[2023-03-18 20:13:32,794] [INFO] DFAST_QC pipeline started.
[2023-03-18 20:13:32,794] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 20:13:32,794] [INFO] DQC Reference Directory: /var/lib/cwl/stg90774366-b8a0-4bd3-915d-8c8c2b103d17/dqc_reference
[2023-03-18 20:13:34,556] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 20:13:34,556] [INFO] Task started: Prodigal
[2023-03-18 20:13:34,557] [INFO] Running command: cat /var/lib/cwl/stg55fdd801-d3da-4844-a17b-646e3c7047db/OceanDNA-b39196.fa | prodigal -d OceanDNA-b39196/cds.fna -a OceanDNA-b39196/protein.faa -g 11 -q > /dev/null
[2023-03-18 20:13:48,234] [INFO] Task succeeded: Prodigal
[2023-03-18 20:13:48,234] [INFO] Task started: HMMsearch
[2023-03-18 20:13:48,234] [INFO] Running command: hmmsearch --tblout OceanDNA-b39196/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg90774366-b8a0-4bd3-915d-8c8c2b103d17/dqc_reference/reference_markers.hmm OceanDNA-b39196/protein.faa > /dev/null
[2023-03-18 20:13:48,430] [INFO] Task succeeded: HMMsearch
[2023-03-18 20:13:48,430] [INFO] Found 6/6 markers.
[2023-03-18 20:13:48,445] [INFO] Query marker FASTA was written to OceanDNA-b39196/markers.fasta
[2023-03-18 20:13:48,445] [INFO] Task started: Blastn
[2023-03-18 20:13:48,445] [INFO] Running command: blastn -query OceanDNA-b39196/markers.fasta -db /var/lib/cwl/stg90774366-b8a0-4bd3-915d-8c8c2b103d17/dqc_reference/reference_markers.fasta -out OceanDNA-b39196/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:13:49,051] [INFO] Task succeeded: Blastn
[2023-03-18 20:13:49,052] [INFO] Selected 34 target genomes.
[2023-03-18 20:13:49,052] [INFO] Target genome list was writen to OceanDNA-b39196/target_genomes.txt
[2023-03-18 20:13:49,069] [INFO] Task started: fastANI
[2023-03-18 20:13:49,069] [INFO] Running command: fastANI --query /var/lib/cwl/stg55fdd801-d3da-4844-a17b-646e3c7047db/OceanDNA-b39196.fa --refList OceanDNA-b39196/target_genomes.txt --output OceanDNA-b39196/fastani_result.tsv --threads 1
[2023-03-18 20:14:10,976] [INFO] Task succeeded: fastANI
[2023-03-18 20:14:10,976] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg90774366-b8a0-4bd3-915d-8c8c2b103d17/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 20:14:10,976] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg90774366-b8a0-4bd3-915d-8c8c2b103d17/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 20:14:10,977] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 20:14:10,977] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 20:14:10,977] [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 20:14:10,977] [INFO] DFAST Taxonomy check result was written to OceanDNA-b39196/tc_result.tsv
[2023-03-18 20:14:10,977] [INFO] ===== Taxonomy check completed =====
[2023-03-18 20:14:10,977] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 20:14:10,977] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg90774366-b8a0-4bd3-915d-8c8c2b103d17/dqc_reference/checkm_data
[2023-03-18 20:14:10,980] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 20:14:10,983] [INFO] Task started: CheckM
[2023-03-18 20:14:10,983] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b39196/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b39196/checkm_input OceanDNA-b39196/checkm_result
[2023-03-18 20:14:48,226] [INFO] Task succeeded: CheckM
[2023-03-18 20:14:48,226] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 20:14:48,228] [INFO] ===== Completeness check finished =====
[2023-03-18 20:14:48,228] [INFO] ===== Start GTDB Search =====
[2023-03-18 20:14:48,228] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b39196/markers.fasta)
[2023-03-18 20:14:48,229] [INFO] Task started: Blastn
[2023-03-18 20:14:48,229] [INFO] Running command: blastn -query OceanDNA-b39196/markers.fasta -db /var/lib/cwl/stg90774366-b8a0-4bd3-915d-8c8c2b103d17/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b39196/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:14:49,238] [INFO] Task succeeded: Blastn
[2023-03-18 20:14:49,239] [INFO] Selected 30 target genomes.
[2023-03-18 20:14:49,239] [INFO] Target genome list was writen to OceanDNA-b39196/target_genomes_gtdb.txt
[2023-03-18 20:14:49,893] [INFO] Task started: fastANI
[2023-03-18 20:14:49,893] [INFO] Running command: fastANI --query /var/lib/cwl/stg55fdd801-d3da-4844-a17b-646e3c7047db/OceanDNA-b39196.fa --refList OceanDNA-b39196/target_genomes_gtdb.txt --output OceanDNA-b39196/fastani_result_gtdb.tsv --threads 1
[2023-03-18 20:15:03,300] [INFO] Task succeeded: fastANI
[2023-03-18 20:15:03,303] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 20:15:03,303] [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_000153445.1	s__HTCC2207 sp000153445	76.393	50	775	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	98.85	98.71	0.89	0.85	4	-
GCA_018664075.1	s__HTCC2207 sp018664075	75.8877	50	775	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.59	99.59	0.81	0.81	2	-
GCA_002334915.1	s__HTCC2207 sp002334915	75.8817	50	775	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.52	99.52	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2023-03-18 20:15:03,303] [INFO] GTDB search result was written to OceanDNA-b39196/result_gtdb.tsv
[2023-03-18 20:15:03,303] [INFO] ===== GTDB Search completed =====
[2023-03-18 20:15:03,304] [INFO] DFAST_QC result json was written to OceanDNA-b39196/dqc_result.json
[2023-03-18 20:15:03,304] [INFO] DFAST_QC completed!
[2023-03-18 20:15:03,304] [INFO] Total running time: 0h1m31s