[2023-03-18 22:14:42,684] [INFO] DFAST_QC pipeline started.
[2023-03-18 22:14:42,684] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 22:14:42,684] [INFO] DQC Reference Directory: /var/lib/cwl/stg8de021f4-a2db-4498-bf60-3f78f11bc880/dqc_reference
[2023-03-18 22:14:43,782] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 22:14:43,783] [INFO] Task started: Prodigal
[2023-03-18 22:14:43,783] [INFO] Running command: cat /var/lib/cwl/stg0ddbb589-3352-48af-94e7-9a2b4bb638f3/OceanDNA-b26917.fa | prodigal -d OceanDNA-b26917/cds.fna -a OceanDNA-b26917/protein.faa -g 11 -q > /dev/null
[2023-03-18 22:14:53,883] [INFO] Task succeeded: Prodigal
[2023-03-18 22:14:53,883] [INFO] Task started: HMMsearch
[2023-03-18 22:14:53,883] [INFO] Running command: hmmsearch --tblout OceanDNA-b26917/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8de021f4-a2db-4498-bf60-3f78f11bc880/dqc_reference/reference_markers.hmm OceanDNA-b26917/protein.faa > /dev/null
[2023-03-18 22:14:54,039] [INFO] Task succeeded: HMMsearch
[2023-03-18 22:14:54,040] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg0ddbb589-3352-48af-94e7-9a2b4bb638f3/OceanDNA-b26917.fa]
[2023-03-18 22:14:54,062] [INFO] Query marker FASTA was written to OceanDNA-b26917/markers.fasta
[2023-03-18 22:14:54,062] [INFO] Task started: Blastn
[2023-03-18 22:14:54,062] [INFO] Running command: blastn -query OceanDNA-b26917/markers.fasta -db /var/lib/cwl/stg8de021f4-a2db-4498-bf60-3f78f11bc880/dqc_reference/reference_markers.fasta -out OceanDNA-b26917/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:14:54,537] [INFO] Task succeeded: Blastn
[2023-03-18 22:14:54,539] [INFO] Selected 17 target genomes.
[2023-03-18 22:14:54,539] [INFO] Target genome list was writen to OceanDNA-b26917/target_genomes.txt
[2023-03-18 22:14:54,550] [INFO] Task started: fastANI
[2023-03-18 22:14:54,551] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ddbb589-3352-48af-94e7-9a2b4bb638f3/OceanDNA-b26917.fa --refList OceanDNA-b26917/target_genomes.txt --output OceanDNA-b26917/fastani_result.tsv --threads 1
[2023-03-18 22:15:07,194] [INFO] Task succeeded: fastANI
[2023-03-18 22:15:07,194] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8de021f4-a2db-4498-bf60-3f78f11bc880/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 22:15:07,194] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8de021f4-a2db-4498-bf60-3f78f11bc880/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 22:15:07,195] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 22:15:07,195] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 22:15:07,195] [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
--------------------------------------------------------------------------------
[2023-03-18 22:15:07,196] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26917/tc_result.tsv
[2023-03-18 22:15:07,196] [INFO] ===== Taxonomy check completed =====
[2023-03-18 22:15:07,196] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 22:15:07,196] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8de021f4-a2db-4498-bf60-3f78f11bc880/dqc_reference/checkm_data
[2023-03-18 22:15:07,199] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 22:15:07,351] [INFO] Task started: CheckM
[2023-03-18 22:15:07,352] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26917/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26917/checkm_input OceanDNA-b26917/checkm_result
[2023-03-18 22:15:37,846] [INFO] Task succeeded: CheckM
[2023-03-18 22:15:37,846] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 41.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 22:15:37,896] [INFO] ===== Completeness check finished =====
[2023-03-18 22:15:37,896] [INFO] ===== Start GTDB Search =====
[2023-03-18 22:15:37,896] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26917/markers.fasta)
[2023-03-18 22:15:37,898] [INFO] Task started: Blastn
[2023-03-18 22:15:37,898] [INFO] Running command: blastn -query OceanDNA-b26917/markers.fasta -db /var/lib/cwl/stg8de021f4-a2db-4498-bf60-3f78f11bc880/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26917/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:15:38,429] [INFO] Task succeeded: Blastn
[2023-03-18 22:15:38,445] [INFO] Selected 17 target genomes.
[2023-03-18 22:15:38,445] [INFO] Target genome list was writen to OceanDNA-b26917/target_genomes_gtdb.txt
[2023-03-18 22:15:38,464] [INFO] Task started: fastANI
[2023-03-18 22:15:38,464] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ddbb589-3352-48af-94e7-9a2b4bb638f3/OceanDNA-b26917.fa --refList OceanDNA-b26917/target_genomes_gtdb.txt --output OceanDNA-b26917/fastani_result_gtdb.tsv --threads 1
[2023-03-18 22:15:49,597] [INFO] Task succeeded: fastANI
[2023-03-18 22:15:49,600] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 22:15:49,600] [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_013214695.1	s__R2A130 sp013214695	77.6377	119	414	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__R2A130	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011087605.1	s__R2A130 sp011087605	77.0963	106	414	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__R2A130	95.0	99.98	99.97	0.98	0.98	3	-
GCA_014238155.1	s__R2A130 sp014238155	76.9701	120	414	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__R2A130	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 22:15:49,607] [INFO] GTDB search result was written to OceanDNA-b26917/result_gtdb.tsv
[2023-03-18 22:15:49,613] [INFO] ===== GTDB Search completed =====
[2023-03-18 22:15:49,618] [INFO] DFAST_QC result json was written to OceanDNA-b26917/dqc_result.json
[2023-03-18 22:15:49,618] [INFO] DFAST_QC completed!
[2023-03-18 22:15:49,618] [INFO] Total running time: 0h1m7s