[2023-03-16 11:24:27,577] [INFO] DFAST_QC pipeline started.
[2023-03-16 11:24:27,577] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 11:24:27,577] [INFO] DQC Reference Directory: /var/lib/cwl/stg50096255-5088-4a65-b3bd-802c01d774b0/dqc_reference
[2023-03-16 11:24:28,945] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 11:24:28,959] [INFO] Task started: Prodigal
[2023-03-16 11:24:28,959] [INFO] Running command: cat /var/lib/cwl/stgb928f60e-b9bd-4bb4-8124-6cf210f17097/OceanDNA-b30850.fa | prodigal -d OceanDNA-b30850/cds.fna -a OceanDNA-b30850/protein.faa -g 11 -q > /dev/null
[2023-03-16 11:24:45,018] [INFO] Task succeeded: Prodigal
[2023-03-16 11:24:45,019] [INFO] Task started: HMMsearch
[2023-03-16 11:24:45,019] [INFO] Running command: hmmsearch --tblout OceanDNA-b30850/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg50096255-5088-4a65-b3bd-802c01d774b0/dqc_reference/reference_markers.hmm OceanDNA-b30850/protein.faa > /dev/null
[2023-03-16 11:24:45,192] [INFO] Task succeeded: HMMsearch
[2023-03-16 11:24:45,193] [INFO] Found 6/6 markers.
[2023-03-16 11:24:45,210] [INFO] Query marker FASTA was written to OceanDNA-b30850/markers.fasta
[2023-03-16 11:24:45,211] [INFO] Task started: Blastn
[2023-03-16 11:24:45,211] [INFO] Running command: blastn -query OceanDNA-b30850/markers.fasta -db /var/lib/cwl/stg50096255-5088-4a65-b3bd-802c01d774b0/dqc_reference/reference_markers.fasta -out OceanDNA-b30850/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 11:24:45,844] [INFO] Task succeeded: Blastn
[2023-03-16 11:24:45,845] [INFO] Selected 25 target genomes.
[2023-03-16 11:24:45,845] [INFO] Target genome list was writen to OceanDNA-b30850/target_genomes.txt
[2023-03-16 11:24:45,860] [INFO] Task started: fastANI
[2023-03-16 11:24:45,860] [INFO] Running command: fastANI --query /var/lib/cwl/stgb928f60e-b9bd-4bb4-8124-6cf210f17097/OceanDNA-b30850.fa --refList OceanDNA-b30850/target_genomes.txt --output OceanDNA-b30850/fastani_result.tsv --threads 1
[2023-03-16 11:25:01,961] [INFO] Task succeeded: fastANI
[2023-03-16 11:25:01,961] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg50096255-5088-4a65-b3bd-802c01d774b0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 11:25:01,961] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg50096255-5088-4a65-b3bd-802c01d774b0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 11:25:01,964] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 11:25:01,964] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 11:25:01,964] [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
Magnetovibrio blakemorei	strain=MV-1	GCA_001746755.1	28181	28181	type	True	77.6931	56	188	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 11:25:01,966] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30850/tc_result.tsv
[2023-03-16 11:25:01,966] [INFO] ===== Taxonomy check completed =====
[2023-03-16 11:25:01,966] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 11:25:01,966] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg50096255-5088-4a65-b3bd-802c01d774b0/dqc_reference/checkm_data
[2023-03-16 11:25:01,967] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 11:25:01,971] [INFO] Task started: CheckM
[2023-03-16 11:25:01,971] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30850/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30850/checkm_input OceanDNA-b30850/checkm_result
[2023-03-16 11:25:27,373] [INFO] Task succeeded: CheckM
[2023-03-16 11:25:27,374] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 65.15%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 11:25:27,376] [INFO] ===== Completeness check finished =====
[2023-03-16 11:25:27,376] [INFO] ===== Start GTDB Search =====
[2023-03-16 11:25:27,376] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30850/markers.fasta)
[2023-03-16 11:25:27,376] [INFO] Task started: Blastn
[2023-03-16 11:25:27,376] [INFO] Running command: blastn -query OceanDNA-b30850/markers.fasta -db /var/lib/cwl/stg50096255-5088-4a65-b3bd-802c01d774b0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30850/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 11:25:28,662] [INFO] Task succeeded: Blastn
[2023-03-16 11:25:28,663] [INFO] Selected 23 target genomes.
[2023-03-16 11:25:28,663] [INFO] Target genome list was writen to OceanDNA-b30850/target_genomes_gtdb.txt
[2023-03-16 11:25:29,304] [INFO] Task started: fastANI
[2023-03-16 11:25:29,304] [INFO] Running command: fastANI --query /var/lib/cwl/stgb928f60e-b9bd-4bb4-8124-6cf210f17097/OceanDNA-b30850.fa --refList OceanDNA-b30850/target_genomes_gtdb.txt --output OceanDNA-b30850/fastani_result_gtdb.tsv --threads 1
[2023-03-16 11:25:40,930] [INFO] Task succeeded: fastANI
[2023-03-16 11:25:40,932] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 11:25:40,932] [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
GCF_001746755.1	s__Magnetovibrio blakemorei	77.6931	56	188	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetovibrionaceae;g__Magnetovibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 11:25:40,932] [INFO] GTDB search result was written to OceanDNA-b30850/result_gtdb.tsv
[2023-03-16 11:25:40,932] [INFO] ===== GTDB Search completed =====
[2023-03-16 11:25:40,933] [INFO] DFAST_QC result json was written to OceanDNA-b30850/dqc_result.json
[2023-03-16 11:25:40,933] [INFO] DFAST_QC completed!
[2023-03-16 11:25:40,933] [INFO] Total running time: 0h1m13s