[2023-03-15 03:25:37,024] [INFO] DFAST_QC pipeline started.
[2023-03-15 03:25:37,024] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 03:25:37,024] [INFO] DQC Reference Directory: /var/lib/cwl/stg72433136-159e-44b7-b449-b65fb34832fd/dqc_reference
[2023-03-15 03:25:38,140] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 03:25:38,140] [INFO] Task started: Prodigal
[2023-03-15 03:25:38,140] [INFO] Running command: cat /var/lib/cwl/stg20892c2b-4402-4640-9a5f-9df78a3ad5db/OceanDNA-b38900.fa | prodigal -d OceanDNA-b38900/cds.fna -a OceanDNA-b38900/protein.faa -g 11 -q > /dev/null
[2023-03-15 03:26:06,895] [INFO] Task succeeded: Prodigal
[2023-03-15 03:26:06,895] [INFO] Task started: HMMsearch
[2023-03-15 03:26:06,895] [INFO] Running command: hmmsearch --tblout OceanDNA-b38900/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg72433136-159e-44b7-b449-b65fb34832fd/dqc_reference/reference_markers.hmm OceanDNA-b38900/protein.faa > /dev/null
[2023-03-15 03:26:07,125] [INFO] Task succeeded: HMMsearch
[2023-03-15 03:26:07,125] [INFO] Found 6/6 markers.
[2023-03-15 03:26:07,155] [INFO] Query marker FASTA was written to OceanDNA-b38900/markers.fasta
[2023-03-15 03:26:07,156] [INFO] Task started: Blastn
[2023-03-15 03:26:07,156] [INFO] Running command: blastn -query OceanDNA-b38900/markers.fasta -db /var/lib/cwl/stg72433136-159e-44b7-b449-b65fb34832fd/dqc_reference/reference_markers.fasta -out OceanDNA-b38900/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:26:07,694] [INFO] Task succeeded: Blastn
[2023-03-15 03:26:07,695] [INFO] Selected 37 target genomes.
[2023-03-15 03:26:07,695] [INFO] Target genome list was writen to OceanDNA-b38900/target_genomes.txt
[2023-03-15 03:26:07,712] [INFO] Task started: fastANI
[2023-03-15 03:26:07,712] [INFO] Running command: fastANI --query /var/lib/cwl/stg20892c2b-4402-4640-9a5f-9df78a3ad5db/OceanDNA-b38900.fa --refList OceanDNA-b38900/target_genomes.txt --output OceanDNA-b38900/fastani_result.tsv --threads 1
[2023-03-15 03:26:30,720] [INFO] Task succeeded: fastANI
[2023-03-15 03:26:30,721] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg72433136-159e-44b7-b449-b65fb34832fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 03:26:30,721] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg72433136-159e-44b7-b449-b65fb34832fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 03:26:30,725] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 03:26:30,725] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 03:26:30,725] [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
Neptunomonas qingdaonensis	strain=CGMCC 1.10971	GCA_900113275.1	1045558	1045558	type	True	76.5002	50	1721	95	below_threshold
Neptunomonas antarctica	strain=S3-22	GCA_001305295.1	619304	619304	type	True	76.4045	62	1721	95	below_threshold
Neptunomonas antarctica	strain=DSM 22306	GCA_900156635.1	619304	619304	type	True	76.3709	61	1721	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 03:26:30,726] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38900/tc_result.tsv
[2023-03-15 03:26:30,726] [INFO] ===== Taxonomy check completed =====
[2023-03-15 03:26:30,726] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 03:26:30,726] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg72433136-159e-44b7-b449-b65fb34832fd/dqc_reference/checkm_data
[2023-03-15 03:26:30,727] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 03:26:30,733] [INFO] Task started: CheckM
[2023-03-15 03:26:30,733] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38900/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38900/checkm_input OceanDNA-b38900/checkm_result
[2023-03-15 03:27:40,550] [INFO] Task succeeded: CheckM
[2023-03-15 03:27:40,550] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.55%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 03:27:40,553] [INFO] ===== Completeness check finished =====
[2023-03-15 03:27:40,553] [INFO] ===== Start GTDB Search =====
[2023-03-15 03:27:40,553] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38900/markers.fasta)
[2023-03-15 03:27:40,555] [INFO] Task started: Blastn
[2023-03-15 03:27:40,555] [INFO] Running command: blastn -query OceanDNA-b38900/markers.fasta -db /var/lib/cwl/stg72433136-159e-44b7-b449-b65fb34832fd/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38900/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:27:41,331] [INFO] Task succeeded: Blastn
[2023-03-15 03:27:41,332] [INFO] Selected 17 target genomes.
[2023-03-15 03:27:41,332] [INFO] Target genome list was writen to OceanDNA-b38900/target_genomes_gtdb.txt
[2023-03-15 03:27:41,381] [INFO] Task started: fastANI
[2023-03-15 03:27:41,381] [INFO] Running command: fastANI --query /var/lib/cwl/stg20892c2b-4402-4640-9a5f-9df78a3ad5db/OceanDNA-b38900.fa --refList OceanDNA-b38900/target_genomes_gtdb.txt --output OceanDNA-b38900/fastani_result_gtdb.tsv --threads 1
[2023-03-15 03:27:54,185] [INFO] Task succeeded: fastANI
[2023-03-15 03:27:54,189] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 03:27:54,189] [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_013215505.1	s__Rs1 sp013215505	99.9722	1702	1721	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Rs1	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002163025.1	s__Rs1 sp002163025	83.5799	940	1721	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Rs1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000416315.1	s__Rs1 sp000416315	82.6715	937	1721	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Rs1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013215445.1	s__Rs1 sp013215445	78.3115	240	1721	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Rs1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013215375.1	s__Rs1 sp013215375	77.8818	232	1721	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Rs1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000416275.1	s__Rs1 sp000416275	77.6178	228	1721	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Rs1	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 03:27:54,190] [INFO] GTDB search result was written to OceanDNA-b38900/result_gtdb.tsv
[2023-03-15 03:27:54,190] [INFO] ===== GTDB Search completed =====
[2023-03-15 03:27:54,191] [INFO] DFAST_QC result json was written to OceanDNA-b38900/dqc_result.json
[2023-03-15 03:27:54,191] [INFO] DFAST_QC completed!
[2023-03-15 03:27:54,191] [INFO] Total running time: 0h2m17s