[2023-03-16 08:41:09,559] [INFO] DFAST_QC pipeline started.
[2023-03-16 08:41:09,560] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 08:41:09,560] [INFO] DQC Reference Directory: /var/lib/cwl/stg9daf6e53-3300-44f0-b872-ac0be61ad5be/dqc_reference
[2023-03-16 08:41:10,643] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 08:41:10,643] [INFO] Task started: Prodigal
[2023-03-16 08:41:10,643] [INFO] Running command: cat /var/lib/cwl/stg59eb3070-d33c-4b2a-9ab2-e3db1caccb90/OceanDNA-b34230.fa | prodigal -d OceanDNA-b34230/cds.fna -a OceanDNA-b34230/protein.faa -g 11 -q > /dev/null
[2023-03-16 08:41:24,753] [INFO] Task succeeded: Prodigal
[2023-03-16 08:41:24,753] [INFO] Task started: HMMsearch
[2023-03-16 08:41:24,753] [INFO] Running command: hmmsearch --tblout OceanDNA-b34230/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9daf6e53-3300-44f0-b872-ac0be61ad5be/dqc_reference/reference_markers.hmm OceanDNA-b34230/protein.faa > /dev/null
[2023-03-16 08:41:24,938] [INFO] Task succeeded: HMMsearch
[2023-03-16 08:41:24,939] [INFO] Found 6/6 markers.
[2023-03-16 08:41:24,978] [INFO] Query marker FASTA was written to OceanDNA-b34230/markers.fasta
[2023-03-16 08:41:24,979] [INFO] Task started: Blastn
[2023-03-16 08:41:24,979] [INFO] Running command: blastn -query OceanDNA-b34230/markers.fasta -db /var/lib/cwl/stg9daf6e53-3300-44f0-b872-ac0be61ad5be/dqc_reference/reference_markers.fasta -out OceanDNA-b34230/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:41:25,557] [INFO] Task succeeded: Blastn
[2023-03-16 08:41:25,558] [INFO] Selected 29 target genomes.
[2023-03-16 08:41:25,558] [INFO] Target genome list was writen to OceanDNA-b34230/target_genomes.txt
[2023-03-16 08:41:25,573] [INFO] Task started: fastANI
[2023-03-16 08:41:25,573] [INFO] Running command: fastANI --query /var/lib/cwl/stg59eb3070-d33c-4b2a-9ab2-e3db1caccb90/OceanDNA-b34230.fa --refList OceanDNA-b34230/target_genomes.txt --output OceanDNA-b34230/fastani_result.tsv --threads 1
[2023-03-16 08:41:43,291] [INFO] Task succeeded: fastANI
[2023-03-16 08:41:43,292] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9daf6e53-3300-44f0-b872-ac0be61ad5be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 08:41:43,292] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9daf6e53-3300-44f0-b872-ac0be61ad5be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 08:41:43,295] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 08:41:43,295] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 08:41:43,295] [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
Sedimenticola selenatireducens	strain=DSM 17993	GCA_000428045.1	191960	191960	type	True	76.4006	61	824	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 08:41:43,295] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34230/tc_result.tsv
[2023-03-16 08:41:43,295] [INFO] ===== Taxonomy check completed =====
[2023-03-16 08:41:43,295] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 08:41:43,295] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9daf6e53-3300-44f0-b872-ac0be61ad5be/dqc_reference/checkm_data
[2023-03-16 08:41:43,296] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 08:41:43,301] [INFO] Task started: CheckM
[2023-03-16 08:41:43,301] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34230/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34230/checkm_input OceanDNA-b34230/checkm_result
[2023-03-16 08:42:21,219] [INFO] Task succeeded: CheckM
[2023-03-16 08:42:21,219] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 08:42:21,224] [INFO] ===== Completeness check finished =====
[2023-03-16 08:42:21,224] [INFO] ===== Start GTDB Search =====
[2023-03-16 08:42:21,224] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34230/markers.fasta)
[2023-03-16 08:42:21,226] [INFO] Task started: Blastn
[2023-03-16 08:42:21,226] [INFO] Running command: blastn -query OceanDNA-b34230/markers.fasta -db /var/lib/cwl/stg9daf6e53-3300-44f0-b872-ac0be61ad5be/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34230/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:42:22,161] [INFO] Task succeeded: Blastn
[2023-03-16 08:42:22,162] [INFO] Selected 32 target genomes.
[2023-03-16 08:42:22,162] [INFO] Target genome list was writen to OceanDNA-b34230/target_genomes_gtdb.txt
[2023-03-16 08:42:22,381] [INFO] Task started: fastANI
[2023-03-16 08:42:22,381] [INFO] Running command: fastANI --query /var/lib/cwl/stg59eb3070-d33c-4b2a-9ab2-e3db1caccb90/OceanDNA-b34230.fa --refList OceanDNA-b34230/target_genomes_gtdb.txt --output OceanDNA-b34230/fastani_result_gtdb.tsv --threads 1
[2023-03-16 08:42:40,423] [INFO] Task succeeded: fastANI
[2023-03-16 08:42:40,425] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 08:42:40,425] [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_000428045.1	s__Sedimenticola selenatireducens	76.4006	61	824	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Sedimenticola	95.0	98.15	98.15	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2023-03-16 08:42:40,436] [INFO] GTDB search result was written to OceanDNA-b34230/result_gtdb.tsv
[2023-03-16 08:42:40,456] [INFO] ===== GTDB Search completed =====
[2023-03-16 08:42:40,456] [INFO] DFAST_QC result json was written to OceanDNA-b34230/dqc_result.json
[2023-03-16 08:42:40,457] [INFO] DFAST_QC completed!
[2023-03-16 08:42:40,457] [INFO] Total running time: 0h1m31s