[2023-03-19 00:01:03,361] [INFO] DFAST_QC pipeline started.
[2023-03-19 00:01:03,361] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 00:01:03,361] [INFO] DQC Reference Directory: /var/lib/cwl/stgc060ccd3-ec61-479c-a569-50e015f55be7/dqc_reference
[2023-03-19 00:01:04,587] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 00:01:04,588] [INFO] Task started: Prodigal
[2023-03-19 00:01:04,588] [INFO] Running command: cat /var/lib/cwl/stg0ad1d700-44e9-46c2-ab78-e2d9b9fd9427/OceanDNA-b46214.fa | prodigal -d OceanDNA-b46214/cds.fna -a OceanDNA-b46214/protein.faa -g 11 -q > /dev/null
[2023-03-19 00:01:32,383] [INFO] Task succeeded: Prodigal
[2023-03-19 00:01:32,383] [INFO] Task started: HMMsearch
[2023-03-19 00:01:32,383] [INFO] Running command: hmmsearch --tblout OceanDNA-b46214/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc060ccd3-ec61-479c-a569-50e015f55be7/dqc_reference/reference_markers.hmm OceanDNA-b46214/protein.faa > /dev/null
[2023-03-19 00:01:32,632] [INFO] Task succeeded: HMMsearch
[2023-03-19 00:01:32,633] [INFO] Found 6/6 markers.
[2023-03-19 00:01:32,655] [INFO] Query marker FASTA was written to OceanDNA-b46214/markers.fasta
[2023-03-19 00:01:32,655] [INFO] Task started: Blastn
[2023-03-19 00:01:32,655] [INFO] Running command: blastn -query OceanDNA-b46214/markers.fasta -db /var/lib/cwl/stgc060ccd3-ec61-479c-a569-50e015f55be7/dqc_reference/reference_markers.fasta -out OceanDNA-b46214/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:01:33,191] [INFO] Task succeeded: Blastn
[2023-03-19 00:01:33,192] [INFO] Selected 16 target genomes.
[2023-03-19 00:01:33,192] [INFO] Target genome list was writen to OceanDNA-b46214/target_genomes.txt
[2023-03-19 00:01:33,200] [INFO] Task started: fastANI
[2023-03-19 00:01:33,200] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ad1d700-44e9-46c2-ab78-e2d9b9fd9427/OceanDNA-b46214.fa --refList OceanDNA-b46214/target_genomes.txt --output OceanDNA-b46214/fastani_result.tsv --threads 1
[2023-03-19 00:01:44,375] [INFO] Task succeeded: fastANI
[2023-03-19 00:01:44,375] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc060ccd3-ec61-479c-a569-50e015f55be7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 00:01:44,375] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc060ccd3-ec61-479c-a569-50e015f55be7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 00:01:44,378] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 00:01:44,378] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 00:01:44,378] [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
Puniceicoccus vermicola	strain=JCM14086	GCA_014230055.1	388746	388746	type	True	77.8661	200	1106	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 00:01:44,378] [INFO] DFAST Taxonomy check result was written to OceanDNA-b46214/tc_result.tsv
[2023-03-19 00:01:44,378] [INFO] ===== Taxonomy check completed =====
[2023-03-19 00:01:44,378] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 00:01:44,379] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc060ccd3-ec61-479c-a569-50e015f55be7/dqc_reference/checkm_data
[2023-03-19 00:01:44,379] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 00:01:44,426] [INFO] Task started: CheckM
[2023-03-19 00:01:44,426] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b46214/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b46214/checkm_input OceanDNA-b46214/checkm_result
[2023-03-19 00:02:53,172] [INFO] Task succeeded: CheckM
[2023-03-19 00:02:53,173] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 00:02:53,175] [INFO] ===== Completeness check finished =====
[2023-03-19 00:02:53,176] [INFO] ===== Start GTDB Search =====
[2023-03-19 00:02:53,176] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b46214/markers.fasta)
[2023-03-19 00:02:53,176] [INFO] Task started: Blastn
[2023-03-19 00:02:53,176] [INFO] Running command: blastn -query OceanDNA-b46214/markers.fasta -db /var/lib/cwl/stgc060ccd3-ec61-479c-a569-50e015f55be7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b46214/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:02:54,077] [INFO] Task succeeded: Blastn
[2023-03-19 00:02:54,078] [INFO] Selected 18 target genomes.
[2023-03-19 00:02:54,078] [INFO] Target genome list was writen to OceanDNA-b46214/target_genomes_gtdb.txt
[2023-03-19 00:02:54,139] [INFO] Task started: fastANI
[2023-03-19 00:02:54,139] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ad1d700-44e9-46c2-ab78-e2d9b9fd9427/OceanDNA-b46214.fa --refList OceanDNA-b46214/target_genomes_gtdb.txt --output OceanDNA-b46214/fastani_result_gtdb.tsv --threads 1
[2023-03-19 00:03:05,306] [INFO] Task succeeded: fastANI
[2023-03-19 00:03:05,309] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 00:03:05,309] [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_002388665.1	s__Puniceicoccus sp002388665	99.9359	1066	1106	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Puniceicoccaceae;g__Puniceicoccus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014230055.1	s__Puniceicoccus vermicola	77.8661	200	1106	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Puniceicoccaceae;g__Puniceicoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 00:03:05,309] [INFO] GTDB search result was written to OceanDNA-b46214/result_gtdb.tsv
[2023-03-19 00:03:05,310] [INFO] ===== GTDB Search completed =====
[2023-03-19 00:03:05,310] [INFO] DFAST_QC result json was written to OceanDNA-b46214/dqc_result.json
[2023-03-19 00:03:05,310] [INFO] DFAST_QC completed!
[2023-03-19 00:03:05,310] [INFO] Total running time: 0h2m2s