[2023-03-16 04:20:43,529] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:20:43,529] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:20:43,529] [INFO] DQC Reference Directory: /var/lib/cwl/stg946ca398-b492-49cd-89db-c2a0ac468641/dqc_reference
[2023-03-16 04:20:44,639] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:20:44,639] [INFO] Task started: Prodigal
[2023-03-16 04:20:44,639] [INFO] Running command: cat /var/lib/cwl/stg3915d5a7-230d-404c-8950-4ca32c83c44e/OceanDNA-b10079.fa | prodigal -d OceanDNA-b10079/cds.fna -a OceanDNA-b10079/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:20:58,226] [INFO] Task succeeded: Prodigal
[2023-03-16 04:20:58,226] [INFO] Task started: HMMsearch
[2023-03-16 04:20:58,226] [INFO] Running command: hmmsearch --tblout OceanDNA-b10079/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg946ca398-b492-49cd-89db-c2a0ac468641/dqc_reference/reference_markers.hmm OceanDNA-b10079/protein.faa > /dev/null
[2023-03-16 04:20:58,387] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:20:58,388] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg3915d5a7-230d-404c-8950-4ca32c83c44e/OceanDNA-b10079.fa]
[2023-03-16 04:20:58,403] [INFO] Query marker FASTA was written to OceanDNA-b10079/markers.fasta
[2023-03-16 04:20:58,403] [INFO] Task started: Blastn
[2023-03-16 04:20:58,403] [INFO] Running command: blastn -query OceanDNA-b10079/markers.fasta -db /var/lib/cwl/stg946ca398-b492-49cd-89db-c2a0ac468641/dqc_reference/reference_markers.fasta -out OceanDNA-b10079/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:20:58,958] [INFO] Task succeeded: Blastn
[2023-03-16 04:20:58,959] [INFO] Selected 24 target genomes.
[2023-03-16 04:20:58,959] [INFO] Target genome list was writen to OceanDNA-b10079/target_genomes.txt
[2023-03-16 04:20:58,971] [INFO] Task started: fastANI
[2023-03-16 04:20:58,971] [INFO] Running command: fastANI --query /var/lib/cwl/stg3915d5a7-230d-404c-8950-4ca32c83c44e/OceanDNA-b10079.fa --refList OceanDNA-b10079/target_genomes.txt --output OceanDNA-b10079/fastani_result.tsv --threads 1
[2023-03-16 04:21:14,040] [INFO] Task succeeded: fastANI
[2023-03-16 04:21:14,040] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg946ca398-b492-49cd-89db-c2a0ac468641/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:21:14,041] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg946ca398-b492-49cd-89db-c2a0ac468641/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:21:14,044] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 04:21:14,044] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 04:21:14,044] [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
Pricia antarctica	strain=DSM 23421	GCA_900101815.1	641691	641691	type	True	76.8437	116	472	95	below_threshold
Zobellia galactanivorans	strain=DsiJT	GCA_000973105.1	63186	63186	type	True	76.2387	57	472	95	below_threshold
Zobellia uliginosa	strain=DSM 2061	GCA_900156625.1	143224	143224	type	True	76.1961	59	472	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 04:21:14,045] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10079/tc_result.tsv
[2023-03-16 04:21:14,045] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:21:14,045] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:21:14,045] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg946ca398-b492-49cd-89db-c2a0ac468641/dqc_reference/checkm_data
[2023-03-16 04:21:14,046] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:21:14,049] [INFO] Task started: CheckM
[2023-03-16 04:21:14,049] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10079/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10079/checkm_input OceanDNA-b10079/checkm_result
[2023-03-16 04:21:51,669] [INFO] Task succeeded: CheckM
[2023-03-16 04:21:51,670] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 67.13%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 04:21:51,672] [INFO] ===== Completeness check finished =====
[2023-03-16 04:21:51,672] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:21:51,672] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10079/markers.fasta)
[2023-03-16 04:21:51,672] [INFO] Task started: Blastn
[2023-03-16 04:21:51,673] [INFO] Running command: blastn -query OceanDNA-b10079/markers.fasta -db /var/lib/cwl/stg946ca398-b492-49cd-89db-c2a0ac468641/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10079/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:21:52,529] [INFO] Task succeeded: Blastn
[2023-03-16 04:21:52,530] [INFO] Selected 25 target genomes.
[2023-03-16 04:21:52,530] [INFO] Target genome list was writen to OceanDNA-b10079/target_genomes_gtdb.txt
[2023-03-16 04:21:52,634] [INFO] Task started: fastANI
[2023-03-16 04:21:52,634] [INFO] Running command: fastANI --query /var/lib/cwl/stg3915d5a7-230d-404c-8950-4ca32c83c44e/OceanDNA-b10079.fa --refList OceanDNA-b10079/target_genomes_gtdb.txt --output OceanDNA-b10079/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:22:08,769] [INFO] Task succeeded: fastANI
[2023-03-16 04:22:08,773] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 04:22:08,773] [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_900101815.1	s__Pricia antarctica	76.8437	116	472	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Pricia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011050085.1	s__Pricia antarctica_A	76.333	69	472	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Pricia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000973105.1	s__Zobellia galactanivorans	76.2387	57	472	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	99.09	99.05	0.92	0.91	3	-
GCF_900156625.1	s__Zobellia uliginosa	76.1961	59	472	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141855.1	s__Pseudozobellia thermophila	76.0744	60	472	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Pseudozobellia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 04:22:08,773] [INFO] GTDB search result was written to OceanDNA-b10079/result_gtdb.tsv
[2023-03-16 04:22:08,773] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:22:08,774] [INFO] DFAST_QC result json was written to OceanDNA-b10079/dqc_result.json
[2023-03-16 04:22:08,774] [INFO] DFAST_QC completed!
[2023-03-16 04:22:08,774] [INFO] Total running time: 0h1m25s