[2023-03-18 06:15:37,958] [INFO] DFAST_QC pipeline started.
[2023-03-18 06:15:37,959] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 06:15:37,959] [INFO] DQC Reference Directory: /var/lib/cwl/stgf5adddc7-fd16-4865-a361-1b0a61be2e78/dqc_reference
[2023-03-18 06:15:39,073] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 06:15:39,073] [INFO] Task started: Prodigal
[2023-03-18 06:15:39,074] [INFO] Running command: cat /var/lib/cwl/stgd07bb554-5289-42f9-9e7c-188b464cd6f9/OceanDNA-b41946.fa | prodigal -d OceanDNA-b41946/cds.fna -a OceanDNA-b41946/protein.faa -g 11 -q > /dev/null
[2023-03-18 06:15:44,040] [INFO] Task succeeded: Prodigal
[2023-03-18 06:15:44,040] [INFO] Task started: HMMsearch
[2023-03-18 06:15:44,040] [INFO] Running command: hmmsearch --tblout OceanDNA-b41946/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf5adddc7-fd16-4865-a361-1b0a61be2e78/dqc_reference/reference_markers.hmm OceanDNA-b41946/protein.faa > /dev/null
[2023-03-18 06:15:44,178] [INFO] Task succeeded: HMMsearch
[2023-03-18 06:15:44,179] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd07bb554-5289-42f9-9e7c-188b464cd6f9/OceanDNA-b41946.fa]
[2023-03-18 06:15:44,188] [INFO] Query marker FASTA was written to OceanDNA-b41946/markers.fasta
[2023-03-18 06:15:44,188] [INFO] Task started: Blastn
[2023-03-18 06:15:44,188] [INFO] Running command: blastn -query OceanDNA-b41946/markers.fasta -db /var/lib/cwl/stgf5adddc7-fd16-4865-a361-1b0a61be2e78/dqc_reference/reference_markers.fasta -out OceanDNA-b41946/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 06:15:44,709] [INFO] Task succeeded: Blastn
[2023-03-18 06:15:44,710] [INFO] Selected 7 target genomes.
[2023-03-18 06:15:44,710] [INFO] Target genome list was writen to OceanDNA-b41946/target_genomes.txt
[2023-03-18 06:15:44,715] [INFO] Task started: fastANI
[2023-03-18 06:15:44,716] [INFO] Running command: fastANI --query /var/lib/cwl/stgd07bb554-5289-42f9-9e7c-188b464cd6f9/OceanDNA-b41946.fa --refList OceanDNA-b41946/target_genomes.txt --output OceanDNA-b41946/fastani_result.tsv --threads 1
[2023-03-18 06:15:46,854] [INFO] Task succeeded: fastANI
[2023-03-18 06:15:46,854] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf5adddc7-fd16-4865-a361-1b0a61be2e78/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 06:15:46,854] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf5adddc7-fd16-4865-a361-1b0a61be2e78/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 06:15:46,854] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 06:15:46,854] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 06:15:46,855] [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
--------------------------------------------------------------------------------
[2023-03-18 06:15:46,855] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41946/tc_result.tsv
[2023-03-18 06:15:46,855] [INFO] ===== Taxonomy check completed =====
[2023-03-18 06:15:46,855] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 06:15:46,855] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf5adddc7-fd16-4865-a361-1b0a61be2e78/dqc_reference/checkm_data
[2023-03-18 06:15:46,908] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 06:15:46,911] [INFO] Task started: CheckM
[2023-03-18 06:15:46,911] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41946/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41946/checkm_input OceanDNA-b41946/checkm_result
[2023-03-18 06:16:08,225] [INFO] Task succeeded: CheckM
[2023-03-18 06:16:08,226] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 61.57%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 06:16:08,227] [INFO] ===== Completeness check finished =====
[2023-03-18 06:16:08,227] [INFO] ===== Start GTDB Search =====
[2023-03-18 06:16:08,228] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41946/markers.fasta)
[2023-03-18 06:16:08,228] [INFO] Task started: Blastn
[2023-03-18 06:16:08,228] [INFO] Running command: blastn -query OceanDNA-b41946/markers.fasta -db /var/lib/cwl/stgf5adddc7-fd16-4865-a361-1b0a61be2e78/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41946/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 06:16:09,545] [INFO] Task succeeded: Blastn
[2023-03-18 06:16:09,545] [INFO] Selected 15 target genomes.
[2023-03-18 06:16:09,546] [INFO] Target genome list was writen to OceanDNA-b41946/target_genomes_gtdb.txt
[2023-03-18 06:16:09,575] [INFO] Task started: fastANI
[2023-03-18 06:16:09,576] [INFO] Running command: fastANI --query /var/lib/cwl/stgd07bb554-5289-42f9-9e7c-188b464cd6f9/OceanDNA-b41946.fa --refList OceanDNA-b41946/target_genomes_gtdb.txt --output OceanDNA-b41946/fastani_result_gtdb.tsv --threads 1
[2023-03-18 06:16:12,729] [INFO] Task succeeded: fastANI
[2023-03-18 06:16:12,735] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 06:16:12,736] [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_902509965.1	s__MED-G78 sp902509965	89.9222	223	312	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__MED-G78	95.0	96.76	96.76	0.83	0.83	2	-
GCA_905181645.1	s__MED-G78 sp905181645	83.841	262	312	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__MED-G78	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905181955.1	s__MED-G78 sp905181955	81.7042	257	312	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__MED-G78	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902557645.1	s__MED-G78 sp902558645	79.8949	177	312	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__MED-G78	95.0	98.05	95.16	0.89	0.87	6	-
GCA_902514105.1	s__MED-G78 sp902514105	78.1084	105	312	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__MED-G78	95.0	98.38	98.38	0.65	0.65	2	-
GCA_905182885.1	s__SCGC-AAA076-P13 sp905182885	77.2526	55	312	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000385055.1	s__SCGC-AAA076-P13 sp000385055	76.9119	65	312	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	98.19	98.19	0.89	0.89	2	-
GCA_905478035.1	s__SCGC-AAA076-P13 sp905478035	76.846	55	312	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000384935.1	s__SCGC-AAA076-P13 sp000384935	76.7157	53	312	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 06:16:12,736] [INFO] GTDB search result was written to OceanDNA-b41946/result_gtdb.tsv
[2023-03-18 06:16:12,736] [INFO] ===== GTDB Search completed =====
[2023-03-18 06:16:12,740] [INFO] DFAST_QC result json was written to OceanDNA-b41946/dqc_result.json
[2023-03-18 06:16:12,740] [INFO] DFAST_QC completed!
[2023-03-18 06:16:12,740] [INFO] Total running time: 0h0m35s