[2023-03-19 04:46:13,840] [INFO] DFAST_QC pipeline started.
[2023-03-19 04:46:13,840] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 04:46:13,840] [INFO] DQC Reference Directory: /var/lib/cwl/stg11e48b1f-aa74-467e-b872-22be443060f3/dqc_reference
[2023-03-19 04:46:14,993] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 04:46:14,993] [INFO] Task started: Prodigal
[2023-03-19 04:46:14,993] [INFO] Running command: cat /var/lib/cwl/stgc7e2fea3-0a84-4fce-9c10-aa4b163eb198/OceanDNA-b42260.fa | prodigal -d OceanDNA-b42260/cds.fna -a OceanDNA-b42260/protein.faa -g 11 -q > /dev/null
[2023-03-19 04:46:19,450] [INFO] Task succeeded: Prodigal
[2023-03-19 04:46:19,450] [INFO] Task started: HMMsearch
[2023-03-19 04:46:19,451] [INFO] Running command: hmmsearch --tblout OceanDNA-b42260/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg11e48b1f-aa74-467e-b872-22be443060f3/dqc_reference/reference_markers.hmm OceanDNA-b42260/protein.faa > /dev/null
[2023-03-19 04:46:19,620] [INFO] Task succeeded: HMMsearch
[2023-03-19 04:46:19,620] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgc7e2fea3-0a84-4fce-9c10-aa4b163eb198/OceanDNA-b42260.fa]
[2023-03-19 04:46:19,630] [INFO] Query marker FASTA was written to OceanDNA-b42260/markers.fasta
[2023-03-19 04:46:19,631] [INFO] Task started: Blastn
[2023-03-19 04:46:19,631] [INFO] Running command: blastn -query OceanDNA-b42260/markers.fasta -db /var/lib/cwl/stg11e48b1f-aa74-467e-b872-22be443060f3/dqc_reference/reference_markers.fasta -out OceanDNA-b42260/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:46:20,182] [INFO] Task succeeded: Blastn
[2023-03-19 04:46:20,183] [INFO] Selected 17 target genomes.
[2023-03-19 04:46:20,183] [INFO] Target genome list was writen to OceanDNA-b42260/target_genomes.txt
[2023-03-19 04:46:20,194] [INFO] Task started: fastANI
[2023-03-19 04:46:20,194] [INFO] Running command: fastANI --query /var/lib/cwl/stgc7e2fea3-0a84-4fce-9c10-aa4b163eb198/OceanDNA-b42260.fa --refList OceanDNA-b42260/target_genomes.txt --output OceanDNA-b42260/fastani_result.tsv --threads 1
[2023-03-19 04:46:26,512] [INFO] Task succeeded: fastANI
[2023-03-19 04:46:26,513] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg11e48b1f-aa74-467e-b872-22be443060f3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 04:46:26,513] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg11e48b1f-aa74-467e-b872-22be443060f3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 04:46:26,513] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 04:46:26,513] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 04:46:26,513] [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
--------------------------------------------------------------------------------
[2023-03-19 04:46:26,513] [INFO] DFAST Taxonomy check result was written to OceanDNA-b42260/tc_result.tsv
[2023-03-19 04:46:26,514] [INFO] ===== Taxonomy check completed =====
[2023-03-19 04:46:26,514] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 04:46:26,514] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg11e48b1f-aa74-467e-b872-22be443060f3/dqc_reference/checkm_data
[2023-03-19 04:46:26,524] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 04:46:26,526] [INFO] Task started: CheckM
[2023-03-19 04:46:26,526] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b42260/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b42260/checkm_input OceanDNA-b42260/checkm_result
[2023-03-19 04:46:44,829] [INFO] Task succeeded: CheckM
[2023-03-19 04:46:44,829] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 1.04%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-19 04:46:44,831] [INFO] ===== Completeness check finished =====
[2023-03-19 04:46:44,831] [INFO] ===== Start GTDB Search =====
[2023-03-19 04:46:44,831] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b42260/markers.fasta)
[2023-03-19 04:46:44,833] [INFO] Task started: Blastn
[2023-03-19 04:46:44,833] [INFO] Running command: blastn -query OceanDNA-b42260/markers.fasta -db /var/lib/cwl/stg11e48b1f-aa74-467e-b872-22be443060f3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b42260/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:46:45,765] [INFO] Task succeeded: Blastn
[2023-03-19 04:46:45,766] [INFO] Selected 17 target genomes.
[2023-03-19 04:46:45,766] [INFO] Target genome list was writen to OceanDNA-b42260/target_genomes_gtdb.txt
[2023-03-19 04:46:45,779] [INFO] Task started: fastANI
[2023-03-19 04:46:45,779] [INFO] Running command: fastANI --query /var/lib/cwl/stgc7e2fea3-0a84-4fce-9c10-aa4b163eb198/OceanDNA-b42260.fa --refList OceanDNA-b42260/target_genomes_gtdb.txt --output OceanDNA-b42260/fastani_result_gtdb.tsv --threads 1
[2023-03-19 04:46:49,305] [INFO] Task succeeded: fastANI
[2023-03-19 04:46:49,314] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 04:46:49,314] [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_902520495.1	s__SAR86A sp902520495	97.8048	220	287	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902558095.1	s__SAR86A sp902558095	81.045	188	287	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902559345.1	s__SAR86A sp902559345	80.7731	158	287	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902517425.1	s__SAR86A sp902517425	80.25	151	287	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902520725.1	s__SAR86A sp902520725	80.2478	160	287	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	99.82	99.82	0.73	0.73	2	-
GCA_002169105.1	s__SAR86A sp002169105	79.4463	114	287	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902517505.1	s__SAR86A sp902517505	79.2837	122	287	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	97.73	97.59	0.82	0.80	3	-
GCA_003213495.1	s__SAR86A sp003213495	78.5211	147	287	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	98.20	96.41	0.97	0.94	3	-
GCA_902586925.1	s__SAR86A sp902586925	78.1874	119	287	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	96.82	96.82	0.89	0.89	2	-
GCA_902591925.1	s__SAR86A sp902591925	78.1349	131	287	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	97.32	97.27	0.90	0.89	3	-
GCA_002690725.1	s__SAR86A sp002690725	77.9915	90	287	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	95.15	95.15	0.80	0.80	2	-
GCA_902541175.1	s__SAR86A sp902541175	77.9867	128	287	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	97.65	95.31	0.89	0.85	3	-
GCA_902547295.1	s__SAR86A sp902547295	77.8355	121	287	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902516285.1	s__SAR86A sp902516285	77.5539	110	287	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	96.51	96.51	0.92	0.92	2	-
GCA_003331505.1	s__MED-G85 sp003331505	77.4662	74	287	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__MED-G85	95.0	98.80	96.15	0.89	0.83	6	-
--------------------------------------------------------------------------------
[2023-03-19 04:46:49,314] [INFO] GTDB search result was written to OceanDNA-b42260/result_gtdb.tsv
[2023-03-19 04:46:49,314] [INFO] ===== GTDB Search completed =====
[2023-03-19 04:46:49,315] [INFO] DFAST_QC result json was written to OceanDNA-b42260/dqc_result.json
[2023-03-19 04:46:49,315] [INFO] DFAST_QC completed!
[2023-03-19 04:46:49,316] [INFO] Total running time: 0h0m35s