[2023-03-15 13:20:51,623] [INFO] DFAST_QC pipeline started.
[2023-03-15 13:20:51,623] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 13:20:51,624] [INFO] DQC Reference Directory: /var/lib/cwl/stge581c2cc-d763-4746-be05-bbfc944b5f7d/dqc_reference
[2023-03-15 13:20:52,770] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 13:20:52,770] [INFO] Task started: Prodigal
[2023-03-15 13:20:52,770] [INFO] Running command: cat /var/lib/cwl/stge70845c0-b014-452c-a0ce-8ce8e709d1ff/OceanDNA-b33568.fa | prodigal -d OceanDNA-b33568/cds.fna -a OceanDNA-b33568/protein.faa -g 11 -q > /dev/null
[2023-03-15 13:21:03,639] [INFO] Task succeeded: Prodigal
[2023-03-15 13:21:03,639] [INFO] Task started: HMMsearch
[2023-03-15 13:21:03,639] [INFO] Running command: hmmsearch --tblout OceanDNA-b33568/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge581c2cc-d763-4746-be05-bbfc944b5f7d/dqc_reference/reference_markers.hmm OceanDNA-b33568/protein.faa > /dev/null
[2023-03-15 13:21:03,849] [INFO] Task succeeded: HMMsearch
[2023-03-15 13:21:03,849] [INFO] Found 6/6 markers.
[2023-03-15 13:21:03,867] [INFO] Query marker FASTA was written to OceanDNA-b33568/markers.fasta
[2023-03-15 13:21:03,868] [INFO] Task started: Blastn
[2023-03-15 13:21:03,868] [INFO] Running command: blastn -query OceanDNA-b33568/markers.fasta -db /var/lib/cwl/stge581c2cc-d763-4746-be05-bbfc944b5f7d/dqc_reference/reference_markers.fasta -out OceanDNA-b33568/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:21:04,406] [INFO] Task succeeded: Blastn
[2023-03-15 13:21:04,407] [INFO] Selected 32 target genomes.
[2023-03-15 13:21:04,408] [INFO] Target genome list was writen to OceanDNA-b33568/target_genomes.txt
[2023-03-15 13:21:04,433] [INFO] Task started: fastANI
[2023-03-15 13:21:04,433] [INFO] Running command: fastANI --query /var/lib/cwl/stge70845c0-b014-452c-a0ce-8ce8e709d1ff/OceanDNA-b33568.fa --refList OceanDNA-b33568/target_genomes.txt --output OceanDNA-b33568/fastani_result.tsv --threads 1
[2023-03-15 13:21:30,813] [INFO] Task succeeded: fastANI
[2023-03-15 13:21:30,814] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge581c2cc-d763-4746-be05-bbfc944b5f7d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 13:21:30,814] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge581c2cc-d763-4746-be05-bbfc944b5f7d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 13:21:30,814] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 13:21:30,814] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 13:21:30,814] [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
--------------------------------------------------------------------------------
[2023-03-15 13:21:30,815] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33568/tc_result.tsv
[2023-03-15 13:21:30,815] [INFO] ===== Taxonomy check completed =====
[2023-03-15 13:21:30,815] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 13:21:30,815] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge581c2cc-d763-4746-be05-bbfc944b5f7d/dqc_reference/checkm_data
[2023-03-15 13:21:30,818] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 13:21:30,824] [INFO] Task started: CheckM
[2023-03-15 13:21:30,824] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33568/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33568/checkm_input OceanDNA-b33568/checkm_result
[2023-03-15 13:22:03,118] [INFO] Task succeeded: CheckM
[2023-03-15 13:22:03,118] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 1.39%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 13:22:03,122] [INFO] ===== Completeness check finished =====
[2023-03-15 13:22:03,122] [INFO] ===== Start GTDB Search =====
[2023-03-15 13:22:03,123] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33568/markers.fasta)
[2023-03-15 13:22:03,123] [INFO] Task started: Blastn
[2023-03-15 13:22:03,123] [INFO] Running command: blastn -query OceanDNA-b33568/markers.fasta -db /var/lib/cwl/stge581c2cc-d763-4746-be05-bbfc944b5f7d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33568/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:22:03,913] [INFO] Task succeeded: Blastn
[2023-03-15 13:22:03,915] [INFO] Selected 29 target genomes.
[2023-03-15 13:22:03,915] [INFO] Target genome list was writen to OceanDNA-b33568/target_genomes_gtdb.txt
[2023-03-15 13:22:03,954] [INFO] Task started: fastANI
[2023-03-15 13:22:03,955] [INFO] Running command: fastANI --query /var/lib/cwl/stge70845c0-b014-452c-a0ce-8ce8e709d1ff/OceanDNA-b33568.fa --refList OceanDNA-b33568/target_genomes_gtdb.txt --output OceanDNA-b33568/fastani_result_gtdb.tsv --threads 1
[2023-03-15 13:22:20,648] [INFO] Task succeeded: fastANI
[2023-03-15 13:22:20,652] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 13:22:20,652] [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_018402635.1	s__UBA2463 sp018402635	92.2607	408	549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__UBA2463	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018401615.1	s__UBA2463 sp018401615	79.1232	50	549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__UBA2463	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016868255.1	s__UBA2463 sp016868255	76.8159	53	549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__UBA2463	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016868305.1	s__UBA2463 sp016868305	76.6856	80	549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__UBA2463	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009646425.1	s__UBA2463 sp009646425	76.6317	66	549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__UBA2463	95.0	95.85	95.85	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2023-03-15 13:22:20,653] [INFO] GTDB search result was written to OceanDNA-b33568/result_gtdb.tsv
[2023-03-15 13:22:20,653] [INFO] ===== GTDB Search completed =====
[2023-03-15 13:22:20,654] [INFO] DFAST_QC result json was written to OceanDNA-b33568/dqc_result.json
[2023-03-15 13:22:20,654] [INFO] DFAST_QC completed!
[2023-03-15 13:22:20,655] [INFO] Total running time: 0h1m29s