[2023-03-19 00:01:03,357] [INFO] DFAST_QC pipeline started.
[2023-03-19 00:01:03,357] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 00:01:03,358] [INFO] DQC Reference Directory: /var/lib/cwl/stgc3a9656c-7ccc-4d88-bfca-1f200a4f1a22/dqc_reference
[2023-03-19 00:01:04,627] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 00:01:04,627] [INFO] Task started: Prodigal
[2023-03-19 00:01:04,627] [INFO] Running command: cat /var/lib/cwl/stg450888da-60e9-41a6-8cad-daf448532aff/OceanDNA-b42188.fa | prodigal -d OceanDNA-b42188/cds.fna -a OceanDNA-b42188/protein.faa -g 11 -q > /dev/null
[2023-03-19 00:01:11,298] [INFO] Task succeeded: Prodigal
[2023-03-19 00:01:11,298] [INFO] Task started: HMMsearch
[2023-03-19 00:01:11,298] [INFO] Running command: hmmsearch --tblout OceanDNA-b42188/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc3a9656c-7ccc-4d88-bfca-1f200a4f1a22/dqc_reference/reference_markers.hmm OceanDNA-b42188/protein.faa > /dev/null
[2023-03-19 00:01:11,484] [INFO] Task succeeded: HMMsearch
[2023-03-19 00:01:11,485] [INFO] Found 6/6 markers.
[2023-03-19 00:01:11,495] [INFO] Query marker FASTA was written to OceanDNA-b42188/markers.fasta
[2023-03-19 00:01:11,495] [INFO] Task started: Blastn
[2023-03-19 00:01:11,495] [INFO] Running command: blastn -query OceanDNA-b42188/markers.fasta -db /var/lib/cwl/stgc3a9656c-7ccc-4d88-bfca-1f200a4f1a22/dqc_reference/reference_markers.fasta -out OceanDNA-b42188/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:01:12,046] [INFO] Task succeeded: Blastn
[2023-03-19 00:01:12,047] [INFO] Selected 11 target genomes.
[2023-03-19 00:01:12,047] [INFO] Target genome list was writen to OceanDNA-b42188/target_genomes.txt
[2023-03-19 00:01:12,053] [INFO] Task started: fastANI
[2023-03-19 00:01:12,053] [INFO] Running command: fastANI --query /var/lib/cwl/stg450888da-60e9-41a6-8cad-daf448532aff/OceanDNA-b42188.fa --refList OceanDNA-b42188/target_genomes.txt --output OceanDNA-b42188/fastani_result.tsv --threads 1
[2023-03-19 00:01:18,011] [INFO] Task succeeded: fastANI
[2023-03-19 00:01:18,011] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc3a9656c-7ccc-4d88-bfca-1f200a4f1a22/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 00:01:18,011] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc3a9656c-7ccc-4d88-bfca-1f200a4f1a22/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 00:01:18,012] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 00:01:18,012] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 00:01:18,012] [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 00:01:18,012] [INFO] DFAST Taxonomy check result was written to OceanDNA-b42188/tc_result.tsv
[2023-03-19 00:01:18,012] [INFO] ===== Taxonomy check completed =====
[2023-03-19 00:01:18,012] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 00:01:18,012] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc3a9656c-7ccc-4d88-bfca-1f200a4f1a22/dqc_reference/checkm_data
[2023-03-19 00:01:18,015] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 00:01:18,018] [INFO] Task started: CheckM
[2023-03-19 00:01:18,018] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b42188/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b42188/checkm_input OceanDNA-b42188/checkm_result
[2023-03-19 00:01:40,399] [INFO] Task succeeded: CheckM
[2023-03-19 00:01:40,399] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 00:01:40,401] [INFO] ===== Completeness check finished =====
[2023-03-19 00:01:40,401] [INFO] ===== Start GTDB Search =====
[2023-03-19 00:01:40,401] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b42188/markers.fasta)
[2023-03-19 00:01:40,401] [INFO] Task started: Blastn
[2023-03-19 00:01:40,402] [INFO] Running command: blastn -query OceanDNA-b42188/markers.fasta -db /var/lib/cwl/stgc3a9656c-7ccc-4d88-bfca-1f200a4f1a22/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b42188/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:01:41,303] [INFO] Task succeeded: Blastn
[2023-03-19 00:01:41,304] [INFO] Selected 16 target genomes.
[2023-03-19 00:01:41,304] [INFO] Target genome list was writen to OceanDNA-b42188/target_genomes_gtdb.txt
[2023-03-19 00:01:41,330] [INFO] Task started: fastANI
[2023-03-19 00:01:41,331] [INFO] Running command: fastANI --query /var/lib/cwl/stg450888da-60e9-41a6-8cad-daf448532aff/OceanDNA-b42188.fa --refList OceanDNA-b42188/target_genomes_gtdb.txt --output OceanDNA-b42188/fastani_result_gtdb.tsv --threads 1
[2023-03-19 00:01:45,109] [INFO] Task succeeded: fastANI
[2023-03-19 00:01:45,117] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 00:01:45,117] [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_002358345.1	s__D2472 sp002358345	96.1986	340	406	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	99.61	97.74	0.92	0.85	27	conclusive
GCA_002469975.1	s__D2472 sp002469975	82.0649	251	406	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	99.56	99.38	0.87	0.81	4	-
GCA_905181595.1	s__D2472 sp905181595	79.4184	221	406	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902595065.1	s__D2472 sp902595065	77.3232	98	406	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	98.09	97.88	0.94	0.91	4	-
GCA_000307935.1	s__D2472 sp000307935	77.2739	103	406	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003284215.1	s__D2472 sp003284215	77.2375	88	406	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	98.26	97.20	0.81	0.71	5	-
GCA_902511575.1	s__D2472 sp902511575	77.2305	104	406	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902593675.1	s__D2472 sp902593675	77.1749	102	406	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902602595.1	s__D2472 sp902602595	77.0926	88	406	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016779505.1	s__D2472 sp016779505	77.0423	82	406	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	98.99	98.50	0.76	0.70	3	-
GCA_902515775.1	s__D2472 sp902515775	76.7993	74	406	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902599315.1	s__D2472 sp902599315	76.6728	83	406	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	97.18	96.37	0.89	0.86	3	-
--------------------------------------------------------------------------------
[2023-03-19 00:01:45,117] [INFO] GTDB search result was written to OceanDNA-b42188/result_gtdb.tsv
[2023-03-19 00:01:45,117] [INFO] ===== GTDB Search completed =====
[2023-03-19 00:01:45,118] [INFO] DFAST_QC result json was written to OceanDNA-b42188/dqc_result.json
[2023-03-19 00:01:45,118] [INFO] DFAST_QC completed!
[2023-03-19 00:01:45,118] [INFO] Total running time: 0h0m42s