[2023-03-16 12:14:10,776] [INFO] DFAST_QC pipeline started.
[2023-03-16 12:14:10,776] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 12:14:10,776] [INFO] DQC Reference Directory: /var/lib/cwl/stg53f71fd4-f339-4fb7-a9c9-f46bfd3e8587/dqc_reference
[2023-03-16 12:14:12,635] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 12:14:12,636] [INFO] Task started: Prodigal
[2023-03-16 12:14:12,636] [INFO] Running command: cat /var/lib/cwl/stg99944b14-928a-493b-8d78-ec771e6b6bb7/OceanDNA-b42316.fa | prodigal -d OceanDNA-b42316/cds.fna -a OceanDNA-b42316/protein.faa -g 11 -q > /dev/null
[2023-03-16 12:14:18,223] [INFO] Task succeeded: Prodigal
[2023-03-16 12:14:18,223] [INFO] Task started: HMMsearch
[2023-03-16 12:14:18,223] [INFO] Running command: hmmsearch --tblout OceanDNA-b42316/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg53f71fd4-f339-4fb7-a9c9-f46bfd3e8587/dqc_reference/reference_markers.hmm OceanDNA-b42316/protein.faa > /dev/null
[2023-03-16 12:14:18,620] [INFO] Task succeeded: HMMsearch
[2023-03-16 12:14:18,620] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg99944b14-928a-493b-8d78-ec771e6b6bb7/OceanDNA-b42316.fa]
[2023-03-16 12:14:18,628] [INFO] Query marker FASTA was written to OceanDNA-b42316/markers.fasta
[2023-03-16 12:14:18,628] [INFO] Task started: Blastn
[2023-03-16 12:14:18,629] [INFO] Running command: blastn -query OceanDNA-b42316/markers.fasta -db /var/lib/cwl/stg53f71fd4-f339-4fb7-a9c9-f46bfd3e8587/dqc_reference/reference_markers.fasta -out OceanDNA-b42316/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 12:14:19,974] [INFO] Task succeeded: Blastn
[2023-03-16 12:14:19,974] [INFO] Selected 19 target genomes.
[2023-03-16 12:14:19,975] [INFO] Target genome list was writen to OceanDNA-b42316/target_genomes.txt
[2023-03-16 12:14:19,985] [INFO] Task started: fastANI
[2023-03-16 12:14:19,986] [INFO] Running command: fastANI --query /var/lib/cwl/stg99944b14-928a-493b-8d78-ec771e6b6bb7/OceanDNA-b42316.fa --refList OceanDNA-b42316/target_genomes.txt --output OceanDNA-b42316/fastani_result.tsv --threads 1
[2023-03-16 12:14:35,618] [INFO] Task succeeded: fastANI
[2023-03-16 12:14:35,618] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg53f71fd4-f339-4fb7-a9c9-f46bfd3e8587/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 12:14:35,619] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg53f71fd4-f339-4fb7-a9c9-f46bfd3e8587/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 12:14:35,619] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 12:14:35,619] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 12:14:35,619] [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
--------------------------------------------------------------------------------
[2023-03-16 12:14:35,619] [INFO] DFAST Taxonomy check result was written to OceanDNA-b42316/tc_result.tsv
[2023-03-16 12:14:35,619] [INFO] ===== Taxonomy check completed =====
[2023-03-16 12:14:35,619] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 12:14:35,619] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg53f71fd4-f339-4fb7-a9c9-f46bfd3e8587/dqc_reference/checkm_data
[2023-03-16 12:14:35,622] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 12:14:35,625] [INFO] Task started: CheckM
[2023-03-16 12:14:35,625] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b42316/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b42316/checkm_input OceanDNA-b42316/checkm_result
[2023-03-16 12:14:58,242] [INFO] Task succeeded: CheckM
[2023-03-16 12:14:58,242] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 12:14:58,244] [INFO] ===== Completeness check finished =====
[2023-03-16 12:14:58,244] [INFO] ===== Start GTDB Search =====
[2023-03-16 12:14:58,244] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b42316/markers.fasta)
[2023-03-16 12:14:58,244] [INFO] Task started: Blastn
[2023-03-16 12:14:58,244] [INFO] Running command: blastn -query OceanDNA-b42316/markers.fasta -db /var/lib/cwl/stg53f71fd4-f339-4fb7-a9c9-f46bfd3e8587/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b42316/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 12:14:59,206] [INFO] Task succeeded: Blastn
[2023-03-16 12:14:59,207] [INFO] Selected 14 target genomes.
[2023-03-16 12:14:59,207] [INFO] Target genome list was writen to OceanDNA-b42316/target_genomes_gtdb.txt
[2023-03-16 12:14:59,709] [INFO] Task started: fastANI
[2023-03-16 12:14:59,709] [INFO] Running command: fastANI --query /var/lib/cwl/stg99944b14-928a-493b-8d78-ec771e6b6bb7/OceanDNA-b42316.fa --refList OceanDNA-b42316/target_genomes_gtdb.txt --output OceanDNA-b42316/fastani_result_gtdb.tsv --threads 1
[2023-03-16 12:15:04,418] [INFO] Task succeeded: fastANI
[2023-03-16 12:15:04,426] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 12:15:04,426] [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_018607365.1	s__SCGC-AAA076-P13 sp018607365	79.0469	135	317	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	78.9868	145	317	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_905478035.1	s__SCGC-AAA076-P13 sp905478035	78.2538	153	317	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	78.0745	131	317	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_902591665.1	s__SCGC-AAA076-P13 sp902591665	77.4793	109	317	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	99.81	99.81	0.85	0.85	2	-
GCA_902558395.1	s__SCGC-AAA076-P13 sp902558395	77.4711	113	317	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	97.77	97.77	0.94	0.94	2	-
GCA_902610905.1	s__SCGC-AAA076-P13 sp902610905	77.4451	98	317	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_902591565.1	s__SCGC-AAA076-P13 sp902591565	77.3276	105	317	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_902558375.1	s__SCGC-AAA076-P13 sp902558375	77.1469	82	317	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_003331505.1	s__MED-G85 sp003331505	77.0135	67	317	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__MED-G85	95.0	98.80	96.15	0.89	0.83	6	-
GCA_902630885.1	s__SAR86A sp902630885	76.5859	66	317	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902631785.1	s__SAR86A sp902631785	76.2856	67	317	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	96.84	96.84	0.79	0.79	2	-
--------------------------------------------------------------------------------
[2023-03-16 12:15:04,426] [INFO] GTDB search result was written to OceanDNA-b42316/result_gtdb.tsv
[2023-03-16 12:15:04,431] [INFO] ===== GTDB Search completed =====
[2023-03-16 12:15:04,432] [INFO] DFAST_QC result json was written to OceanDNA-b42316/dqc_result.json
[2023-03-16 12:15:04,432] [INFO] DFAST_QC completed!
[2023-03-16 12:15:04,432] [INFO] Total running time: 0h0m54s