[2023-03-16 21:45:15,237] [INFO] DFAST_QC pipeline started.
[2023-03-16 21:45:15,237] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 21:45:15,237] [INFO] DQC Reference Directory: /var/lib/cwl/stg42fc580c-a16d-48bb-a3f9-248d5bcfdcbf/dqc_reference
[2023-03-16 21:45:16,434] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 21:45:16,434] [INFO] Task started: Prodigal
[2023-03-16 21:45:16,434] [INFO] Running command: cat /var/lib/cwl/stgd7bde321-b863-41a6-9cc0-0e43c45529a5/OceanDNA-b46181.fa | prodigal -d OceanDNA-b46181/cds.fna -a OceanDNA-b46181/protein.faa -g 11 -q > /dev/null
[2023-03-16 21:45:31,320] [INFO] Task succeeded: Prodigal
[2023-03-16 21:45:31,321] [INFO] Task started: HMMsearch
[2023-03-16 21:45:31,321] [INFO] Running command: hmmsearch --tblout OceanDNA-b46181/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg42fc580c-a16d-48bb-a3f9-248d5bcfdcbf/dqc_reference/reference_markers.hmm OceanDNA-b46181/protein.faa > /dev/null
[2023-03-16 21:45:31,511] [INFO] Task succeeded: HMMsearch
[2023-03-16 21:45:31,512] [INFO] Found 6/6 markers.
[2023-03-16 21:45:31,523] [INFO] Query marker FASTA was written to OceanDNA-b46181/markers.fasta
[2023-03-16 21:45:31,523] [INFO] Task started: Blastn
[2023-03-16 21:45:31,523] [INFO] Running command: blastn -query OceanDNA-b46181/markers.fasta -db /var/lib/cwl/stg42fc580c-a16d-48bb-a3f9-248d5bcfdcbf/dqc_reference/reference_markers.fasta -out OceanDNA-b46181/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 21:45:32,127] [INFO] Task succeeded: Blastn
[2023-03-16 21:45:32,128] [INFO] Selected 16 target genomes.
[2023-03-16 21:45:32,128] [INFO] Target genome list was writen to OceanDNA-b46181/target_genomes.txt
[2023-03-16 21:45:32,138] [INFO] Task started: fastANI
[2023-03-16 21:45:32,138] [INFO] Running command: fastANI --query /var/lib/cwl/stgd7bde321-b863-41a6-9cc0-0e43c45529a5/OceanDNA-b46181.fa --refList OceanDNA-b46181/target_genomes.txt --output OceanDNA-b46181/fastani_result.tsv --threads 1
[2023-03-16 21:45:40,469] [INFO] Task succeeded: fastANI
[2023-03-16 21:45:40,469] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg42fc580c-a16d-48bb-a3f9-248d5bcfdcbf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 21:45:40,470] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg42fc580c-a16d-48bb-a3f9-248d5bcfdcbf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 21:45:40,473] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 21:45:40,473] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 21:45:40,473] [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
Coraliomargarita sinensis	strain=WN38	GCA_003185655.1	2174842	2174842	type	True	76.6947	91	597	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 21:45:40,473] [INFO] DFAST Taxonomy check result was written to OceanDNA-b46181/tc_result.tsv
[2023-03-16 21:45:40,473] [INFO] ===== Taxonomy check completed =====
[2023-03-16 21:45:40,473] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 21:45:40,473] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg42fc580c-a16d-48bb-a3f9-248d5bcfdcbf/dqc_reference/checkm_data
[2023-03-16 21:45:40,474] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 21:45:40,478] [INFO] Task started: CheckM
[2023-03-16 21:45:40,478] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b46181/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b46181/checkm_input OceanDNA-b46181/checkm_result
[2023-03-16 21:46:20,921] [INFO] Task succeeded: CheckM
[2023-03-16 21:46:20,921] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 21:46:20,923] [INFO] ===== Completeness check finished =====
[2023-03-16 21:46:20,924] [INFO] ===== Start GTDB Search =====
[2023-03-16 21:46:20,924] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b46181/markers.fasta)
[2023-03-16 21:46:20,924] [INFO] Task started: Blastn
[2023-03-16 21:46:20,924] [INFO] Running command: blastn -query OceanDNA-b46181/markers.fasta -db /var/lib/cwl/stg42fc580c-a16d-48bb-a3f9-248d5bcfdcbf/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b46181/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 21:46:21,885] [INFO] Task succeeded: Blastn
[2023-03-16 21:46:21,886] [INFO] Selected 26 target genomes.
[2023-03-16 21:46:21,886] [INFO] Target genome list was writen to OceanDNA-b46181/target_genomes_gtdb.txt
[2023-03-16 21:46:21,963] [INFO] Task started: fastANI
[2023-03-16 21:46:21,963] [INFO] Running command: fastANI --query /var/lib/cwl/stgd7bde321-b863-41a6-9cc0-0e43c45529a5/OceanDNA-b46181.fa --refList OceanDNA-b46181/target_genomes_gtdb.txt --output OceanDNA-b46181/fastani_result_gtdb.tsv --threads 1
[2023-03-16 21:46:33,357] [INFO] Task succeeded: fastANI
[2023-03-16 21:46:33,362] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 21:46:33,362] [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_018402305.1	s__UBA7441 sp018402305	77.6353	73	597	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__UBA7441	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007692545.1	s__UBA7441 sp007692545	76.8944	55	597	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__UBA7441	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003185655.1	s__WN38 sp003185655	76.6947	91	597	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__WN38	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003566795.1	s__WN38 sp003566795	76.6848	63	597	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__WN38	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 21:46:33,362] [INFO] GTDB search result was written to OceanDNA-b46181/result_gtdb.tsv
[2023-03-16 21:46:33,362] [INFO] ===== GTDB Search completed =====
[2023-03-16 21:46:33,363] [INFO] DFAST_QC result json was written to OceanDNA-b46181/dqc_result.json
[2023-03-16 21:46:33,363] [INFO] DFAST_QC completed!
[2023-03-16 21:46:33,363] [INFO] Total running time: 0h1m18s