[2023-03-16 13:29:11,829] [INFO] DFAST_QC pipeline started.
[2023-03-16 13:29:11,830] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 13:29:11,830] [INFO] DQC Reference Directory: /var/lib/cwl/stg7f8d3ed2-0280-4c11-bdf7-955778812921/dqc_reference
[2023-03-16 13:29:13,486] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 13:29:13,486] [INFO] Task started: Prodigal
[2023-03-16 13:29:13,486] [INFO] Running command: cat /var/lib/cwl/stg16f285ef-1938-4ada-997a-af2c3519c02d/OceanDNA-b40027.fa | prodigal -d OceanDNA-b40027/cds.fna -a OceanDNA-b40027/protein.faa -g 11 -q > /dev/null
[2023-03-16 13:29:27,788] [INFO] Task succeeded: Prodigal
[2023-03-16 13:29:27,788] [INFO] Task started: HMMsearch
[2023-03-16 13:29:27,788] [INFO] Running command: hmmsearch --tblout OceanDNA-b40027/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7f8d3ed2-0280-4c11-bdf7-955778812921/dqc_reference/reference_markers.hmm OceanDNA-b40027/protein.faa > /dev/null
[2023-03-16 13:29:27,960] [INFO] Task succeeded: HMMsearch
[2023-03-16 13:29:27,961] [INFO] Found 6/6 markers.
[2023-03-16 13:29:27,975] [INFO] Query marker FASTA was written to OceanDNA-b40027/markers.fasta
[2023-03-16 13:29:27,975] [INFO] Task started: Blastn
[2023-03-16 13:29:27,975] [INFO] Running command: blastn -query OceanDNA-b40027/markers.fasta -db /var/lib/cwl/stg7f8d3ed2-0280-4c11-bdf7-955778812921/dqc_reference/reference_markers.fasta -out OceanDNA-b40027/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 13:29:28,570] [INFO] Task succeeded: Blastn
[2023-03-16 13:29:28,571] [INFO] Selected 35 target genomes.
[2023-03-16 13:29:28,571] [INFO] Target genome list was writen to OceanDNA-b40027/target_genomes.txt
[2023-03-16 13:29:28,593] [INFO] Task started: fastANI
[2023-03-16 13:29:28,593] [INFO] Running command: fastANI --query /var/lib/cwl/stg16f285ef-1938-4ada-997a-af2c3519c02d/OceanDNA-b40027.fa --refList OceanDNA-b40027/target_genomes.txt --output OceanDNA-b40027/fastani_result.tsv --threads 1
[2023-03-16 13:29:48,563] [INFO] Task succeeded: fastANI
[2023-03-16 13:29:48,563] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7f8d3ed2-0280-4c11-bdf7-955778812921/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 13:29:48,563] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7f8d3ed2-0280-4c11-bdf7-955778812921/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 13:29:48,566] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 13:29:48,566] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 13:29:48,566] [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
Porticoccus hydrocarbonoclasticus	strain=MCTG13d	GCA_000744735.1	1073414	1073414	type	True	76.6111	79	830	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 13:29:48,566] [INFO] DFAST Taxonomy check result was written to OceanDNA-b40027/tc_result.tsv
[2023-03-16 13:29:48,566] [INFO] ===== Taxonomy check completed =====
[2023-03-16 13:29:48,566] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 13:29:48,567] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7f8d3ed2-0280-4c11-bdf7-955778812921/dqc_reference/checkm_data
[2023-03-16 13:29:48,567] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 13:29:48,571] [INFO] Task started: CheckM
[2023-03-16 13:29:48,571] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b40027/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b40027/checkm_input OceanDNA-b40027/checkm_result
[2023-03-16 13:30:39,201] [INFO] Task succeeded: CheckM
[2023-03-16 13:30:39,201] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 13:30:39,203] [INFO] ===== Completeness check finished =====
[2023-03-16 13:30:39,204] [INFO] ===== Start GTDB Search =====
[2023-03-16 13:30:39,204] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b40027/markers.fasta)
[2023-03-16 13:30:39,205] [INFO] Task started: Blastn
[2023-03-16 13:30:39,205] [INFO] Running command: blastn -query OceanDNA-b40027/markers.fasta -db /var/lib/cwl/stg7f8d3ed2-0280-4c11-bdf7-955778812921/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b40027/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 13:30:40,202] [INFO] Task succeeded: Blastn
[2023-03-16 13:30:40,203] [INFO] Selected 25 target genomes.
[2023-03-16 13:30:40,203] [INFO] Target genome list was writen to OceanDNA-b40027/target_genomes_gtdb.txt
[2023-03-16 13:30:41,100] [INFO] Task started: fastANI
[2023-03-16 13:30:41,100] [INFO] Running command: fastANI --query /var/lib/cwl/stg16f285ef-1938-4ada-997a-af2c3519c02d/OceanDNA-b40027.fa --refList OceanDNA-b40027/target_genomes_gtdb.txt --output OceanDNA-b40027/fastani_result_gtdb.tsv --threads 1
[2023-03-16 13:30:58,919] [INFO] Task succeeded: fastANI
[2023-03-16 13:30:58,923] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 13:30:58,923] [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_002746985.1	s__Porticoccus sp002746985	78.9949	405	830	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__Porticoccus	95.0	97.07	97.07	0.91	0.91	2	-
GCA_018066715.1	s__Porticoccus sp018066715	78.7255	213	830	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__Porticoccus	95.0	99.88	99.88	0.93	0.93	2	-
GCA_002390285.1	s__Porticoccus sp002390285	78.5621	212	830	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__Porticoccus	95.0	99.85	99.48	0.95	0.89	6	-
GCA_011049795.1	s__Porticoccus sp011049795	78.151	160	830	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__Porticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002707685.1	s__Porticoccus sp002707685	77.0593	71	830	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__Porticoccus	95.0	99.58	99.58	0.96	0.96	2	-
GCA_002341315.1	s__Porticoccus sp002341315	76.6502	69	830	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__Porticoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 13:30:58,924] [INFO] GTDB search result was written to OceanDNA-b40027/result_gtdb.tsv
[2023-03-16 13:30:58,924] [INFO] ===== GTDB Search completed =====
[2023-03-16 13:30:58,924] [INFO] DFAST_QC result json was written to OceanDNA-b40027/dqc_result.json
[2023-03-16 13:30:58,925] [INFO] DFAST_QC completed!
[2023-03-16 13:30:58,925] [INFO] Total running time: 0h1m47s