[2024-01-24 11:18:17,698] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:18:17,701] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:18:17,701] [INFO] DQC Reference Directory: /var/lib/cwl/stg8bb79d2c-c6e1-4a82-b724-93185441984d/dqc_reference
[2024-01-24 11:18:19,086] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:18:19,087] [INFO] Task started: Prodigal
[2024-01-24 11:18:19,087] [INFO] Running command: gunzip -c /var/lib/cwl/stg82dcb0a6-2aa0-48c8-b375-ead6fd8cc17c/GCF_001592435.1_ASM159243v1_genomic.fna.gz | prodigal -d GCF_001592435.1_ASM159243v1_genomic.fna/cds.fna -a GCF_001592435.1_ASM159243v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:18:23,547] [INFO] Task succeeded: Prodigal
[2024-01-24 11:18:23,547] [INFO] Task started: HMMsearch
[2024-01-24 11:18:23,547] [INFO] Running command: hmmsearch --tblout GCF_001592435.1_ASM159243v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8bb79d2c-c6e1-4a82-b724-93185441984d/dqc_reference/reference_markers.hmm GCF_001592435.1_ASM159243v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:18:23,755] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:18:23,756] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg82dcb0a6-2aa0-48c8-b375-ead6fd8cc17c/GCF_001592435.1_ASM159243v1_genomic.fna.gz]
[2024-01-24 11:18:23,776] [INFO] Query marker FASTA was written to GCF_001592435.1_ASM159243v1_genomic.fna/markers.fasta
[2024-01-24 11:18:23,777] [INFO] Task started: Blastn
[2024-01-24 11:18:23,777] [INFO] Running command: blastn -query GCF_001592435.1_ASM159243v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8bb79d2c-c6e1-4a82-b724-93185441984d/dqc_reference/reference_markers.fasta -out GCF_001592435.1_ASM159243v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:18:24,285] [INFO] Task succeeded: Blastn
[2024-01-24 11:18:24,289] [INFO] Selected 7 target genomes.
[2024-01-24 11:18:24,290] [INFO] Target genome list was writen to GCF_001592435.1_ASM159243v1_genomic.fna/target_genomes.txt
[2024-01-24 11:18:24,299] [INFO] Task started: fastANI
[2024-01-24 11:18:24,299] [INFO] Running command: fastANI --query /var/lib/cwl/stg82dcb0a6-2aa0-48c8-b375-ead6fd8cc17c/GCF_001592435.1_ASM159243v1_genomic.fna.gz --refList GCF_001592435.1_ASM159243v1_genomic.fna/target_genomes.txt --output GCF_001592435.1_ASM159243v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:18:27,417] [INFO] Task succeeded: fastANI
[2024-01-24 11:18:27,417] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8bb79d2c-c6e1-4a82-b724-93185441984d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:18:27,418] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8bb79d2c-c6e1-4a82-b724-93185441984d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:18:27,431] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:18:27,431] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:18:27,431] [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 peptonophilus	strain=OG-1	GCA_001592435.1	53952	53952	type	True	100.0	631	631	95	conclusive
Thermococcus kodakarensis	strain=KOD1	GCA_000009965.1	311400	311400	type	True	89.167	500	631	95	below_threshold
Thermococcus stetteri	strain=DSM 5262	GCA_017873335.1	49900	49900	type	True	85.3664	486	631	95	below_threshold
Thermococcus profundus	strain=DT 5432	GCA_002214585.1	49899	49899	type	True	81.1239	364	631	95	below_threshold
Thermococcus siculi	strain=RG-20	GCA_002214505.1	72803	72803	type	True	80.4182	335	631	95	below_threshold
Thermococcus litoralis	strain=DSM 5473	GCA_000246985.3	2265	2265	type	True	78.1511	89	631	95	below_threshold
Thermococcus alcaliphilus	strain=AEDII12	GCA_024054535.1	139207	139207	type	True	77.6055	84	631	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:18:27,432] [INFO] DFAST Taxonomy check result was written to GCF_001592435.1_ASM159243v1_genomic.fna/tc_result.tsv
[2024-01-24 11:18:27,433] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:18:27,433] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:18:27,433] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8bb79d2c-c6e1-4a82-b724-93185441984d/dqc_reference/checkm_data
[2024-01-24 11:18:27,434] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:18:27,460] [INFO] Task started: CheckM
[2024-01-24 11:18:27,460] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001592435.1_ASM159243v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001592435.1_ASM159243v1_genomic.fna/checkm_input GCF_001592435.1_ASM159243v1_genomic.fna/checkm_result
[2024-01-24 11:18:47,907] [INFO] Task succeeded: CheckM
[2024-01-24 11:18:47,909] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:18:47,929] [INFO] ===== Completeness check finished =====
[2024-01-24 11:18:47,930] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:18:47,930] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001592435.1_ASM159243v1_genomic.fna/markers.fasta)
[2024-01-24 11:18:47,931] [INFO] Task started: Blastn
[2024-01-24 11:18:47,931] [INFO] Running command: blastn -query GCF_001592435.1_ASM159243v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8bb79d2c-c6e1-4a82-b724-93185441984d/dqc_reference/reference_markers_gtdb.fasta -out GCF_001592435.1_ASM159243v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:18:48,488] [INFO] Task succeeded: Blastn
[2024-01-24 11:18:48,491] [INFO] Selected 7 target genomes.
[2024-01-24 11:18:48,491] [INFO] Target genome list was writen to GCF_001592435.1_ASM159243v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:18:48,499] [INFO] Task started: fastANI
[2024-01-24 11:18:48,500] [INFO] Running command: fastANI --query /var/lib/cwl/stg82dcb0a6-2aa0-48c8-b375-ead6fd8cc17c/GCF_001592435.1_ASM159243v1_genomic.fna.gz --refList GCF_001592435.1_ASM159243v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001592435.1_ASM159243v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:18:51,613] [INFO] Task succeeded: fastANI
[2024-01-24 11:18:51,623] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:18:51,623] [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_001592435.1	s__Thermococcus peptonophilus	100.0	631	631	d__Archaea;p__Methanobacteriota_B;c__Thermococci;o__Thermococcales;f__Thermococcaceae;g__Thermococcus	95.0	99.53	99.53	0.99	0.99	2	conclusive
GCF_000009965.1	s__Thermococcus kodakarensis	89.167	500	631	d__Archaea;p__Methanobacteriota_B;c__Thermococci;o__Thermococcales;f__Thermococcaceae;g__Thermococcus	95.0	97.75	97.75	0.93	0.93	2	-
GCF_017873335.1	s__Thermococcus stetteri	85.3664	486	631	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	81.1309	364	631	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	80.5823	327	631	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_000246985.2	s__Thermococcus_A litoralis	78.1912	88	631	d__Archaea;p__Methanobacteriota_B;c__Thermococci;o__Thermococcales;f__Thermococcaceae;g__Thermococcus_A	95.0	96.93	96.93	0.89	0.89	2	-
GCF_001484685.1	s__Thermococcus_A sp001484685	77.5683	91	631	d__Archaea;p__Methanobacteriota_B;c__Thermococci;o__Thermococcales;f__Thermococcaceae;g__Thermococcus_A	95.0	98.39	98.39	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:18:51,624] [INFO] GTDB search result was written to GCF_001592435.1_ASM159243v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:18:51,625] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:18:51,628] [INFO] DFAST_QC result json was written to GCF_001592435.1_ASM159243v1_genomic.fna/dqc_result.json
[2024-01-24 11:18:51,628] [INFO] DFAST_QC completed!
[2024-01-24 11:18:51,628] [INFO] Total running time: 0h0m34s