[2024-01-24 11:42:20,301] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:42:20,303] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:42:20,303] [INFO] DQC Reference Directory: /var/lib/cwl/stg0eb31aa3-f912-44c6-9da2-47e2902b3982/dqc_reference
[2024-01-24 11:42:24,522] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:42:24,524] [INFO] Task started: Prodigal
[2024-01-24 11:42:24,524] [INFO] Running command: gunzip -c /var/lib/cwl/stga10e04d3-72dc-4f56-8cc2-244f359b2593/GCF_008329965.1_ASM832996v1_genomic.fna.gz | prodigal -d GCF_008329965.1_ASM832996v1_genomic.fna/cds.fna -a GCF_008329965.1_ASM832996v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:42:33,954] [INFO] Task succeeded: Prodigal
[2024-01-24 11:42:33,955] [INFO] Task started: HMMsearch
[2024-01-24 11:42:33,955] [INFO] Running command: hmmsearch --tblout GCF_008329965.1_ASM832996v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0eb31aa3-f912-44c6-9da2-47e2902b3982/dqc_reference/reference_markers.hmm GCF_008329965.1_ASM832996v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:42:34,205] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:42:34,207] [INFO] Found 6/6 markers.
[2024-01-24 11:42:34,243] [INFO] Query marker FASTA was written to GCF_008329965.1_ASM832996v1_genomic.fna/markers.fasta
[2024-01-24 11:42:34,244] [INFO] Task started: Blastn
[2024-01-24 11:42:34,244] [INFO] Running command: blastn -query GCF_008329965.1_ASM832996v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0eb31aa3-f912-44c6-9da2-47e2902b3982/dqc_reference/reference_markers.fasta -out GCF_008329965.1_ASM832996v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:42:34,801] [INFO] Task succeeded: Blastn
[2024-01-24 11:42:34,806] [INFO] Selected 19 target genomes.
[2024-01-24 11:42:34,806] [INFO] Target genome list was writen to GCF_008329965.1_ASM832996v1_genomic.fna/target_genomes.txt
[2024-01-24 11:42:34,860] [INFO] Task started: fastANI
[2024-01-24 11:42:34,860] [INFO] Running command: fastANI --query /var/lib/cwl/stga10e04d3-72dc-4f56-8cc2-244f359b2593/GCF_008329965.1_ASM832996v1_genomic.fna.gz --refList GCF_008329965.1_ASM832996v1_genomic.fna/target_genomes.txt --output GCF_008329965.1_ASM832996v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:42:44,345] [INFO] Task succeeded: fastANI
[2024-01-24 11:42:44,346] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0eb31aa3-f912-44c6-9da2-47e2902b3982/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:42:44,347] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0eb31aa3-f912-44c6-9da2-47e2902b3982/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:42:44,350] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:42:44,351] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:42:44,351] [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
Oceanispirochaeta crateris	strain=K2	GCA_008329965.1	2518645	2518645	type	True	100.0	1336	1337	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 11:42:44,352] [INFO] DFAST Taxonomy check result was written to GCF_008329965.1_ASM832996v1_genomic.fna/tc_result.tsv
[2024-01-24 11:42:44,352] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:42:44,353] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:42:44,353] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0eb31aa3-f912-44c6-9da2-47e2902b3982/dqc_reference/checkm_data
[2024-01-24 11:42:44,354] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:42:44,396] [INFO] Task started: CheckM
[2024-01-24 11:42:44,396] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008329965.1_ASM832996v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008329965.1_ASM832996v1_genomic.fna/checkm_input GCF_008329965.1_ASM832996v1_genomic.fna/checkm_result
[2024-01-24 11:43:17,999] [INFO] Task succeeded: CheckM
[2024-01-24 11:43:18,000] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:43:18,021] [INFO] ===== Completeness check finished =====
[2024-01-24 11:43:18,022] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:43:18,022] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008329965.1_ASM832996v1_genomic.fna/markers.fasta)
[2024-01-24 11:43:18,023] [INFO] Task started: Blastn
[2024-01-24 11:43:18,023] [INFO] Running command: blastn -query GCF_008329965.1_ASM832996v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0eb31aa3-f912-44c6-9da2-47e2902b3982/dqc_reference/reference_markers_gtdb.fasta -out GCF_008329965.1_ASM832996v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:43:18,796] [INFO] Task succeeded: Blastn
[2024-01-24 11:43:18,799] [INFO] Selected 24 target genomes.
[2024-01-24 11:43:18,800] [INFO] Target genome list was writen to GCF_008329965.1_ASM832996v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:43:18,820] [INFO] Task started: fastANI
[2024-01-24 11:43:18,820] [INFO] Running command: fastANI --query /var/lib/cwl/stga10e04d3-72dc-4f56-8cc2-244f359b2593/GCF_008329965.1_ASM832996v1_genomic.fna.gz --refList GCF_008329965.1_ASM832996v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008329965.1_ASM832996v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:43:30,859] [INFO] Task succeeded: fastANI
[2024-01-24 11:43:30,870] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:43:30,870] [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_008329965.1	s__Oceanispirochaeta crateris	100.0	1337	1337	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Spirochaetales_E;f__Spirochaetaceae_B;g__Oceanispirochaeta	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003346715.1	s__Oceanispirochaeta sp003346715	77.7425	242	1337	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Spirochaetales_E;f__Spirochaetaceae_B;g__Oceanispirochaeta	95.0	100.00	100.00	1.00	1.00	3	-
GCA_003249275.1	s__Oceanispirochaeta sp003249275	77.5883	79	1337	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Spirochaetales_E;f__Spirochaetaceae_B;g__Oceanispirochaeta	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002408085.1	s__Oceanispirochaeta sp002408085	77.0336	153	1337	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Spirochaetales_E;f__Spirochaetaceae_B;g__Oceanispirochaeta	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002084805.1	s__Oceanispirochaeta sp002084805	76.6409	96	1337	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Spirochaetales_E;f__Spirochaetaceae_B;g__Oceanispirochaeta	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:43:30,873] [INFO] GTDB search result was written to GCF_008329965.1_ASM832996v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:43:30,873] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:43:30,876] [INFO] DFAST_QC result json was written to GCF_008329965.1_ASM832996v1_genomic.fna/dqc_result.json
[2024-01-24 11:43:30,876] [INFO] DFAST_QC completed!
[2024-01-24 11:43:30,876] [INFO] Total running time: 0h1m11s