[2023-03-16 10:08:11,079] [INFO] DFAST_QC pipeline started.
[2023-03-16 10:08:11,079] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 10:08:11,079] [INFO] DQC Reference Directory: /var/lib/cwl/stg2fbea310-4f3c-43b1-b086-6f073df2b161/dqc_reference
[2023-03-16 10:08:12,222] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 10:08:12,222] [INFO] Task started: Prodigal
[2023-03-16 10:08:12,222] [INFO] Running command: cat /var/lib/cwl/stg022a7b91-0b70-47cb-ab9b-15348f945782/OceanDNA-b37906.fa | prodigal -d OceanDNA-b37906/cds.fna -a OceanDNA-b37906/protein.faa -g 11 -q > /dev/null
[2023-03-16 10:08:23,835] [INFO] Task succeeded: Prodigal
[2023-03-16 10:08:23,835] [INFO] Task started: HMMsearch
[2023-03-16 10:08:23,835] [INFO] Running command: hmmsearch --tblout OceanDNA-b37906/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2fbea310-4f3c-43b1-b086-6f073df2b161/dqc_reference/reference_markers.hmm OceanDNA-b37906/protein.faa > /dev/null
[2023-03-16 10:08:24,028] [INFO] Task succeeded: HMMsearch
[2023-03-16 10:08:24,028] [INFO] Found 6/6 markers.
[2023-03-16 10:08:24,043] [INFO] Query marker FASTA was written to OceanDNA-b37906/markers.fasta
[2023-03-16 10:08:24,044] [INFO] Task started: Blastn
[2023-03-16 10:08:24,044] [INFO] Running command: blastn -query OceanDNA-b37906/markers.fasta -db /var/lib/cwl/stg2fbea310-4f3c-43b1-b086-6f073df2b161/dqc_reference/reference_markers.fasta -out OceanDNA-b37906/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:08:24,654] [INFO] Task succeeded: Blastn
[2023-03-16 10:08:24,655] [INFO] Selected 30 target genomes.
[2023-03-16 10:08:24,655] [INFO] Target genome list was writen to OceanDNA-b37906/target_genomes.txt
[2023-03-16 10:08:24,673] [INFO] Task started: fastANI
[2023-03-16 10:08:24,673] [INFO] Running command: fastANI --query /var/lib/cwl/stg022a7b91-0b70-47cb-ab9b-15348f945782/OceanDNA-b37906.fa --refList OceanDNA-b37906/target_genomes.txt --output OceanDNA-b37906/fastani_result.tsv --threads 1
[2023-03-16 10:08:41,721] [INFO] Task succeeded: fastANI
[2023-03-16 10:08:41,721] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2fbea310-4f3c-43b1-b086-6f073df2b161/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 10:08:41,721] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2fbea310-4f3c-43b1-b086-6f073df2b161/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 10:08:41,722] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 10:08:41,722] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 10:08:41,722] [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 10:08:41,722] [INFO] DFAST Taxonomy check result was written to OceanDNA-b37906/tc_result.tsv
[2023-03-16 10:08:41,722] [INFO] ===== Taxonomy check completed =====
[2023-03-16 10:08:41,722] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 10:08:41,722] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2fbea310-4f3c-43b1-b086-6f073df2b161/dqc_reference/checkm_data
[2023-03-16 10:08:41,725] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 10:08:41,729] [INFO] Task started: CheckM
[2023-03-16 10:08:41,729] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b37906/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b37906/checkm_input OceanDNA-b37906/checkm_result
[2023-03-16 10:09:14,659] [INFO] Task succeeded: CheckM
[2023-03-16 10:09:14,659] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 10:09:14,661] [INFO] ===== Completeness check finished =====
[2023-03-16 10:09:14,662] [INFO] ===== Start GTDB Search =====
[2023-03-16 10:09:14,662] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b37906/markers.fasta)
[2023-03-16 10:09:14,663] [INFO] Task started: Blastn
[2023-03-16 10:09:14,663] [INFO] Running command: blastn -query OceanDNA-b37906/markers.fasta -db /var/lib/cwl/stg2fbea310-4f3c-43b1-b086-6f073df2b161/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b37906/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:09:15,610] [INFO] Task succeeded: Blastn
[2023-03-16 10:09:15,611] [INFO] Selected 25 target genomes.
[2023-03-16 10:09:15,611] [INFO] Target genome list was writen to OceanDNA-b37906/target_genomes_gtdb.txt
[2023-03-16 10:09:15,729] [INFO] Task started: fastANI
[2023-03-16 10:09:15,729] [INFO] Running command: fastANI --query /var/lib/cwl/stg022a7b91-0b70-47cb-ab9b-15348f945782/OceanDNA-b37906.fa --refList OceanDNA-b37906/target_genomes_gtdb.txt --output OceanDNA-b37906/fastani_result_gtdb.tsv --threads 1
[2023-03-16 10:09:27,187] [INFO] Task succeeded: fastANI
[2023-03-16 10:09:27,192] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 10:09:27,192] [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_018666295.1	s__Luminiphilus sp018666295	99.3799	502	624	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	99.15	99.01	0.84	0.82	4	conclusive
GCA_002390485.1	s__Luminiphilus sp002390485	94.4885	542	624	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	99.01	96.90	0.92	0.88	5	-
GCA_009937065.1	s__Luminiphilus sp009937065	78.3031	118	624	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002689915.1	s__Luminiphilus sp002689915	77.8558	72	624	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	100.00	100.00	0.97	0.97	2	-
GCA_003523185.1	s__Luminiphilus sp003523185	77.2086	113	624	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000227505.4	s__Luminiphilus sp000227505	77.2076	104	624	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011524755.1	s__Luminiphilus sp011524755	77.0487	94	624	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	95.11	95.11	0.58	0.58	2	-
GCA_002862405.1	s__Luminiphilus sp002862405	76.6422	95	624	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	95.70	95.58	0.78	0.76	4	-
GCA_002469785.1	s__Luminiphilus sp002469785	76.4444	67	624	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 10:09:27,193] [INFO] GTDB search result was written to OceanDNA-b37906/result_gtdb.tsv
[2023-03-16 10:09:27,193] [INFO] ===== GTDB Search completed =====
[2023-03-16 10:09:27,194] [INFO] DFAST_QC result json was written to OceanDNA-b37906/dqc_result.json
[2023-03-16 10:09:27,194] [INFO] DFAST_QC completed!
[2023-03-16 10:09:27,194] [INFO] Total running time: 0h1m16s