[2024-01-24 12:37:37,928] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:37:37,930] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:37:37,930] [INFO] DQC Reference Directory: /var/lib/cwl/stg4d106e9a-a856-4f02-b53e-39d32e691cdc/dqc_reference
[2024-01-24 12:37:41,026] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:37:41,030] [INFO] Task started: Prodigal
[2024-01-24 12:37:41,031] [INFO] Running command: gunzip -c /var/lib/cwl/stg9121c059-c500-4b33-bf8d-62c2ddf23b4e/GCF_000769655.1_ASM76965v1_genomic.fna.gz | prodigal -d GCF_000769655.1_ASM76965v1_genomic.fna/cds.fna -a GCF_000769655.1_ASM76965v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:46,080] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:46,080] [INFO] Task started: HMMsearch
[2024-01-24 12:37:46,081] [INFO] Running command: hmmsearch --tblout GCF_000769655.1_ASM76965v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4d106e9a-a856-4f02-b53e-39d32e691cdc/dqc_reference/reference_markers.hmm GCF_000769655.1_ASM76965v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:46,408] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:46,410] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg9121c059-c500-4b33-bf8d-62c2ddf23b4e/GCF_000769655.1_ASM76965v1_genomic.fna.gz]
[2024-01-24 12:37:46,435] [INFO] Query marker FASTA was written to GCF_000769655.1_ASM76965v1_genomic.fna/markers.fasta
[2024-01-24 12:37:46,436] [INFO] Task started: Blastn
[2024-01-24 12:37:46,436] [INFO] Running command: blastn -query GCF_000769655.1_ASM76965v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4d106e9a-a856-4f02-b53e-39d32e691cdc/dqc_reference/reference_markers.fasta -out GCF_000769655.1_ASM76965v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:48,475] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:48,479] [INFO] Selected 6 target genomes.
[2024-01-24 12:37:48,480] [INFO] Target genome list was writen to GCF_000769655.1_ASM76965v1_genomic.fna/target_genomes.txt
[2024-01-24 12:37:48,530] [INFO] Task started: fastANI
[2024-01-24 12:37:48,531] [INFO] Running command: fastANI --query /var/lib/cwl/stg9121c059-c500-4b33-bf8d-62c2ddf23b4e/GCF_000769655.1_ASM76965v1_genomic.fna.gz --refList GCF_000769655.1_ASM76965v1_genomic.fna/target_genomes.txt --output GCF_000769655.1_ASM76965v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:37:51,594] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:51,595] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4d106e9a-a856-4f02-b53e-39d32e691cdc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:37:51,596] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4d106e9a-a856-4f02-b53e-39d32e691cdc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:37:51,604] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:37:51,604] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:37:51,605] [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 eurythermalis	strain=A501	GCA_000769655.1	1505907	1505907	type	True	100.0	708	708	95	conclusive
Thermococcus guaymasensis	strain=DSM 11113	GCA_000816105.1	110164	110164	type	True	86.9724	433	708	95	below_threshold
Thermococcus nautili	strain=30-1	GCA_000585495.1	195522	195522	type	True	84.5447	493	708	95	below_threshold
Thermococcus henrietii	strain=EXT12c	GCA_900198835.1	2016361	2016361	type	True	84.0041	485	708	95	below_threshold
Thermococcus gammatolerans	strain=EJ3; DSM 15229	GCA_000022365.1	187878	187878	type	True	83.6488	379	708	95	below_threshold
Thermococcus celer	strain=Vu 13	GCA_002214365.1	2264	2264	type	True	79.5374	337	708	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:37:51,607] [INFO] DFAST Taxonomy check result was written to GCF_000769655.1_ASM76965v1_genomic.fna/tc_result.tsv
[2024-01-24 12:37:51,607] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:37:51,608] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:37:51,608] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4d106e9a-a856-4f02-b53e-39d32e691cdc/dqc_reference/checkm_data
[2024-01-24 12:37:51,609] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:37:51,634] [INFO] Task started: CheckM
[2024-01-24 12:37:51,635] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000769655.1_ASM76965v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000769655.1_ASM76965v1_genomic.fna/checkm_input GCF_000769655.1_ASM76965v1_genomic.fna/checkm_result
[2024-01-24 12:38:16,264] [INFO] Task succeeded: CheckM
[2024-01-24 12:38:16,266] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:38:16,291] [INFO] ===== Completeness check finished =====
[2024-01-24 12:38:16,292] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:38:16,292] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000769655.1_ASM76965v1_genomic.fna/markers.fasta)
[2024-01-24 12:38:16,292] [INFO] Task started: Blastn
[2024-01-24 12:38:16,292] [INFO] Running command: blastn -query GCF_000769655.1_ASM76965v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4d106e9a-a856-4f02-b53e-39d32e691cdc/dqc_reference/reference_markers_gtdb.fasta -out GCF_000769655.1_ASM76965v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:38:16,898] [INFO] Task succeeded: Blastn
[2024-01-24 12:38:16,901] [INFO] Selected 7 target genomes.
[2024-01-24 12:38:16,901] [INFO] Target genome list was writen to GCF_000769655.1_ASM76965v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:38:16,912] [INFO] Task started: fastANI
[2024-01-24 12:38:16,912] [INFO] Running command: fastANI --query /var/lib/cwl/stg9121c059-c500-4b33-bf8d-62c2ddf23b4e/GCF_000769655.1_ASM76965v1_genomic.fna.gz --refList GCF_000769655.1_ASM76965v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000769655.1_ASM76965v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:38:20,567] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:20,574] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:38:20,574] [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_000769655.1	s__Thermococcus eurythermalis	100.0	708	708	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_000816105.1	s__Thermococcus guaymasensis	86.9472	433	708	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_000585495.1	s__Thermococcus nautili	84.5092	495	708	d__Archaea;p__Methanobacteriota_B;c__Thermococci;o__Thermococcales;f__Thermococcaceae;g__Thermococcus	95.0	97.44	97.44	0.91	0.91	2	-
GCF_012027635.1	s__Thermococcus sp012027635	84.0587	452	708	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_900198835.1	s__Thermococcus sp900198835	83.9893	486	708	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	83.6655	378	708	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_000151205.2	s__Thermococcus sp000151205	82.6729	402	708	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 12:38:20,576] [INFO] GTDB search result was written to GCF_000769655.1_ASM76965v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:38:20,577] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:38:20,582] [INFO] DFAST_QC result json was written to GCF_000769655.1_ASM76965v1_genomic.fna/dqc_result.json
[2024-01-24 12:38:20,583] [INFO] DFAST_QC completed!
[2024-01-24 12:38:20,583] [INFO] Total running time: 0h0m43s