[2023-03-17 23:54:11,283] [INFO] DFAST_QC pipeline started.
[2023-03-17 23:54:11,284] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 23:54:11,284] [INFO] DQC Reference Directory: /var/lib/cwl/stgb51b143e-8c72-4aae-9216-ccb9d39b7d33/dqc_reference
[2023-03-17 23:54:13,839] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 23:54:13,840] [INFO] Task started: Prodigal
[2023-03-17 23:54:13,840] [INFO] Running command: cat /var/lib/cwl/stga03ff843-c6cd-4d93-9ad0-e7d53de6af23/OceanDNA-b46876.fa | prodigal -d OceanDNA-b46876/cds.fna -a OceanDNA-b46876/protein.faa -g 11 -q > /dev/null
[2023-03-17 23:54:23,350] [INFO] Task succeeded: Prodigal
[2023-03-17 23:54:23,350] [INFO] Task started: HMMsearch
[2023-03-17 23:54:23,350] [INFO] Running command: hmmsearch --tblout OceanDNA-b46876/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb51b143e-8c72-4aae-9216-ccb9d39b7d33/dqc_reference/reference_markers.hmm OceanDNA-b46876/protein.faa > /dev/null
[2023-03-17 23:54:23,522] [INFO] Task succeeded: HMMsearch
[2023-03-17 23:54:23,522] [INFO] Found 6/6 markers.
[2023-03-17 23:54:23,538] [INFO] Query marker FASTA was written to OceanDNA-b46876/markers.fasta
[2023-03-17 23:54:23,539] [INFO] Task started: Blastn
[2023-03-17 23:54:23,539] [INFO] Running command: blastn -query OceanDNA-b46876/markers.fasta -db /var/lib/cwl/stgb51b143e-8c72-4aae-9216-ccb9d39b7d33/dqc_reference/reference_markers.fasta -out OceanDNA-b46876/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:54:24,048] [INFO] Task succeeded: Blastn
[2023-03-17 23:54:24,052] [INFO] Selected 13 target genomes.
[2023-03-17 23:54:24,052] [INFO] Target genome list was writen to OceanDNA-b46876/target_genomes.txt
[2023-03-17 23:54:24,060] [INFO] Task started: fastANI
[2023-03-17 23:54:24,060] [INFO] Running command: fastANI --query /var/lib/cwl/stga03ff843-c6cd-4d93-9ad0-e7d53de6af23/OceanDNA-b46876.fa --refList OceanDNA-b46876/target_genomes.txt --output OceanDNA-b46876/fastani_result.tsv --threads 1
[2023-03-17 23:54:31,330] [INFO] Task succeeded: fastANI
[2023-03-17 23:54:31,331] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb51b143e-8c72-4aae-9216-ccb9d39b7d33/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 23:54:31,331] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb51b143e-8c72-4aae-9216-ccb9d39b7d33/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 23:54:31,332] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 23:54:31,332] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 23:54:31,332] [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
--------------------------------------------------------------------------------
[2023-03-17 23:54:31,334] [INFO] DFAST Taxonomy check result was written to OceanDNA-b46876/tc_result.tsv
[2023-03-17 23:54:31,335] [INFO] ===== Taxonomy check completed =====
[2023-03-17 23:54:31,335] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 23:54:31,335] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb51b143e-8c72-4aae-9216-ccb9d39b7d33/dqc_reference/checkm_data
[2023-03-17 23:54:31,340] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 23:54:31,431] [INFO] Task started: CheckM
[2023-03-17 23:54:31,432] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b46876/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b46876/checkm_input OceanDNA-b46876/checkm_result
[2023-03-17 23:55:00,068] [INFO] Task succeeded: CheckM
[2023-03-17 23:55:00,068] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 23:55:00,075] [INFO] ===== Completeness check finished =====
[2023-03-17 23:55:00,075] [INFO] ===== Start GTDB Search =====
[2023-03-17 23:55:00,075] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b46876/markers.fasta)
[2023-03-17 23:55:00,076] [INFO] Task started: Blastn
[2023-03-17 23:55:00,076] [INFO] Running command: blastn -query OceanDNA-b46876/markers.fasta -db /var/lib/cwl/stgb51b143e-8c72-4aae-9216-ccb9d39b7d33/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b46876/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:55:00,766] [INFO] Task succeeded: Blastn
[2023-03-17 23:55:00,770] [INFO] Selected 19 target genomes.
[2023-03-17 23:55:00,770] [INFO] Target genome list was writen to OceanDNA-b46876/target_genomes_gtdb.txt
[2023-03-17 23:55:00,790] [INFO] Task started: fastANI
[2023-03-17 23:55:00,790] [INFO] Running command: fastANI --query /var/lib/cwl/stga03ff843-c6cd-4d93-9ad0-e7d53de6af23/OceanDNA-b46876.fa --refList OceanDNA-b46876/target_genomes_gtdb.txt --output OceanDNA-b46876/fastani_result_gtdb.tsv --threads 1
[2023-03-17 23:55:08,129] [INFO] Task succeeded: fastANI
[2023-03-17 23:55:08,132] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 23:55:08,132] [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_002386905.1	s__UBA4581 sp002386905	99.947	462	484	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__UBA4581	95.0	99.78	99.78	0.92	0.92	2	conclusive
GCA_002387565.1	s__UBA4581 sp002387565	84.3434	340	484	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__UBA4581	95.0	99.92	99.92	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2023-03-17 23:55:08,132] [INFO] GTDB search result was written to OceanDNA-b46876/result_gtdb.tsv
[2023-03-17 23:55:08,132] [INFO] ===== GTDB Search completed =====
[2023-03-17 23:55:08,134] [INFO] DFAST_QC result json was written to OceanDNA-b46876/dqc_result.json
[2023-03-17 23:55:08,134] [INFO] DFAST_QC completed!
[2023-03-17 23:55:08,134] [INFO] Total running time: 0h0m57s