[2023-03-14 12:29:45,284] [INFO] DFAST_QC pipeline started.
[2023-03-14 12:29:45,284] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 12:29:45,284] [INFO] DQC Reference Directory: /var/lib/cwl/stg9fabe259-28c6-434a-9ce0-aa69001b07cf/dqc_reference
[2023-03-14 12:29:46,366] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 12:29:46,367] [INFO] Task started: Prodigal
[2023-03-14 12:29:46,368] [INFO] Running command: cat /var/lib/cwl/stge382dbe4-2913-4865-ba47-1ab4079fe677/OceanDNA-b38893.fa | prodigal -d OceanDNA-b38893/cds.fna -a OceanDNA-b38893/protein.faa -g 11 -q > /dev/null
[2023-03-14 12:30:11,992] [INFO] Task succeeded: Prodigal
[2023-03-14 12:30:11,993] [INFO] Task started: HMMsearch
[2023-03-14 12:30:11,993] [INFO] Running command: hmmsearch --tblout OceanDNA-b38893/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9fabe259-28c6-434a-9ce0-aa69001b07cf/dqc_reference/reference_markers.hmm OceanDNA-b38893/protein.faa > /dev/null
[2023-03-14 12:30:12,216] [INFO] Task succeeded: HMMsearch
[2023-03-14 12:30:12,216] [INFO] Found 6/6 markers.
[2023-03-14 12:30:12,257] [INFO] Query marker FASTA was written to OceanDNA-b38893/markers.fasta
[2023-03-14 12:30:12,258] [INFO] Task started: Blastn
[2023-03-14 12:30:12,258] [INFO] Running command: blastn -query OceanDNA-b38893/markers.fasta -db /var/lib/cwl/stg9fabe259-28c6-434a-9ce0-aa69001b07cf/dqc_reference/reference_markers.fasta -out OceanDNA-b38893/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:30:12,808] [INFO] Task succeeded: Blastn
[2023-03-14 12:30:12,830] [INFO] Selected 36 target genomes.
[2023-03-14 12:30:12,830] [INFO] Target genome list was writen to OceanDNA-b38893/target_genomes.txt
[2023-03-14 12:30:12,845] [INFO] Task started: fastANI
[2023-03-14 12:30:12,845] [INFO] Running command: fastANI --query /var/lib/cwl/stge382dbe4-2913-4865-ba47-1ab4079fe677/OceanDNA-b38893.fa --refList OceanDNA-b38893/target_genomes.txt --output OceanDNA-b38893/fastani_result.tsv --threads 1
[2023-03-14 12:30:32,560] [INFO] Task succeeded: fastANI
[2023-03-14 12:30:32,561] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9fabe259-28c6-434a-9ce0-aa69001b07cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 12:30:32,561] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9fabe259-28c6-434a-9ce0-aa69001b07cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 12:30:32,565] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 12:30:32,565] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 12:30:32,566] [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
Neptunomonas antarctica	strain=DSM 22306	GCA_900156635.1	619304	619304	type	True	76.7817	53	1542	95	below_threshold
Neptunomonas japonica	strain=DSM 18939	GCA_000422765.1	417574	417574	type	True	76.6671	56	1542	95	below_threshold
Neptunomonas concharum	strain=JCM 17730	GCA_006148955.1	1031538	1031538	type	True	76.6062	55	1542	95	below_threshold
Neptunomonas concharum	strain=JCM17730	GCA_008630635.1	1031538	1031538	type	True	76.481	54	1542	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 12:30:32,568] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38893/tc_result.tsv
[2023-03-14 12:30:32,568] [INFO] ===== Taxonomy check completed =====
[2023-03-14 12:30:32,568] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 12:30:32,568] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9fabe259-28c6-434a-9ce0-aa69001b07cf/dqc_reference/checkm_data
[2023-03-14 12:30:32,569] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 12:30:32,578] [INFO] Task started: CheckM
[2023-03-14 12:30:32,579] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38893/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38893/checkm_input OceanDNA-b38893/checkm_result
[2023-03-14 12:31:35,521] [INFO] Task succeeded: CheckM
[2023-03-14 12:31:35,521] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 12:31:35,526] [INFO] ===== Completeness check finished =====
[2023-03-14 12:31:35,526] [INFO] ===== Start GTDB Search =====
[2023-03-14 12:31:35,527] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38893/markers.fasta)
[2023-03-14 12:31:35,528] [INFO] Task started: Blastn
[2023-03-14 12:31:35,528] [INFO] Running command: blastn -query OceanDNA-b38893/markers.fasta -db /var/lib/cwl/stg9fabe259-28c6-434a-9ce0-aa69001b07cf/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38893/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:31:36,264] [INFO] Task succeeded: Blastn
[2023-03-14 12:31:36,265] [INFO] Selected 21 target genomes.
[2023-03-14 12:31:36,265] [INFO] Target genome list was writen to OceanDNA-b38893/target_genomes_gtdb.txt
[2023-03-14 12:31:36,289] [INFO] Task started: fastANI
[2023-03-14 12:31:36,290] [INFO] Running command: fastANI --query /var/lib/cwl/stge382dbe4-2913-4865-ba47-1ab4079fe677/OceanDNA-b38893.fa --refList OceanDNA-b38893/target_genomes_gtdb.txt --output OceanDNA-b38893/fastani_result_gtdb.tsv --threads 1
[2023-03-14 12:31:50,292] [INFO] Task succeeded: fastANI
[2023-03-14 12:31:50,299] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 12:31:50,299] [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_013215375.1	s__Rs1 sp013215375	99.9183	1450	1542	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_013215445.1	s__Rs1 sp013215445	79.4802	514	1542	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	78.5168	250	1542	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Rs1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002163025.1	s__Rs1 sp002163025	78.3	187	1542	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Rs1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013215505.1	s__Rs1 sp013215505	78.2478	249	1542	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	77.4542	190	1542	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Rs1	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008630635.1	s__Neptunomonas concharum	76.5171	54	1542	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Neptunomonas	95.0	100.00	100.00	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2023-03-14 12:31:50,577] [INFO] GTDB search result was written to OceanDNA-b38893/result_gtdb.tsv
[2023-03-14 12:31:50,578] [INFO] ===== GTDB Search completed =====
[2023-03-14 12:31:50,580] [INFO] DFAST_QC result json was written to OceanDNA-b38893/dqc_result.json
[2023-03-14 12:31:50,580] [INFO] DFAST_QC completed!
[2023-03-14 12:31:50,580] [INFO] Total running time: 0h2m5s