024-01-25 19:45:41,443] [INFO] Running command: fastANI --query /var/lib/cwl/stgeaa587bb-0a5a-44a0-bc71-a9ab6dde9f2e/GCF_001647085.1_ASM164708v1_genomic.fna.gz --refList GCF_001647085.1_ASM164708v1_genomic.fna/target_genomes.txt --output GCF_001647085.1_ASM164708v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:45:43,982] [INFO] Task succeeded: fastANI
[2024-01-25 19:45:43,982] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg77f94cfd-c72a-4d41-872d-8c8f82d04b75/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:45:43,983] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg77f94cfd-c72a-4d41-872d-8c8f82d04b75/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:45:43,988] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:45:43,988] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:45:43,988] [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 piezophilus	strain=CDGS	GCA_001647085.1	1712654	1712654	type	True	100.0	642	642	95	conclusive
Thermococcus onnurineus	strain=NA1	GCA_000018365.1	342948	342948	type	True	87.5812	479	642	95	below_threshold
Thermococcus radiotolerans	strain=EJ2	GCA_002214565.1	187880	187880	type	True	79.9062	351	642	95	below_threshold
Thermococcus indicus	strain=IOH1	GCA_006274605.1	2586643	2586643	type	True	79.7237	347	642	95	below_threshold
Thermococcus profundus	strain=DT 5432	GCA_002214585.1	49899	49899	type	True	79.0149	229	642	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:45:43,990] [INFO] DFAST Taxonomy check result was written to GCF_001647085.1_ASM164708v1_genomic.fna/tc_result.tsv
[2024-01-25 19:45:43,990] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:45:43,990] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:45:43,991] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg77f94cfd-c72a-4d41-872d-8c8f82d04b75/dqc_reference/checkm_data
[2024-01-25 19:45:43,991] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:45:44,013] [INFO] Task started: CheckM
[2024-01-25 19:45:44,014] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001647085.1_ASM164708v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001647085.1_ASM164708v1_genomic.fna/checkm_input GCF_001647085.1_ASM164708v1_genomic.fna/checkm_result
[2024-01-25 19:46:02,155] [INFO] Task succeeded: CheckM
[2024-01-25 19:46:02,156] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:46:02,169] [INFO] ===== Completeness check finished =====
[2024-01-25 19:46:02,169] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:46:02,169] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001647085.1_ASM164708v1_genomic.fna/markers.fasta)
[2024-01-25 19:46:02,169] [INFO] Task started: Blastn
[2024-01-25 19:46:02,169] [INFO] Running command: blastn -query GCF_001647085.1_ASM164708v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg77f94cfd-c72a-4d41-872d-8c8f82d04b75/dqc_reference/reference_markers_gtdb.fasta -out GCF_001647085.1_ASM164708v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:46:02,643] [INFO] Task succeeded: Blastn
[2024-01-25 19:46:02,650] [INFO] Selected 5 target genomes.
[2024-01-25 19:46:02,650] [INFO] Target genome list was writen to GCF_001647085.1_ASM164708v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:46:02,654] [INFO] Task started: fastANI
[2024-01-25 19:46:02,654] [INFO] Running command: fastANI --query /var/lib/cwl/stgeaa587bb-0a5a-44a0-bc71-a9ab6dde9f2e/GCF_001647085.1_ASM164708v1_genomic.fna.gz --refList GCF_001647085.1_ASM164708v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001647085.1_ASM164708v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:46:05,173] [INFO] Task succeeded: fastANI
[2024-01-25 19:46:05,177] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:46:05,178] [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_001647085.1	s__Thermococcus piezophilus	100.0	642	642	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_012027555.1	s__Thermococcus sp012027555	94.2225	524	642	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_000018365.1	s__Thermococcus onnurineus	87.5896	479	642	d__Archaea;p__Methanobacteriota_B;c__Thermococci;o__Thermococcales;f__Thermococcaceae;g__Thermococcus	95.0	98.12	96.29	0.92	0.90	5	-
GCF_012027395.1	s__Thermococcus sp012027395	87.3696	491	642	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_002214565.1	s__Thermococcus radiotolerans	79.9062	351	642	d__Archaea;p__Methanobacteriota_B;c__Thermococci;o__Thermococcales;f__Thermococcaceae;g__Thermococcus	95.0	95.62	95.62	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:46:05,179] [INFO] GTDB search result was written to GCF_001647085.1_ASM164708v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:46:05,179] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:46:05,181] [INFO] DFAST_QC result json was written to GCF_001647085.1_ASM164708v1_genomic.fna/dqc_result.json
[2024-01-25 19:46:05,182] [INFO] DFAST_QC completed!
[2024-01-25 19:46:05,182] [INFO] Total running time: 0h0m30s