[2024-01-24 13:49:27,519] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:27,529] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:27,529] [INFO] DQC Reference Directory: /var/lib/cwl/stg8c2005a5-3a6c-41bf-85d9-8e484570df7f/dqc_reference
[2024-01-24 13:49:28,865] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:28,865] [INFO] Task started: Prodigal
[2024-01-24 13:49:28,866] [INFO] Running command: gunzip -c /var/lib/cwl/stg2e39e02c-d6b5-4358-8c8d-10c955f854a2/GCF_900258485.1_PRJEB22822_genomic.fna.gz | prodigal -d GCF_900258485.1_PRJEB22822_genomic.fna/cds.fna -a GCF_900258485.1_PRJEB22822_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:31,202] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:31,203] [INFO] Task started: HMMsearch
[2024-01-24 13:49:31,203] [INFO] Running command: hmmsearch --tblout GCF_900258485.1_PRJEB22822_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8c2005a5-3a6c-41bf-85d9-8e484570df7f/dqc_reference/reference_markers.hmm GCF_900258485.1_PRJEB22822_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:31,404] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:31,405] [INFO] Found 6/6 markers.
[2024-01-24 13:49:31,419] [INFO] Query marker FASTA was written to GCF_900258485.1_PRJEB22822_genomic.fna/markers.fasta
[2024-01-24 13:49:31,420] [INFO] Task started: Blastn
[2024-01-24 13:49:31,420] [INFO] Running command: blastn -query GCF_900258485.1_PRJEB22822_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c2005a5-3a6c-41bf-85d9-8e484570df7f/dqc_reference/reference_markers.fasta -out GCF_900258485.1_PRJEB22822_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:31,983] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:31,985] [INFO] Selected 18 target genomes.
[2024-01-24 13:49:31,986] [INFO] Target genome list was writen to GCF_900258485.1_PRJEB22822_genomic.fna/target_genomes.txt
[2024-01-24 13:49:32,007] [INFO] Task started: fastANI
[2024-01-24 13:49:32,007] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e39e02c-d6b5-4358-8c8d-10c955f854a2/GCF_900258485.1_PRJEB22822_genomic.fna.gz --refList GCF_900258485.1_PRJEB22822_genomic.fna/target_genomes.txt --output GCF_900258485.1_PRJEB22822_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:39,862] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:39,863] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8c2005a5-3a6c-41bf-85d9-8e484570df7f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:39,863] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8c2005a5-3a6c-41bf-85d9-8e484570df7f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:39,867] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:49:39,867] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:39,867] [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
Helcococcus massiliensis	strain=Marseille-P4590	GCA_900258485.1	2040290	2040290	type	True	100.0	446	447	95	conclusive
Helcococcus sueciensis	strain=DSM 17243	GCA_000423145.1	241555	241555	type	True	79.867	121	447	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:39,869] [INFO] DFAST Taxonomy check result was written to GCF_900258485.1_PRJEB22822_genomic.fna/tc_result.tsv
[2024-01-24 13:49:39,870] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:39,870] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:39,870] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8c2005a5-3a6c-41bf-85d9-8e484570df7f/dqc_reference/checkm_data
[2024-01-24 13:49:39,871] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:39,886] [INFO] Task started: CheckM
[2024-01-24 13:49:39,887] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900258485.1_PRJEB22822_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900258485.1_PRJEB22822_genomic.fna/checkm_input GCF_900258485.1_PRJEB22822_genomic.fna/checkm_result
[2024-01-24 13:49:55,178] [INFO] Task succeeded: CheckM
[2024-01-24 13:49:55,179] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:49:55,201] [INFO] ===== Completeness check finished =====
[2024-01-24 13:49:55,201] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:49:55,202] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900258485.1_PRJEB22822_genomic.fna/markers.fasta)
[2024-01-24 13:49:55,202] [INFO] Task started: Blastn
[2024-01-24 13:49:55,202] [INFO] Running command: blastn -query GCF_900258485.1_PRJEB22822_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c2005a5-3a6c-41bf-85d9-8e484570df7f/dqc_reference/reference_markers_gtdb.fasta -out GCF_900258485.1_PRJEB22822_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:56,025] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:56,028] [INFO] Selected 24 target genomes.
[2024-01-24 13:49:56,029] [INFO] Target genome list was writen to GCF_900258485.1_PRJEB22822_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:49:56,088] [INFO] Task started: fastANI
[2024-01-24 13:49:56,089] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e39e02c-d6b5-4358-8c8d-10c955f854a2/GCF_900258485.1_PRJEB22822_genomic.fna.gz --refList GCF_900258485.1_PRJEB22822_genomic.fna/target_genomes_gtdb.txt --output GCF_900258485.1_PRJEB22822_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:05,347] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:05,351] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:05,351] [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_900258485.1	s__Helcococcus massiliensis	100.0	446	447	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Helcococcus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000423145.1	s__Helcococcus sueciensis	79.867	121	447	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Helcococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004524775.1	s__Helcococcus ovis	77.1905	72	447	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Helcococcus	95.0	99.42	99.12	0.95	0.90	4	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:05,353] [INFO] GTDB search result was written to GCF_900258485.1_PRJEB22822_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:05,353] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:05,356] [INFO] DFAST_QC result json was written to GCF_900258485.1_PRJEB22822_genomic.fna/dqc_result.json
[2024-01-24 13:50:05,356] [INFO] DFAST_QC completed!
[2024-01-24 13:50:05,356] [INFO] Total running time: 0h0m38s