[2023-03-17 07:44:36,996] [INFO] DFAST_QC pipeline started.
[2023-03-17 07:44:36,996] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 07:44:36,996] [INFO] DQC Reference Directory: /var/lib/cwl/stg906e745a-9554-411f-b4fb-0f1255b686df/dqc_reference
[2023-03-17 07:44:38,848] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 07:44:38,849] [INFO] Task started: Prodigal
[2023-03-17 07:44:38,849] [INFO] Running command: cat /var/lib/cwl/stg351d7a3d-a615-4fac-a18d-e92135f92245/OceanDNA-b4525.fa | prodigal -d OceanDNA-b4525/cds.fna -a OceanDNA-b4525/protein.faa -g 11 -q > /dev/null
[2023-03-17 07:44:56,954] [INFO] Task succeeded: Prodigal
[2023-03-17 07:44:56,954] [INFO] Task started: HMMsearch
[2023-03-17 07:44:56,955] [INFO] Running command: hmmsearch --tblout OceanDNA-b4525/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg906e745a-9554-411f-b4fb-0f1255b686df/dqc_reference/reference_markers.hmm OceanDNA-b4525/protein.faa > /dev/null
[2023-03-17 07:44:57,154] [INFO] Task succeeded: HMMsearch
[2023-03-17 07:44:57,154] [INFO] Found 6/6 markers.
[2023-03-17 07:44:57,174] [INFO] Query marker FASTA was written to OceanDNA-b4525/markers.fasta
[2023-03-17 07:44:57,174] [INFO] Task started: Blastn
[2023-03-17 07:44:57,174] [INFO] Running command: blastn -query OceanDNA-b4525/markers.fasta -db /var/lib/cwl/stg906e745a-9554-411f-b4fb-0f1255b686df/dqc_reference/reference_markers.fasta -out OceanDNA-b4525/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:44:57,717] [INFO] Task succeeded: Blastn
[2023-03-17 07:44:57,718] [INFO] Selected 33 target genomes.
[2023-03-17 07:44:57,718] [INFO] Target genome list was writen to OceanDNA-b4525/target_genomes.txt
[2023-03-17 07:44:57,749] [INFO] Task started: fastANI
[2023-03-17 07:44:57,749] [INFO] Running command: fastANI --query /var/lib/cwl/stg351d7a3d-a615-4fac-a18d-e92135f92245/OceanDNA-b4525.fa --refList OceanDNA-b4525/target_genomes.txt --output OceanDNA-b4525/fastani_result.tsv --threads 1
[2023-03-17 07:45:14,255] [INFO] Task succeeded: fastANI
[2023-03-17 07:45:14,256] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg906e745a-9554-411f-b4fb-0f1255b686df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 07:45:14,256] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg906e745a-9554-411f-b4fb-0f1255b686df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 07:45:14,259] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 07:45:14,259] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 07:45:14,259] [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
Vicingus serpentipes	strain=NCIMB 15042	GCA_007993035.1	1926625	1926625	type	True	75.5983	53	919	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 07:45:14,259] [INFO] DFAST Taxonomy check result was written to OceanDNA-b4525/tc_result.tsv
[2023-03-17 07:45:14,259] [INFO] ===== Taxonomy check completed =====
[2023-03-17 07:45:14,259] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 07:45:14,259] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg906e745a-9554-411f-b4fb-0f1255b686df/dqc_reference/checkm_data
[2023-03-17 07:45:14,260] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 07:45:14,264] [INFO] Task started: CheckM
[2023-03-17 07:45:14,264] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b4525/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b4525/checkm_input OceanDNA-b4525/checkm_result
[2023-03-17 07:46:01,219] [INFO] Task succeeded: CheckM
[2023-03-17 07:46:01,220] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 07:46:01,222] [INFO] ===== Completeness check finished =====
[2023-03-17 07:46:01,222] [INFO] ===== Start GTDB Search =====
[2023-03-17 07:46:01,222] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b4525/markers.fasta)
[2023-03-17 07:46:01,223] [INFO] Task started: Blastn
[2023-03-17 07:46:01,223] [INFO] Running command: blastn -query OceanDNA-b4525/markers.fasta -db /var/lib/cwl/stg906e745a-9554-411f-b4fb-0f1255b686df/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b4525/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:46:01,952] [INFO] Task succeeded: Blastn
[2023-03-17 07:46:01,953] [INFO] Selected 26 target genomes.
[2023-03-17 07:46:01,953] [INFO] Target genome list was writen to OceanDNA-b4525/target_genomes_gtdb.txt
[2023-03-17 07:46:02,011] [INFO] Task started: fastANI
[2023-03-17 07:46:02,011] [INFO] Running command: fastANI --query /var/lib/cwl/stg351d7a3d-a615-4fac-a18d-e92135f92245/OceanDNA-b4525.fa --refList OceanDNA-b4525/target_genomes_gtdb.txt --output OceanDNA-b4525/fastani_result_gtdb.tsv --threads 1
[2023-03-17 07:46:15,135] [INFO] Task succeeded: fastANI
[2023-03-17 07:46:15,138] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 07:46:15,138] [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_018609045.1	s__JAAZVO01 sp018609045	99.7833	838	919	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Salibacteraceae;g__JAAZVO01	95.0	99.59	99.59	0.92	0.92	2	conclusive
GCA_018623405.1	s__JAAZVO01 sp018623405	76.9599	188	919	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Salibacteraceae;g__JAAZVO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905181855.1	s__CAJIZE01 sp905181855	76.4749	65	919	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Salibacteraceae;g__CAJIZE01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 07:46:15,138] [INFO] GTDB search result was written to OceanDNA-b4525/result_gtdb.tsv
[2023-03-17 07:46:15,139] [INFO] ===== GTDB Search completed =====
[2023-03-17 07:46:15,139] [INFO] DFAST_QC result json was written to OceanDNA-b4525/dqc_result.json
[2023-03-17 07:46:15,139] [INFO] DFAST_QC completed!
[2023-03-17 07:46:15,139] [INFO] Total running time: 0h1m38s