[2024-01-24 14:20:01,498] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:20:01,500] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:20:01,500] [INFO] DQC Reference Directory: /var/lib/cwl/stga7947e44-2e04-45c7-84a2-a2c7c5fb41c9/dqc_reference
[2024-01-24 14:20:03,423] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:20:03,424] [INFO] Task started: Prodigal
[2024-01-24 14:20:03,424] [INFO] Running command: gunzip -c /var/lib/cwl/stg0f8e6da0-addb-4eb0-a664-76919dbebe50/GCF_023746595.1_ASM2374659v1_genomic.fna.gz | prodigal -d GCF_023746595.1_ASM2374659v1_genomic.fna/cds.fna -a GCF_023746595.1_ASM2374659v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:20:08,431] [INFO] Task succeeded: Prodigal
[2024-01-24 14:20:08,431] [INFO] Task started: HMMsearch
[2024-01-24 14:20:08,431] [INFO] Running command: hmmsearch --tblout GCF_023746595.1_ASM2374659v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga7947e44-2e04-45c7-84a2-a2c7c5fb41c9/dqc_reference/reference_markers.hmm GCF_023746595.1_ASM2374659v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:20:08,782] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:20:08,783] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg0f8e6da0-addb-4eb0-a664-76919dbebe50/GCF_023746595.1_ASM2374659v1_genomic.fna.gz]
[2024-01-24 14:20:08,810] [INFO] Query marker FASTA was written to GCF_023746595.1_ASM2374659v1_genomic.fna/markers.fasta
[2024-01-24 14:20:08,811] [INFO] Task started: Blastn
[2024-01-24 14:20:08,811] [INFO] Running command: blastn -query GCF_023746595.1_ASM2374659v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga7947e44-2e04-45c7-84a2-a2c7c5fb41c9/dqc_reference/reference_markers.fasta -out GCF_023746595.1_ASM2374659v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:09,384] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:09,387] [INFO] Selected 3 target genomes.
[2024-01-24 14:20:09,388] [INFO] Target genome list was writen to GCF_023746595.1_ASM2374659v1_genomic.fna/target_genomes.txt
[2024-01-24 14:20:09,390] [INFO] Task started: fastANI
[2024-01-24 14:20:09,390] [INFO] Running command: fastANI --query /var/lib/cwl/stg0f8e6da0-addb-4eb0-a664-76919dbebe50/GCF_023746595.1_ASM2374659v1_genomic.fna.gz --refList GCF_023746595.1_ASM2374659v1_genomic.fna/target_genomes.txt --output GCF_023746595.1_ASM2374659v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:20:10,863] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:10,863] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga7947e44-2e04-45c7-84a2-a2c7c5fb41c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:20:10,864] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga7947e44-2e04-45c7-84a2-a2c7c5fb41c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:20:10,868] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:20:10,868] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:20:10,868] [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 barophilus	strain=MP	GCA_000151105.2	55802	55802	type	True	77.7886	96	648	95	below_threshold
Thermococcus paralvinellae	strain=ES1	GCA_000517445.1	582419	582419	type	True	77.5155	103	648	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:20:10,870] [INFO] DFAST Taxonomy check result was written to GCF_023746595.1_ASM2374659v1_genomic.fna/tc_result.tsv
[2024-01-24 14:20:10,871] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:20:10,871] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:20:10,871] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga7947e44-2e04-45c7-84a2-a2c7c5fb41c9/dqc_reference/checkm_data
[2024-01-24 14:20:10,873] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:20:10,909] [INFO] Task started: CheckM
[2024-01-24 14:20:10,909] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_023746595.1_ASM2374659v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_023746595.1_ASM2374659v1_genomic.fna/checkm_input GCF_023746595.1_ASM2374659v1_genomic.fna/checkm_result
[2024-01-24 14:20:35,125] [INFO] Task succeeded: CheckM
[2024-01-24 14:20:35,126] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:20:35,157] [INFO] ===== Completeness check finished =====
[2024-01-24 14:20:35,158] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:20:35,158] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_023746595.1_ASM2374659v1_genomic.fna/markers.fasta)
[2024-01-24 14:20:35,158] [INFO] Task started: Blastn
[2024-01-24 14:20:35,159] [INFO] Running command: blastn -query GCF_023746595.1_ASM2374659v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga7947e44-2e04-45c7-84a2-a2c7c5fb41c9/dqc_reference/reference_markers_gtdb.fasta -out GCF_023746595.1_ASM2374659v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:35,678] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:35,681] [INFO] Selected 6 target genomes.
[2024-01-24 14:20:35,681] [INFO] Target genome list was writen to GCF_023746595.1_ASM2374659v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:20:35,685] [INFO] Task started: fastANI
[2024-01-24 14:20:35,685] [INFO] Running command: fastANI --query /var/lib/cwl/stg0f8e6da0-addb-4eb0-a664-76919dbebe50/GCF_023746595.1_ASM2374659v1_genomic.fna.gz --refList GCF_023746595.1_ASM2374659v1_genomic.fna/target_genomes_gtdb.txt --output GCF_023746595.1_ASM2374659v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:20:38,293] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:38,303] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:20:38,304] [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_001317345.1	s__Thermococcus_A sp001317345	93.9837	557	648	d__Archaea;p__Methanobacteriota_B;c__Thermococci;o__Thermococcales;f__Thermococcaceae;g__Thermococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012027425.1	s__Thermococcus_A sp012027425	91.4662	529	648	d__Archaea;p__Methanobacteriota_B;c__Thermococci;o__Thermococcales;f__Thermococcaceae;g__Thermococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000430485.1	s__Thermococcus_A sp000430485	78.1484	202	648	d__Archaea;p__Methanobacteriota_B;c__Thermococci;o__Thermococcales;f__Thermococcaceae;g__Thermococcus_A	95.0	96.03	95.46	0.86	0.83	4	-
GCF_000151105.2	s__Thermococcus_B barophilus	77.7921	96	648	d__Archaea;p__Methanobacteriota_B;c__Thermococci;o__Thermococcales;f__Thermococcaceae;g__Thermococcus_B	95.0	97.81	97.81	0.90	0.90	2	-
GCF_000517445.1	s__Thermococcus_B paralvinellae	77.553	103	648	d__Archaea;p__Methanobacteriota_B;c__Thermococci;o__Thermococcales;f__Thermococcaceae;g__Thermococcus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012027325.1	s__Thermococcus_B sp012027325	77.4688	101	648	d__Archaea;p__Methanobacteriota_B;c__Thermococci;o__Thermococcales;f__Thermococcaceae;g__Thermococcus_B	95.0	99.41	99.41	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:20:38,305] [INFO] GTDB search result was written to GCF_023746595.1_ASM2374659v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:20:38,306] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:20:38,309] [INFO] DFAST_QC result json was written to GCF_023746595.1_ASM2374659v1_genomic.fna/dqc_result.json
[2024-01-24 14:20:38,310] [INFO] DFAST_QC completed!
[2024-01-24 14:20:38,310] [INFO] Total running time: 0h0m37s