[2024-01-24 13:33:11,391] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:33:11,392] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:33:11,393] [INFO] DQC Reference Directory: /var/lib/cwl/stgd7873067-76c4-4211-9946-3721642da6f7/dqc_reference
[2024-01-24 13:33:12,723] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:33:12,724] [INFO] Task started: Prodigal
[2024-01-24 13:33:12,724] [INFO] Running command: gunzip -c /var/lib/cwl/stga4172679-720c-491b-8389-4615dda0ab53/GCF_001049895.1_Rubeoparvulum_massiliensis_genomic.fna.gz | prodigal -d GCF_001049895.1_Rubeoparvulum_massiliensis_genomic.fna/cds.fna -a GCF_001049895.1_Rubeoparvulum_massiliensis_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:33:19,731] [INFO] Task succeeded: Prodigal
[2024-01-24 13:33:19,731] [INFO] Task started: HMMsearch
[2024-01-24 13:33:19,731] [INFO] Running command: hmmsearch --tblout GCF_001049895.1_Rubeoparvulum_massiliensis_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd7873067-76c4-4211-9946-3721642da6f7/dqc_reference/reference_markers.hmm GCF_001049895.1_Rubeoparvulum_massiliensis_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:33:19,988] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:33:19,990] [INFO] Found 6/6 markers.
[2024-01-24 13:33:20,021] [INFO] Query marker FASTA was written to GCF_001049895.1_Rubeoparvulum_massiliensis_genomic.fna/markers.fasta
[2024-01-24 13:33:20,022] [INFO] Task started: Blastn
[2024-01-24 13:33:20,022] [INFO] Running command: blastn -query GCF_001049895.1_Rubeoparvulum_massiliensis_genomic.fna/markers.fasta -db /var/lib/cwl/stgd7873067-76c4-4211-9946-3721642da6f7/dqc_reference/reference_markers.fasta -out GCF_001049895.1_Rubeoparvulum_massiliensis_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:20,637] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:20,641] [INFO] Selected 23 target genomes.
[2024-01-24 13:33:20,641] [INFO] Target genome list was writen to GCF_001049895.1_Rubeoparvulum_massiliensis_genomic.fna/target_genomes.txt
[2024-01-24 13:33:20,674] [INFO] Task started: fastANI
[2024-01-24 13:33:20,674] [INFO] Running command: fastANI --query /var/lib/cwl/stga4172679-720c-491b-8389-4615dda0ab53/GCF_001049895.1_Rubeoparvulum_massiliensis_genomic.fna.gz --refList GCF_001049895.1_Rubeoparvulum_massiliensis_genomic.fna/target_genomes.txt --output GCF_001049895.1_Rubeoparvulum_massiliensis_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:33,735] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:33,736] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd7873067-76c4-4211-9946-3721642da6f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:33,736] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd7873067-76c4-4211-9946-3721642da6f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:33,743] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:33:33,743] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:33:33,743] [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
Rubeoparvulum massiliense	strain=mt6	GCA_001049895.1	1631346	1631346	type	True	100.0	946	946	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 13:33:33,745] [INFO] DFAST Taxonomy check result was written to GCF_001049895.1_Rubeoparvulum_massiliensis_genomic.fna/tc_result.tsv
[2024-01-24 13:33:33,746] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:33,746] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:33,746] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd7873067-76c4-4211-9946-3721642da6f7/dqc_reference/checkm_data
[2024-01-24 13:33:33,748] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:33,777] [INFO] Task started: CheckM
[2024-01-24 13:33:33,777] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001049895.1_Rubeoparvulum_massiliensis_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001049895.1_Rubeoparvulum_massiliensis_genomic.fna/checkm_input GCF_001049895.1_Rubeoparvulum_massiliensis_genomic.fna/checkm_result
[2024-01-24 13:34:00,925] [INFO] Task succeeded: CheckM
[2024-01-24 13:34:00,926] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:34:00,944] [INFO] ===== Completeness check finished =====
[2024-01-24 13:34:00,944] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:34:00,944] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001049895.1_Rubeoparvulum_massiliensis_genomic.fna/markers.fasta)
[2024-01-24 13:34:00,945] [INFO] Task started: Blastn
[2024-01-24 13:34:00,945] [INFO] Running command: blastn -query GCF_001049895.1_Rubeoparvulum_massiliensis_genomic.fna/markers.fasta -db /var/lib/cwl/stgd7873067-76c4-4211-9946-3721642da6f7/dqc_reference/reference_markers_gtdb.fasta -out GCF_001049895.1_Rubeoparvulum_massiliensis_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:34:01,697] [INFO] Task succeeded: Blastn
[2024-01-24 13:34:01,701] [INFO] Selected 24 target genomes.
[2024-01-24 13:34:01,701] [INFO] Target genome list was writen to GCF_001049895.1_Rubeoparvulum_massiliensis_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:34:01,740] [INFO] Task started: fastANI
[2024-01-24 13:34:01,740] [INFO] Running command: fastANI --query /var/lib/cwl/stga4172679-720c-491b-8389-4615dda0ab53/GCF_001049895.1_Rubeoparvulum_massiliensis_genomic.fna.gz --refList GCF_001049895.1_Rubeoparvulum_massiliensis_genomic.fna/target_genomes_gtdb.txt --output GCF_001049895.1_Rubeoparvulum_massiliensis_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:34:16,284] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:16,289] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:34:16,289] [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_001049895.1	s__Rubeoparvulum massiliense	100.0	946	946	d__Bacteria;p__Firmicutes;c__Bacilli;o__Rubeoparvulales;f__Rubeoparvulaceae;g__Rubeoparvulum	95.0	100.00	100.00	1.00	1.00	2	conclusive
--------------------------------------------------------------------------------
[2024-01-24 13:34:16,290] [INFO] GTDB search result was written to GCF_001049895.1_Rubeoparvulum_massiliensis_genomic.fna/result_gtdb.tsv
[2024-01-24 13:34:16,291] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:34:16,293] [INFO] DFAST_QC result json was written to GCF_001049895.1_Rubeoparvulum_massiliensis_genomic.fna/dqc_result.json
[2024-01-24 13:34:16,293] [INFO] DFAST_QC completed!
[2024-01-24 13:34:16,293] [INFO] Total running time: 0h1m5s