[2023-03-15 08:55:06,629] [INFO] DFAST_QC pipeline started.
[2023-03-15 08:55:06,629] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 08:55:06,629] [INFO] DQC Reference Directory: /var/lib/cwl/stg7514dbe3-b82d-4877-9b91-06bbe2daeb30/dqc_reference
[2023-03-15 08:55:08,348] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 08:55:08,348] [INFO] Task started: Prodigal
[2023-03-15 08:55:08,348] [INFO] Running command: cat /var/lib/cwl/stgbab36da7-9b1b-45a7-b5fa-96d497c476b0/OceanDNA-b39354.fa | prodigal -d OceanDNA-b39354/cds.fna -a OceanDNA-b39354/protein.faa -g 11 -q > /dev/null
[2023-03-15 08:55:15,555] [INFO] Task succeeded: Prodigal
[2023-03-15 08:55:15,556] [INFO] Task started: HMMsearch
[2023-03-15 08:55:15,556] [INFO] Running command: hmmsearch --tblout OceanDNA-b39354/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7514dbe3-b82d-4877-9b91-06bbe2daeb30/dqc_reference/reference_markers.hmm OceanDNA-b39354/protein.faa > /dev/null
[2023-03-15 08:55:15,754] [INFO] Task succeeded: HMMsearch
[2023-03-15 08:55:15,755] [INFO] Found 6/6 markers.
[2023-03-15 08:55:15,768] [INFO] Query marker FASTA was written to OceanDNA-b39354/markers.fasta
[2023-03-15 08:55:15,768] [INFO] Task started: Blastn
[2023-03-15 08:55:15,768] [INFO] Running command: blastn -query OceanDNA-b39354/markers.fasta -db /var/lib/cwl/stg7514dbe3-b82d-4877-9b91-06bbe2daeb30/dqc_reference/reference_markers.fasta -out OceanDNA-b39354/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:55:16,304] [INFO] Task succeeded: Blastn
[2023-03-15 08:55:16,305] [INFO] Selected 38 target genomes.
[2023-03-15 08:55:16,305] [INFO] Target genome list was writen to OceanDNA-b39354/target_genomes.txt
[2023-03-15 08:55:16,322] [INFO] Task started: fastANI
[2023-03-15 08:55:16,322] [INFO] Running command: fastANI --query /var/lib/cwl/stgbab36da7-9b1b-45a7-b5fa-96d497c476b0/OceanDNA-b39354.fa --refList OceanDNA-b39354/target_genomes.txt --output OceanDNA-b39354/fastani_result.tsv --threads 1
[2023-03-15 08:55:42,425] [INFO] Task succeeded: fastANI
[2023-03-15 08:55:42,425] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7514dbe3-b82d-4877-9b91-06bbe2daeb30/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 08:55:42,426] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7514dbe3-b82d-4877-9b91-06bbe2daeb30/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 08:55:42,426] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 08:55:42,426] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 08:55:42,426] [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 08:55:42,426] [INFO] DFAST Taxonomy check result was written to OceanDNA-b39354/tc_result.tsv
[2023-03-15 08:55:42,426] [INFO] ===== Taxonomy check completed =====
[2023-03-15 08:55:42,426] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 08:55:42,426] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7514dbe3-b82d-4877-9b91-06bbe2daeb30/dqc_reference/checkm_data
[2023-03-15 08:55:42,429] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 08:55:42,433] [INFO] Task started: CheckM
[2023-03-15 08:55:42,433] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b39354/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b39354/checkm_input OceanDNA-b39354/checkm_result
[2023-03-15 08:56:06,325] [INFO] Task succeeded: CheckM
[2023-03-15 08:56:06,326] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 40.62%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 08:56:06,331] [INFO] ===== Completeness check finished =====
[2023-03-15 08:56:06,331] [INFO] ===== Start GTDB Search =====
[2023-03-15 08:56:06,331] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b39354/markers.fasta)
[2023-03-15 08:56:06,331] [INFO] Task started: Blastn
[2023-03-15 08:56:06,331] [INFO] Running command: blastn -query OceanDNA-b39354/markers.fasta -db /var/lib/cwl/stg7514dbe3-b82d-4877-9b91-06bbe2daeb30/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b39354/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:56:07,113] [INFO] Task succeeded: Blastn
[2023-03-15 08:56:07,114] [INFO] Selected 12 target genomes.
[2023-03-15 08:56:07,114] [INFO] Target genome list was writen to OceanDNA-b39354/target_genomes_gtdb.txt
[2023-03-15 08:56:07,174] [INFO] Task started: fastANI
[2023-03-15 08:56:07,174] [INFO] Running command: fastANI --query /var/lib/cwl/stgbab36da7-9b1b-45a7-b5fa-96d497c476b0/OceanDNA-b39354.fa --refList OceanDNA-b39354/target_genomes_gtdb.txt --output OceanDNA-b39354/fastani_result_gtdb.tsv --threads 1
[2023-03-15 08:56:12,228] [INFO] Task succeeded: fastANI
[2023-03-15 08:56:12,234] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 08:56:12,234] [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_000153445.1	s__HTCC2207 sp000153445	84.6016	310	383	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	98.85	98.71	0.89	0.85	4	-
GCA_905478975.1	s__HTCC2207 sp905478975	83.8288	257	383	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905478725.1	s__HTCC2207 sp905478725	82.8907	228	383	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017858295.1	s__HTCC2207 sp017858295	81.9042	221	383	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	97.83	97.83	0.77	0.77	2	-
GCA_000511875.1	s__HTCC2207 sp000511875	81.603	289	383	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017858135.1	s__HTCC2207 sp017858135	79.4925	199	383	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	98.96	98.94	0.87	0.86	3	-
GCA_018607545.1	s__HTCC2207 sp018607545	78.1486	64	383	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018664075.1	s__HTCC2207 sp018664075	76.7853	80	383	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.59	99.59	0.81	0.81	2	-
--------------------------------------------------------------------------------
[2023-03-15 08:56:12,234] [INFO] GTDB search result was written to OceanDNA-b39354/result_gtdb.tsv
[2023-03-15 08:56:12,234] [INFO] ===== GTDB Search completed =====
[2023-03-15 08:56:12,235] [INFO] DFAST_QC result json was written to OceanDNA-b39354/dqc_result.json
[2023-03-15 08:56:12,235] [INFO] DFAST_QC completed!
[2023-03-15 08:56:12,235] [INFO] Total running time: 0h1m6s