[2023-03-18 20:40:39,434] [INFO] DFAST_QC pipeline started.
[2023-03-18 20:40:39,434] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 20:40:39,434] [INFO] DQC Reference Directory: /var/lib/cwl/stgcbbec134-bacb-4a6e-9f12-9c89200650e8/dqc_reference
[2023-03-18 20:40:41,213] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 20:40:41,213] [INFO] Task started: Prodigal
[2023-03-18 20:40:41,213] [INFO] Running command: cat /var/lib/cwl/stgf3a3358d-82a9-4b17-a3d8-04b141380a0a/OceanDNA-b46867.fa | prodigal -d OceanDNA-b46867/cds.fna -a OceanDNA-b46867/protein.faa -g 11 -q > /dev/null
[2023-03-18 20:40:59,351] [INFO] Task succeeded: Prodigal
[2023-03-18 20:40:59,351] [INFO] Task started: HMMsearch
[2023-03-18 20:40:59,351] [INFO] Running command: hmmsearch --tblout OceanDNA-b46867/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcbbec134-bacb-4a6e-9f12-9c89200650e8/dqc_reference/reference_markers.hmm OceanDNA-b46867/protein.faa > /dev/null
[2023-03-18 20:40:59,598] [INFO] Task succeeded: HMMsearch
[2023-03-18 20:40:59,599] [INFO] Found 6/6 markers.
[2023-03-18 20:40:59,622] [INFO] Query marker FASTA was written to OceanDNA-b46867/markers.fasta
[2023-03-18 20:40:59,622] [INFO] Task started: Blastn
[2023-03-18 20:40:59,622] [INFO] Running command: blastn -query OceanDNA-b46867/markers.fasta -db /var/lib/cwl/stgcbbec134-bacb-4a6e-9f12-9c89200650e8/dqc_reference/reference_markers.fasta -out OceanDNA-b46867/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:41:00,187] [INFO] Task succeeded: Blastn
[2023-03-18 20:41:00,188] [INFO] Selected 14 target genomes.
[2023-03-18 20:41:00,189] [INFO] Target genome list was writen to OceanDNA-b46867/target_genomes.txt
[2023-03-18 20:41:00,194] [INFO] Task started: fastANI
[2023-03-18 20:41:00,194] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3a3358d-82a9-4b17-a3d8-04b141380a0a/OceanDNA-b46867.fa --refList OceanDNA-b46867/target_genomes.txt --output OceanDNA-b46867/fastani_result.tsv --threads 1
[2023-03-18 20:41:09,993] [INFO] Task succeeded: fastANI
[2023-03-18 20:41:09,994] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcbbec134-bacb-4a6e-9f12-9c89200650e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 20:41:09,994] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcbbec134-bacb-4a6e-9f12-9c89200650e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 20:41:09,997] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 20:41:09,997] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 20:41:09,997] [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
Luteolibacter yonseiensis	strain=JCM 18052	GCA_016595465.1	1144680	1144680	type	True	75.9445	54	614	95	below_threshold
Luteolibacter ambystomatis	strain=32A	GCA_018137965.1	2824561	2824561	type	True	75.8549	54	614	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 20:41:09,998] [INFO] DFAST Taxonomy check result was written to OceanDNA-b46867/tc_result.tsv
[2023-03-18 20:41:09,998] [INFO] ===== Taxonomy check completed =====
[2023-03-18 20:41:09,998] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 20:41:09,998] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcbbec134-bacb-4a6e-9f12-9c89200650e8/dqc_reference/checkm_data
[2023-03-18 20:41:09,999] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 20:41:10,003] [INFO] Task started: CheckM
[2023-03-18 20:41:10,003] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b46867/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b46867/checkm_input OceanDNA-b46867/checkm_result
[2023-03-18 20:41:59,558] [INFO] Task succeeded: CheckM
[2023-03-18 20:41:59,559] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.03%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 20:41:59,561] [INFO] ===== Completeness check finished =====
[2023-03-18 20:41:59,561] [INFO] ===== Start GTDB Search =====
[2023-03-18 20:41:59,562] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b46867/markers.fasta)
[2023-03-18 20:41:59,562] [INFO] Task started: Blastn
[2023-03-18 20:41:59,562] [INFO] Running command: blastn -query OceanDNA-b46867/markers.fasta -db /var/lib/cwl/stgcbbec134-bacb-4a6e-9f12-9c89200650e8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b46867/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:42:00,349] [INFO] Task succeeded: Blastn
[2023-03-18 20:42:00,350] [INFO] Selected 23 target genomes.
[2023-03-18 20:42:00,350] [INFO] Target genome list was writen to OceanDNA-b46867/target_genomes_gtdb.txt
[2023-03-18 20:42:00,500] [INFO] Task started: fastANI
[2023-03-18 20:42:00,501] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3a3358d-82a9-4b17-a3d8-04b141380a0a/OceanDNA-b46867.fa --refList OceanDNA-b46867/target_genomes_gtdb.txt --output OceanDNA-b46867/fastani_result_gtdb.tsv --threads 1
[2023-03-18 20:42:15,296] [INFO] Task succeeded: fastANI
[2023-03-18 20:42:15,299] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 20:42:15,299] [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_016595465.1	s__Luteolibacter yonseiensis	75.9445	54	614	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017798145.1	s__Luteolibacter sp017798145	75.8727	58	614	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 20:42:15,299] [INFO] GTDB search result was written to OceanDNA-b46867/result_gtdb.tsv
[2023-03-18 20:42:15,299] [INFO] ===== GTDB Search completed =====
[2023-03-18 20:42:15,300] [INFO] DFAST_QC result json was written to OceanDNA-b46867/dqc_result.json
[2023-03-18 20:42:15,300] [INFO] DFAST_QC completed!
[2023-03-18 20:42:15,300] [INFO] Total running time: 0h1m36s