[2023-03-15 11:10:12,690] [INFO] DFAST_QC pipeline started.
[2023-03-15 11:10:12,692] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 11:10:12,692] [INFO] DQC Reference Directory: /var/lib/cwl/stge07c7241-56ea-45ef-b36f-66d8a5e0c8cd/dqc_reference
[2023-03-15 11:10:13,789] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 11:10:13,789] [INFO] Task started: Prodigal
[2023-03-15 11:10:13,789] [INFO] Running command: cat /var/lib/cwl/stg92afa677-3408-4cf6-a112-acc68084bbd1/OceanDNA-b42102.fa | prodigal -d OceanDNA-b42102/cds.fna -a OceanDNA-b42102/protein.faa -g 11 -q > /dev/null
[2023-03-15 11:10:19,527] [INFO] Task succeeded: Prodigal
[2023-03-15 11:10:19,528] [INFO] Task started: HMMsearch
[2023-03-15 11:10:19,528] [INFO] Running command: hmmsearch --tblout OceanDNA-b42102/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge07c7241-56ea-45ef-b36f-66d8a5e0c8cd/dqc_reference/reference_markers.hmm OceanDNA-b42102/protein.faa > /dev/null
[2023-03-15 11:10:19,698] [INFO] Task succeeded: HMMsearch
[2023-03-15 11:10:19,698] [INFO] Found 6/6 markers.
[2023-03-15 11:10:19,737] [INFO] Query marker FASTA was written to OceanDNA-b42102/markers.fasta
[2023-03-15 11:10:19,738] [INFO] Task started: Blastn
[2023-03-15 11:10:19,738] [INFO] Running command: blastn -query OceanDNA-b42102/markers.fasta -db /var/lib/cwl/stge07c7241-56ea-45ef-b36f-66d8a5e0c8cd/dqc_reference/reference_markers.fasta -out OceanDNA-b42102/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:10:20,298] [INFO] Task succeeded: Blastn
[2023-03-15 11:10:20,304] [INFO] Selected 19 target genomes.
[2023-03-15 11:10:20,305] [INFO] Target genome list was writen to OceanDNA-b42102/target_genomes.txt
[2023-03-15 11:10:20,315] [INFO] Task started: fastANI
[2023-03-15 11:10:20,315] [INFO] Running command: fastANI --query /var/lib/cwl/stg92afa677-3408-4cf6-a112-acc68084bbd1/OceanDNA-b42102.fa --refList OceanDNA-b42102/target_genomes.txt --output OceanDNA-b42102/fastani_result.tsv --threads 1
[2023-03-15 11:10:28,814] [INFO] Task succeeded: fastANI
[2023-03-15 11:10:28,815] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge07c7241-56ea-45ef-b36f-66d8a5e0c8cd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 11:10:28,815] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge07c7241-56ea-45ef-b36f-66d8a5e0c8cd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 11:10:28,815] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 11:10:28,815] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 11:10:28,815] [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
--------------------------------------------------------------------------------
[2023-03-15 11:10:28,819] [INFO] DFAST Taxonomy check result was written to OceanDNA-b42102/tc_result.tsv
[2023-03-15 11:10:28,825] [INFO] ===== Taxonomy check completed =====
[2023-03-15 11:10:28,825] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 11:10:28,825] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge07c7241-56ea-45ef-b36f-66d8a5e0c8cd/dqc_reference/checkm_data
[2023-03-15 11:10:28,829] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 11:10:28,835] [INFO] Task started: CheckM
[2023-03-15 11:10:28,835] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b42102/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b42102/checkm_input OceanDNA-b42102/checkm_result
[2023-03-15 11:10:49,339] [INFO] Task succeeded: CheckM
[2023-03-15 11:10:49,339] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 1.85%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-15 11:10:49,588] [INFO] ===== Completeness check finished =====
[2023-03-15 11:10:49,588] [INFO] ===== Start GTDB Search =====
[2023-03-15 11:10:49,588] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b42102/markers.fasta)
[2023-03-15 11:10:49,590] [INFO] Task started: Blastn
[2023-03-15 11:10:49,590] [INFO] Running command: blastn -query OceanDNA-b42102/markers.fasta -db /var/lib/cwl/stge07c7241-56ea-45ef-b36f-66d8a5e0c8cd/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b42102/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:10:50,531] [INFO] Task succeeded: Blastn
[2023-03-15 11:10:50,537] [INFO] Selected 15 target genomes.
[2023-03-15 11:10:50,537] [INFO] Target genome list was writen to OceanDNA-b42102/target_genomes_gtdb.txt
[2023-03-15 11:10:50,556] [INFO] Task started: fastANI
[2023-03-15 11:10:50,556] [INFO] Running command: fastANI --query /var/lib/cwl/stg92afa677-3408-4cf6-a112-acc68084bbd1/OceanDNA-b42102.fa --refList OceanDNA-b42102/target_genomes_gtdb.txt --output OceanDNA-b42102/fastani_result_gtdb.tsv --threads 1
[2023-03-15 11:10:54,516] [INFO] Task succeeded: fastANI
[2023-03-15 11:10:54,525] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 11:10:54,525] [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_016779505.1	s__D2472 sp016779505	98.5916	231	350	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	98.99	98.50	0.76	0.70	3	conclusive
GCA_016779285.1	s__D2472 sp016779285	83.6401	180	350	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902511575.1	s__D2472 sp902511575	83.3167	272	350	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902593675.1	s__D2472 sp902593675	82.9118	271	350	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003283765.1	s__D2472 sp003283765	82.8584	240	350	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	100.00	100.00	0.99	0.99	2	-
GCA_902509555.1	s__D2472 sp902509555	82.6549	205	350	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902596165.1	s__D2472 sp902596165	82.4127	254	350	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902512655.1	s__D2472 sp902512655	82.3173	176	350	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902513515.1	s__D2472 sp902513515	82.2892	210	350	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902595065.1	s__D2472 sp902595065	82.2637	277	350	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	98.09	97.88	0.94	0.91	4	-
GCA_902602595.1	s__D2472 sp902602595	82.2627	248	350	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003284215.1	s__D2472 sp003284215	82.0226	228	350	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	98.26	97.20	0.81	0.71	5	-
GCA_000307935.1	s__D2472 sp000307935	81.6864	212	350	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902623685.1	s__D2472 sp902623685	79.0759	155	350	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	99.90	99.90	0.83	0.83	2	-
--------------------------------------------------------------------------------
[2023-03-15 11:10:54,525] [INFO] GTDB search result was written to OceanDNA-b42102/result_gtdb.tsv
[2023-03-15 11:10:54,525] [INFO] ===== GTDB Search completed =====
[2023-03-15 11:10:54,526] [INFO] DFAST_QC result json was written to OceanDNA-b42102/dqc_result.json
[2023-03-15 11:10:54,526] [INFO] DFAST_QC completed!
[2023-03-15 11:10:54,526] [INFO] Total running time: 0h0m42s