[2023-03-18 21:29:07,937] [INFO] DFAST_QC pipeline started.
[2023-03-18 21:29:07,937] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 21:29:07,937] [INFO] DQC Reference Directory: /var/lib/cwl/stg2e34f902-42bd-460b-82dd-9bd676f6ea91/dqc_reference
[2023-03-18 21:29:09,086] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 21:29:09,086] [INFO] Task started: Prodigal
[2023-03-18 21:29:09,087] [INFO] Running command: cat /var/lib/cwl/stg17245313-31f2-4425-a427-b0410e575ea9/OceanDNA-b25474.fa | prodigal -d OceanDNA-b25474/cds.fna -a OceanDNA-b25474/protein.faa -g 11 -q > /dev/null
[2023-03-18 21:29:11,511] [INFO] Task succeeded: Prodigal
[2023-03-18 21:29:11,511] [INFO] Task started: HMMsearch
[2023-03-18 21:29:11,511] [INFO] Running command: hmmsearch --tblout OceanDNA-b25474/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2e34f902-42bd-460b-82dd-9bd676f6ea91/dqc_reference/reference_markers.hmm OceanDNA-b25474/protein.faa > /dev/null
[2023-03-18 21:29:11,640] [INFO] Task succeeded: HMMsearch
[2023-03-18 21:29:11,640] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg17245313-31f2-4425-a427-b0410e575ea9/OceanDNA-b25474.fa]
[2023-03-18 21:29:11,645] [INFO] Query marker FASTA was written to OceanDNA-b25474/markers.fasta
[2023-03-18 21:29:11,646] [INFO] Task started: Blastn
[2023-03-18 21:29:11,646] [INFO] Running command: blastn -query OceanDNA-b25474/markers.fasta -db /var/lib/cwl/stg2e34f902-42bd-460b-82dd-9bd676f6ea91/dqc_reference/reference_markers.fasta -out OceanDNA-b25474/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:29:12,256] [INFO] Task succeeded: Blastn
[2023-03-18 21:29:12,257] [INFO] Selected 6 target genomes.
[2023-03-18 21:29:12,257] [INFO] Target genome list was writen to OceanDNA-b25474/target_genomes.txt
[2023-03-18 21:29:12,264] [INFO] Task started: fastANI
[2023-03-18 21:29:12,264] [INFO] Running command: fastANI --query /var/lib/cwl/stg17245313-31f2-4425-a427-b0410e575ea9/OceanDNA-b25474.fa --refList OceanDNA-b25474/target_genomes.txt --output OceanDNA-b25474/fastani_result.tsv --threads 1
[2023-03-18 21:29:14,865] [INFO] Task succeeded: fastANI
[2023-03-18 21:29:14,865] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2e34f902-42bd-460b-82dd-9bd676f6ea91/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 21:29:14,865] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2e34f902-42bd-460b-82dd-9bd676f6ea91/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 21:29:14,865] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 21:29:14,865] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 21:29:14,865] [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 21:29:14,866] [INFO] DFAST Taxonomy check result was written to OceanDNA-b25474/tc_result.tsv
[2023-03-18 21:29:14,866] [INFO] ===== Taxonomy check completed =====
[2023-03-18 21:29:14,866] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 21:29:14,866] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2e34f902-42bd-460b-82dd-9bd676f6ea91/dqc_reference/checkm_data
[2023-03-18 21:29:14,869] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 21:29:14,878] [INFO] Task started: CheckM
[2023-03-18 21:29:14,878] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b25474/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b25474/checkm_input OceanDNA-b25474/checkm_result
[2023-03-18 21:29:27,877] [INFO] Task succeeded: CheckM
[2023-03-18 21:29:27,877] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 52.35%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 21:29:27,879] [INFO] ===== Completeness check finished =====
[2023-03-18 21:29:27,879] [INFO] ===== Start GTDB Search =====
[2023-03-18 21:29:27,879] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b25474/markers.fasta)
[2023-03-18 21:29:27,880] [INFO] Task started: Blastn
[2023-03-18 21:29:27,880] [INFO] Running command: blastn -query OceanDNA-b25474/markers.fasta -db /var/lib/cwl/stg2e34f902-42bd-460b-82dd-9bd676f6ea91/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b25474/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:29:28,583] [INFO] Task succeeded: Blastn
[2023-03-18 21:29:28,584] [INFO] Selected 18 target genomes.
[2023-03-18 21:29:28,584] [INFO] Target genome list was writen to OceanDNA-b25474/target_genomes_gtdb.txt
[2023-03-18 21:29:28,595] [INFO] Task started: fastANI
[2023-03-18 21:29:28,595] [INFO] Running command: fastANI --query /var/lib/cwl/stg17245313-31f2-4425-a427-b0410e575ea9/OceanDNA-b25474.fa --refList OceanDNA-b25474/target_genomes_gtdb.txt --output OceanDNA-b25474/fastani_result_gtdb.tsv --threads 1
[2023-03-18 21:29:32,461] [INFO] Task succeeded: fastANI
[2023-03-18 21:29:32,468] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 21:29:32,468] [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_902554135.1	s__GCA-2704625 sp902554135	89.2148	53	117	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__GCA-2704625	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902588585.1	s__GCA-2704625 sp902588585	85.6643	104	117	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__GCA-2704625	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902634325.1	s__GCA-2704625 sp902634325	82.3587	59	117	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__GCA-2704625	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902591045.1	s__GCA-2704625 sp902591045	82.1791	63	117	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__GCA-2704625	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902578935.1	s__GCA-2704625 sp902578935	82.0648	83	117	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__GCA-2704625	95.0	97.21	97.21	0.85	0.85	2	-
GCA_902530635.1	s__GCA-2704625 sp902530635	80.3403	80	117	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__GCA-2704625	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902582475.1	s__GCA-2704625 sp902582475	79.0547	65	117	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__GCA-2704625	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902609645.1	s__GCA-2704625 sp902609645	78.7558	56	117	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__GCA-2704625	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902578115.1	s__GCA-2704625 sp902578115	78.3007	73	117	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__GCA-2704625	95.0	95.38	95.38	0.77	0.77	2	-
GCA_902573065.1	s__GCA-2704625 sp902573065	78.2803	62	117	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__GCA-2704625	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003209895.1	s__GCA-2704625 sp003209895	77.7417	51	117	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__GCA-2704625	95.0	99.93	99.90	0.90	0.84	4	-
--------------------------------------------------------------------------------
[2023-03-18 21:29:32,471] [INFO] GTDB search result was written to OceanDNA-b25474/result_gtdb.tsv
[2023-03-18 21:29:32,471] [INFO] ===== GTDB Search completed =====
[2023-03-18 21:29:32,472] [INFO] DFAST_QC result json was written to OceanDNA-b25474/dqc_result.json
[2023-03-18 21:29:32,472] [INFO] DFAST_QC completed!
[2023-03-18 21:29:32,472] [INFO] Total running time: 0h0m25s