[2023-03-17 23:54:11,282] [INFO] DFAST_QC pipeline started.
[2023-03-17 23:54:11,282] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 23:54:11,282] [INFO] DQC Reference Directory: /var/lib/cwl/stg70fc35f5-2fbd-4d38-aa03-1533021efa9f/dqc_reference
[2023-03-17 23:54:13,854] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 23:54:13,855] [INFO] Task started: Prodigal
[2023-03-17 23:54:13,855] [INFO] Running command: cat /var/lib/cwl/stgbee6cfa5-5bf6-46cf-b9fb-edde6af71273/OceanDNA-b31513.fa | prodigal -d OceanDNA-b31513/cds.fna -a OceanDNA-b31513/protein.faa -g 11 -q > /dev/null
[2023-03-17 23:54:24,588] [INFO] Task succeeded: Prodigal
[2023-03-17 23:54:24,588] [INFO] Task started: HMMsearch
[2023-03-17 23:54:24,588] [INFO] Running command: hmmsearch --tblout OceanDNA-b31513/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg70fc35f5-2fbd-4d38-aa03-1533021efa9f/dqc_reference/reference_markers.hmm OceanDNA-b31513/protein.faa > /dev/null
[2023-03-17 23:54:24,765] [INFO] Task succeeded: HMMsearch
[2023-03-17 23:54:24,766] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgbee6cfa5-5bf6-46cf-b9fb-edde6af71273/OceanDNA-b31513.fa]
[2023-03-17 23:54:24,785] [INFO] Query marker FASTA was written to OceanDNA-b31513/markers.fasta
[2023-03-17 23:54:24,785] [INFO] Task started: Blastn
[2023-03-17 23:54:24,785] [INFO] Running command: blastn -query OceanDNA-b31513/markers.fasta -db /var/lib/cwl/stg70fc35f5-2fbd-4d38-aa03-1533021efa9f/dqc_reference/reference_markers.fasta -out OceanDNA-b31513/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:54:25,333] [INFO] Task succeeded: Blastn
[2023-03-17 23:54:25,335] [INFO] Selected 19 target genomes.
[2023-03-17 23:54:25,336] [INFO] Target genome list was writen to OceanDNA-b31513/target_genomes.txt
[2023-03-17 23:54:25,347] [INFO] Task started: fastANI
[2023-03-17 23:54:25,347] [INFO] Running command: fastANI --query /var/lib/cwl/stgbee6cfa5-5bf6-46cf-b9fb-edde6af71273/OceanDNA-b31513.fa --refList OceanDNA-b31513/target_genomes.txt --output OceanDNA-b31513/fastani_result.tsv --threads 1
[2023-03-17 23:54:35,529] [INFO] Task succeeded: fastANI
[2023-03-17 23:54:35,530] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg70fc35f5-2fbd-4d38-aa03-1533021efa9f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 23:54:35,530] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg70fc35f5-2fbd-4d38-aa03-1533021efa9f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 23:54:35,533] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 23:54:35,534] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 23:54:35,534] [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
Pseudemcibacter aquimaris	strain=Y4	GCA_020748165.1	2857064	2857064	type	True	76.8597	109	629	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 23:54:35,535] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31513/tc_result.tsv
[2023-03-17 23:54:35,535] [INFO] ===== Taxonomy check completed =====
[2023-03-17 23:54:35,536] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 23:54:35,536] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg70fc35f5-2fbd-4d38-aa03-1533021efa9f/dqc_reference/checkm_data
[2023-03-17 23:54:35,536] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 23:54:35,543] [INFO] Task started: CheckM
[2023-03-17 23:54:35,543] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31513/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31513/checkm_input OceanDNA-b31513/checkm_result
[2023-03-17 23:55:06,352] [INFO] Task succeeded: CheckM
[2023-03-17 23:55:06,353] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 1.50%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-17 23:55:06,360] [INFO] ===== Completeness check finished =====
[2023-03-17 23:55:06,360] [INFO] ===== Start GTDB Search =====
[2023-03-17 23:55:06,361] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31513/markers.fasta)
[2023-03-17 23:55:06,362] [INFO] Task started: Blastn
[2023-03-17 23:55:06,362] [INFO] Running command: blastn -query OceanDNA-b31513/markers.fasta -db /var/lib/cwl/stg70fc35f5-2fbd-4d38-aa03-1533021efa9f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31513/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:55:07,305] [INFO] Task succeeded: Blastn
[2023-03-17 23:55:07,306] [INFO] Selected 18 target genomes.
[2023-03-17 23:55:07,306] [INFO] Target genome list was writen to OceanDNA-b31513/target_genomes_gtdb.txt
[2023-03-17 23:55:07,325] [INFO] Task started: fastANI
[2023-03-17 23:55:07,325] [INFO] Running command: fastANI --query /var/lib/cwl/stgbee6cfa5-5bf6-46cf-b9fb-edde6af71273/OceanDNA-b31513.fa --refList OceanDNA-b31513/target_genomes_gtdb.txt --output OceanDNA-b31513/fastani_result_gtdb.tsv --threads 1
[2023-03-17 23:55:14,357] [INFO] Task succeeded: fastANI
[2023-03-17 23:55:14,360] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 23:55:14,360] [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_018660225.1	s__UBA4441 sp018660225	77.215	169	629	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Emcibacteraceae;g__UBA4441	95.0	99.68	99.64	0.89	0.88	3	-
GCA_018699075.1	s__UBA4441 sp018699075	77.2073	141	629	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Emcibacteraceae;g__UBA4441	95.0	99.25	99.25	0.75	0.75	2	-
GCA_016763335.1	s__UBA4441 sp016763335	77.0023	146	629	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Emcibacteraceae;g__UBA4441	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002390425.1	s__UBA4441 sp002390425	76.7262	97	629	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Emcibacteraceae;g__UBA4441	95.0	99.08	99.08	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2023-03-17 23:55:14,360] [INFO] GTDB search result was written to OceanDNA-b31513/result_gtdb.tsv
[2023-03-17 23:55:14,361] [INFO] ===== GTDB Search completed =====
[2023-03-17 23:55:14,361] [INFO] DFAST_QC result json was written to OceanDNA-b31513/dqc_result.json
[2023-03-17 23:55:14,361] [INFO] DFAST_QC completed!
[2023-03-17 23:55:14,361] [INFO] Total running time: 0h1m3s