[2023-03-17 13:46:30,402] [INFO] DFAST_QC pipeline started.
[2023-03-17 13:46:30,402] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 13:46:30,402] [INFO] DQC Reference Directory: /var/lib/cwl/stg95981700-b1dd-47af-ac03-26df871b2234/dqc_reference
[2023-03-17 13:46:32,763] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 13:46:32,777] [INFO] Task started: Prodigal
[2023-03-17 13:46:32,777] [INFO] Running command: cat /var/lib/cwl/stg47b1b61e-2610-41e9-bb19-d91973510e30/OceanDNA-b25900.fa | prodigal -d OceanDNA-b25900/cds.fna -a OceanDNA-b25900/protein.faa -g 11 -q > /dev/null
[2023-03-17 13:46:35,367] [INFO] Task succeeded: Prodigal
[2023-03-17 13:46:35,367] [INFO] Task started: HMMsearch
[2023-03-17 13:46:35,367] [INFO] Running command: hmmsearch --tblout OceanDNA-b25900/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg95981700-b1dd-47af-ac03-26df871b2234/dqc_reference/reference_markers.hmm OceanDNA-b25900/protein.faa > /dev/null
[2023-03-17 13:46:35,557] [INFO] Task succeeded: HMMsearch
[2023-03-17 13:46:35,558] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg47b1b61e-2610-41e9-bb19-d91973510e30/OceanDNA-b25900.fa]
[2023-03-17 13:46:35,563] [INFO] Query marker FASTA was written to OceanDNA-b25900/markers.fasta
[2023-03-17 13:46:35,565] [INFO] Task started: Blastn
[2023-03-17 13:46:35,565] [INFO] Running command: blastn -query OceanDNA-b25900/markers.fasta -db /var/lib/cwl/stg95981700-b1dd-47af-ac03-26df871b2234/dqc_reference/reference_markers.fasta -out OceanDNA-b25900/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 13:46:39,541] [INFO] Task succeeded: Blastn
[2023-03-17 13:46:39,541] [INFO] Selected 5 target genomes.
[2023-03-17 13:46:39,542] [INFO] Target genome list was writen to OceanDNA-b25900/target_genomes.txt
[2023-03-17 13:46:39,545] [INFO] Task started: fastANI
[2023-03-17 13:46:39,545] [INFO] Running command: fastANI --query /var/lib/cwl/stg47b1b61e-2610-41e9-bb19-d91973510e30/OceanDNA-b25900.fa --refList OceanDNA-b25900/target_genomes.txt --output OceanDNA-b25900/fastani_result.tsv --threads 1
[2023-03-17 13:46:41,035] [INFO] Task succeeded: fastANI
[2023-03-17 13:46:41,036] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg95981700-b1dd-47af-ac03-26df871b2234/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 13:46:41,036] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg95981700-b1dd-47af-ac03-26df871b2234/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 13:46:41,107] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 13:46:41,107] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 13:46:41,108] [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
Candidatus Pelagibacter ubique	strain=HTCC1062	GCA_000012345.1	198252	198252	suspected-type	True	77.9024	50	100	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 13:46:41,108] [INFO] DFAST Taxonomy check result was written to OceanDNA-b25900/tc_result.tsv
[2023-03-17 13:46:41,108] [INFO] ===== Taxonomy check completed =====
[2023-03-17 13:46:41,108] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 13:46:41,108] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg95981700-b1dd-47af-ac03-26df871b2234/dqc_reference/checkm_data
[2023-03-17 13:46:41,109] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 13:46:41,111] [INFO] Task started: CheckM
[2023-03-17 13:46:41,111] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b25900/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b25900/checkm_input OceanDNA-b25900/checkm_result
[2023-03-17 13:47:04,916] [INFO] Task succeeded: CheckM
[2023-03-17 13:47:04,916] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 40.03%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 13:47:04,918] [INFO] ===== Completeness check finished =====
[2023-03-17 13:47:04,918] [INFO] ===== Start GTDB Search =====
[2023-03-17 13:47:04,918] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b25900/markers.fasta)
[2023-03-17 13:47:04,920] [INFO] Task started: Blastn
[2023-03-17 13:47:04,920] [INFO] Running command: blastn -query OceanDNA-b25900/markers.fasta -db /var/lib/cwl/stg95981700-b1dd-47af-ac03-26df871b2234/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b25900/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 13:47:06,482] [INFO] Task succeeded: Blastn
[2023-03-17 13:47:06,483] [INFO] Selected 13 target genomes.
[2023-03-17 13:47:06,483] [INFO] Target genome list was writen to OceanDNA-b25900/target_genomes_gtdb.txt
[2023-03-17 13:47:06,710] [INFO] Task started: fastANI
[2023-03-17 13:47:06,710] [INFO] Running command: fastANI --query /var/lib/cwl/stg47b1b61e-2610-41e9-bb19-d91973510e30/OceanDNA-b25900.fa --refList OceanDNA-b25900/target_genomes_gtdb.txt --output OceanDNA-b25900/fastani_result_gtdb.tsv --threads 1
[2023-03-17 13:47:10,330] [INFO] Task succeeded: fastANI
[2023-03-17 13:47:10,338] [INFO] Found 12 fastANI hits (10 hits with ANI > circumscription radius)
[2023-03-17 13:47:10,338] [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
GCA_902616725.1	s__Pelagibacter sp902616725	97.1946	94	100	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	95.39	95.04	0.85	0.83	5	inconclusive
GCA_902609685.1	s__Pelagibacter sp902609685	96.9532	100	100	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	96.69	95.28	0.90	0.86	8	inconclusive
GCA_003213155.1	s__Pelagibacter sp003213155	96.7991	90	100	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	96.52	95.06	0.83	0.73	7	inconclusive
GCA_902582605.1	s__Pelagibacter sp902582605	96.746	79	100	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	99.82	99.82	0.81	0.81	2	inconclusive
GCA_003212275.1	s__Pelagibacter sp003212275	96.5793	95	100	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	100.00	100.00	1.00	1.00	2	inconclusive
GCA_902597675.1	s__Pelagibacter sp902597675	96.1686	73	100	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	95.60	95.15	0.72	0.69	5	inconclusive
GCA_902528645.1	s__Pelagibacter sp902528645	96.0382	75	100	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCA_003281045.1	s__Pelagibacter sp003281045	96.0216	63	100	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	100.00	100.00	0.99	0.99	2	inconclusive
GCA_902632935.1	s__Pelagibacter sp902632935	95.9873	65	100	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCA_902574345.1	s__Pelagibacter sp902574345	95.7943	63	100	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCA_902627805.1	s__Pelagibacter sp902627805	93.0724	89	100	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902624465.1	s__Pelagibacter sp902624465	90.7546	67	100	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 13:47:10,338] [INFO] GTDB search result was written to OceanDNA-b25900/result_gtdb.tsv
[2023-03-17 13:47:10,339] [INFO] ===== GTDB Search completed =====
[2023-03-17 13:47:10,340] [INFO] DFAST_QC result json was written to OceanDNA-b25900/dqc_result.json
[2023-03-17 13:47:10,340] [INFO] DFAST_QC completed!
[2023-03-17 13:47:10,340] [INFO] Total running time: 0h0m40s