[2023-03-17 09:59:00,773] [INFO] DFAST_QC pipeline started.
[2023-03-17 09:59:00,778] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 09:59:00,778] [INFO] DQC Reference Directory: /var/lib/cwl/stgd8fe42ac-5ed3-4937-89e3-4fa74cae9266/dqc_reference
[2023-03-17 09:59:02,026] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 09:59:02,027] [INFO] Task started: Prodigal
[2023-03-17 09:59:02,027] [INFO] Running command: cat /var/lib/cwl/stg60719207-2acb-4e58-857e-bf548c07d1bf/OceanDNA-b40198.fa | prodigal -d OceanDNA-b40198/cds.fna -a OceanDNA-b40198/protein.faa -g 11 -q > /dev/null
[2023-03-17 09:59:12,852] [INFO] Task succeeded: Prodigal
[2023-03-17 09:59:12,852] [INFO] Task started: HMMsearch
[2023-03-17 09:59:12,853] [INFO] Running command: hmmsearch --tblout OceanDNA-b40198/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd8fe42ac-5ed3-4937-89e3-4fa74cae9266/dqc_reference/reference_markers.hmm OceanDNA-b40198/protein.faa > /dev/null
[2023-03-17 09:59:13,040] [INFO] Task succeeded: HMMsearch
[2023-03-17 09:59:13,041] [INFO] Found 6/6 markers.
[2023-03-17 09:59:13,208] [INFO] Query marker FASTA was written to OceanDNA-b40198/markers.fasta
[2023-03-17 09:59:13,208] [INFO] Task started: Blastn
[2023-03-17 09:59:13,208] [INFO] Running command: blastn -query OceanDNA-b40198/markers.fasta -db /var/lib/cwl/stgd8fe42ac-5ed3-4937-89e3-4fa74cae9266/dqc_reference/reference_markers.fasta -out OceanDNA-b40198/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:59:13,773] [INFO] Task succeeded: Blastn
[2023-03-17 09:59:13,806] [INFO] Selected 23 target genomes.
[2023-03-17 09:59:13,807] [INFO] Target genome list was writen to OceanDNA-b40198/target_genomes.txt
[2023-03-17 09:59:13,967] [INFO] Task started: fastANI
[2023-03-17 09:59:13,967] [INFO] Running command: fastANI --query /var/lib/cwl/stg60719207-2acb-4e58-857e-bf548c07d1bf/OceanDNA-b40198.fa --refList OceanDNA-b40198/target_genomes.txt --output OceanDNA-b40198/fastani_result.tsv --threads 1
[2023-03-17 09:59:26,717] [INFO] Task succeeded: fastANI
[2023-03-17 09:59:26,718] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd8fe42ac-5ed3-4937-89e3-4fa74cae9266/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 09:59:26,718] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd8fe42ac-5ed3-4937-89e3-4fa74cae9266/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 09:59:26,718] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 09:59:26,718] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 09:59:26,718] [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
--------------------------------------------------------------------------------
[2023-03-17 09:59:26,727] [INFO] DFAST Taxonomy check result was written to OceanDNA-b40198/tc_result.tsv
[2023-03-17 09:59:26,743] [INFO] ===== Taxonomy check completed =====
[2023-03-17 09:59:26,743] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 09:59:26,743] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd8fe42ac-5ed3-4937-89e3-4fa74cae9266/dqc_reference/checkm_data
[2023-03-17 09:59:26,746] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 09:59:26,811] [INFO] Task started: CheckM
[2023-03-17 09:59:26,811] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b40198/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b40198/checkm_input OceanDNA-b40198/checkm_result
[2023-03-17 09:59:58,261] [INFO] Task succeeded: CheckM
[2023-03-17 09:59:58,261] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 09:59:58,415] [INFO] ===== Completeness check finished =====
[2023-03-17 09:59:58,415] [INFO] ===== Start GTDB Search =====
[2023-03-17 09:59:58,415] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b40198/markers.fasta)
[2023-03-17 09:59:58,417] [INFO] Task started: Blastn
[2023-03-17 09:59:58,417] [INFO] Running command: blastn -query OceanDNA-b40198/markers.fasta -db /var/lib/cwl/stgd8fe42ac-5ed3-4937-89e3-4fa74cae9266/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b40198/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:59:59,339] [INFO] Task succeeded: Blastn
[2023-03-17 09:59:59,366] [INFO] Selected 13 target genomes.
[2023-03-17 09:59:59,366] [INFO] Target genome list was writen to OceanDNA-b40198/target_genomes_gtdb.txt
[2023-03-17 09:59:59,508] [INFO] Task started: fastANI
[2023-03-17 09:59:59,508] [INFO] Running command: fastANI --query /var/lib/cwl/stg60719207-2acb-4e58-857e-bf548c07d1bf/OceanDNA-b40198.fa --refList OceanDNA-b40198/target_genomes_gtdb.txt --output OceanDNA-b40198/fastani_result_gtdb.tsv --threads 1
[2023-03-17 10:00:04,766] [INFO] Task succeeded: fastANI
[2023-03-17 10:00:04,770] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 10:00:04,770] [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_002591625.1	s__TMED48 sp002591625	99.2054	589	647	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__TMED48	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002701765.1	s__TMED48 sp002701765	93.3511	444	647	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__TMED48	95.0	97.58	97.58	0.65	0.65	2	-
GCA_902557735.1	s__TMED48 sp902557735	79.3204	253	647	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__TMED48	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002692165.1	s__TMED48 sp002692165	79.2575	238	647	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__TMED48	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2023-03-17 10:00:04,778] [INFO] GTDB search result was written to OceanDNA-b40198/result_gtdb.tsv
[2023-03-17 10:00:04,794] [INFO] ===== GTDB Search completed =====
[2023-03-17 10:00:04,804] [INFO] DFAST_QC result json was written to OceanDNA-b40198/dqc_result.json
[2023-03-17 10:00:04,804] [INFO] DFAST_QC completed!
[2023-03-17 10:00:04,805] [INFO] Total running time: 0h1m4s