[2023-03-14 13:29:09,756] [INFO] DFAST_QC pipeline started.
[2023-03-14 13:29:09,756] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 13:29:09,756] [INFO] DQC Reference Directory: /var/lib/cwl/stgd5110d50-60a2-4216-b417-fa2fab996bcf/dqc_reference
[2023-03-14 13:29:10,894] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 13:29:10,895] [INFO] Task started: Prodigal
[2023-03-14 13:29:10,895] [INFO] Running command: cat /var/lib/cwl/stgdb80df05-6a03-4d32-b440-7e091e8329f2/OceanDNA-b43704.fa | prodigal -d OceanDNA-b43704/cds.fna -a OceanDNA-b43704/protein.faa -g 11 -q > /dev/null
[2023-03-14 13:29:21,412] [INFO] Task succeeded: Prodigal
[2023-03-14 13:29:21,412] [INFO] Task started: HMMsearch
[2023-03-14 13:29:21,413] [INFO] Running command: hmmsearch --tblout OceanDNA-b43704/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd5110d50-60a2-4216-b417-fa2fab996bcf/dqc_reference/reference_markers.hmm OceanDNA-b43704/protein.faa > /dev/null
[2023-03-14 13:29:21,590] [INFO] Task succeeded: HMMsearch
[2023-03-14 13:29:21,590] [INFO] Found 6/6 markers.
[2023-03-14 13:29:21,605] [INFO] Query marker FASTA was written to OceanDNA-b43704/markers.fasta
[2023-03-14 13:29:21,606] [INFO] Task started: Blastn
[2023-03-14 13:29:21,606] [INFO] Running command: blastn -query OceanDNA-b43704/markers.fasta -db /var/lib/cwl/stgd5110d50-60a2-4216-b417-fa2fab996bcf/dqc_reference/reference_markers.fasta -out OceanDNA-b43704/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:29:22,186] [INFO] Task succeeded: Blastn
[2023-03-14 13:29:22,187] [INFO] Selected 27 target genomes.
[2023-03-14 13:29:22,188] [INFO] Target genome list was writen to OceanDNA-b43704/target_genomes.txt
[2023-03-14 13:29:22,200] [INFO] Task started: fastANI
[2023-03-14 13:29:22,200] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb80df05-6a03-4d32-b440-7e091e8329f2/OceanDNA-b43704.fa --refList OceanDNA-b43704/target_genomes.txt --output OceanDNA-b43704/fastani_result.tsv --threads 1
[2023-03-14 13:29:37,863] [INFO] Task succeeded: fastANI
[2023-03-14 13:29:37,864] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd5110d50-60a2-4216-b417-fa2fab996bcf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 13:29:37,864] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd5110d50-60a2-4216-b417-fa2fab996bcf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 13:29:37,864] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 13:29:37,864] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 13:29:37,864] [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
--------------------------------------------------------------------------------
[2023-03-14 13:29:37,864] [INFO] DFAST Taxonomy check result was written to OceanDNA-b43704/tc_result.tsv
[2023-03-14 13:29:37,864] [INFO] ===== Taxonomy check completed =====
[2023-03-14 13:29:37,864] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 13:29:37,864] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd5110d50-60a2-4216-b417-fa2fab996bcf/dqc_reference/checkm_data
[2023-03-14 13:29:37,867] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 13:29:37,871] [INFO] Task started: CheckM
[2023-03-14 13:29:37,871] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b43704/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b43704/checkm_input OceanDNA-b43704/checkm_result
[2023-03-14 13:30:10,160] [INFO] Task succeeded: CheckM
[2023-03-14 13:30:10,161] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 5.07%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-03-14 13:30:10,163] [INFO] ===== Completeness check finished =====
[2023-03-14 13:30:10,163] [INFO] ===== Start GTDB Search =====
[2023-03-14 13:30:10,163] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b43704/markers.fasta)
[2023-03-14 13:30:10,166] [INFO] Task started: Blastn
[2023-03-14 13:30:10,166] [INFO] Running command: blastn -query OceanDNA-b43704/markers.fasta -db /var/lib/cwl/stgd5110d50-60a2-4216-b417-fa2fab996bcf/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b43704/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:30:12,190] [INFO] Task succeeded: Blastn
[2023-03-14 13:30:12,190] [INFO] Selected 17 target genomes.
[2023-03-14 13:30:12,191] [INFO] Target genome list was writen to OceanDNA-b43704/target_genomes_gtdb.txt
[2023-03-14 13:30:12,203] [INFO] Task started: fastANI
[2023-03-14 13:30:12,203] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb80df05-6a03-4d32-b440-7e091e8329f2/OceanDNA-b43704.fa --refList OceanDNA-b43704/target_genomes_gtdb.txt --output OceanDNA-b43704/fastani_result_gtdb.tsv --threads 1
[2023-03-14 13:30:24,153] [INFO] Task succeeded: fastANI
[2023-03-14 13:30:24,159] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 13:30:24,159] [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_018661145.1	s__UBA868 sp018661145	98.3331	441	566	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Arenicellales;f__UBA868;g__UBA868	95.0	99.09	98.72	0.78	0.74	4	conclusive
GCA_002171735.1	s__UBA868 sp002171735	89.727	455	566	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Arenicellales;f__UBA868;g__UBA868	95.0	98.83	98.60	0.84	0.82	3	-
GCA_003529705.1	s__UBA868 sp003529705	82.2815	224	566	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Arenicellales;f__UBA868;g__UBA868	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002327725.1	s__UBA868 sp002327725	80.1508	319	566	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Arenicellales;f__UBA868;g__UBA868	95.0	99.85	99.69	0.88	0.82	5	-
GCA_016845525.1	s__UBA868 sp016845525	78.209	197	566	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Arenicellales;f__UBA868;g__UBA868	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011523045.1	s__UBA868 sp011523045	78.0148	194	566	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Arenicellales;f__UBA868;g__UBA868	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002713825.1	s__UBA868 sp002713825	77.526	113	566	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Arenicellales;f__UBA868;g__UBA868	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002477475.1	s__UBA868 sp002477475	77.4073	198	566	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Arenicellales;f__UBA868;g__UBA868	95.0	99.71	99.58	0.88	0.75	11	-
--------------------------------------------------------------------------------
[2023-03-14 13:30:24,159] [INFO] GTDB search result was written to OceanDNA-b43704/result_gtdb.tsv
[2023-03-14 13:30:24,159] [INFO] ===== GTDB Search completed =====
[2023-03-14 13:30:24,160] [INFO] DFAST_QC result json was written to OceanDNA-b43704/dqc_result.json
[2023-03-14 13:30:24,160] [INFO] DFAST_QC completed!
[2023-03-14 13:30:24,160] [INFO] Total running time: 0h1m14s