[2023-03-14 12:28:23,286] [INFO] DFAST_QC pipeline started.
[2023-03-14 12:28:23,286] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 12:28:23,286] [INFO] DQC Reference Directory: /var/lib/cwl/stg8aca440f-a4f5-463a-82ea-800f770cdf16/dqc_reference
[2023-03-14 12:28:25,336] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 12:28:25,337] [INFO] Task started: Prodigal
[2023-03-14 12:28:25,337] [INFO] Running command: cat /var/lib/cwl/stga156df69-9f16-49a9-86e4-edbee1e4bf71/OceanDNA-b4102.fa | prodigal -d OceanDNA-b4102/cds.fna -a OceanDNA-b4102/protein.faa -g 11 -q > /dev/null
[2023-03-14 12:28:53,993] [INFO] Task succeeded: Prodigal
[2023-03-14 12:28:53,993] [INFO] Task started: HMMsearch
[2023-03-14 12:28:53,993] [INFO] Running command: hmmsearch --tblout OceanDNA-b4102/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8aca440f-a4f5-463a-82ea-800f770cdf16/dqc_reference/reference_markers.hmm OceanDNA-b4102/protein.faa > /dev/null
[2023-03-14 12:28:54,219] [INFO] Task succeeded: HMMsearch
[2023-03-14 12:28:54,219] [WARNING] Found 5/6 markers. [/var/lib/cwl/stga156df69-9f16-49a9-86e4-edbee1e4bf71/OceanDNA-b4102.fa]
[2023-03-14 12:28:54,251] [INFO] Query marker FASTA was written to OceanDNA-b4102/markers.fasta
[2023-03-14 12:28:54,253] [INFO] Task started: Blastn
[2023-03-14 12:28:54,253] [INFO] Running command: blastn -query OceanDNA-b4102/markers.fasta -db /var/lib/cwl/stg8aca440f-a4f5-463a-82ea-800f770cdf16/dqc_reference/reference_markers.fasta -out OceanDNA-b4102/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:28:54,783] [INFO] Task succeeded: Blastn
[2023-03-14 12:28:54,783] [INFO] Selected 20 target genomes.
[2023-03-14 12:28:54,784] [INFO] Target genome list was writen to OceanDNA-b4102/target_genomes.txt
[2023-03-14 12:28:54,798] [INFO] Task started: fastANI
[2023-03-14 12:28:54,798] [INFO] Running command: fastANI --query /var/lib/cwl/stga156df69-9f16-49a9-86e4-edbee1e4bf71/OceanDNA-b4102.fa --refList OceanDNA-b4102/target_genomes.txt --output OceanDNA-b4102/fastani_result.tsv --threads 1
[2023-03-14 12:29:09,101] [INFO] Task succeeded: fastANI
[2023-03-14 12:29:09,101] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8aca440f-a4f5-463a-82ea-800f770cdf16/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 12:29:09,101] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8aca440f-a4f5-463a-82ea-800f770cdf16/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 12:29:09,108] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 12:29:09,108] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 12:29:09,108] [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
Fulvivirga sediminis	strain=2943	GCA_016757215.1	2803949	2803949	type	True	78.0702	336	1384	95	below_threshold
Fulvivirga kasyanovii	strain=JCM 16186	GCA_009711405.1	396812	396812	type	True	76.3166	74	1384	95	below_threshold
Fulvivirga marina	strain=29W222	GCA_016775155.1	2494733	2494733	type	True	76.2825	104	1384	95	below_threshold
Fulvivirga aurantia	strain=RKSG066	GCA_009711475.1	2529383	2529383	type	True	76.1899	58	1384	95	below_threshold
Fulvivirga imtechensis	strain=AK7	GCA_000331535.1	881893	881893	type	True	76.189	88	1384	95	below_threshold
Fulvivirga lutimaris	strain=KCTC 42720	GCA_009711525.1	1819566	1819566	type	True	75.9545	61	1384	95	below_threshold
Fulvivirga lutea	strain=S481	GCA_017068455.1	2810512	2810512	type	True	75.4636	58	1384	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 12:29:09,108] [INFO] DFAST Taxonomy check result was written to OceanDNA-b4102/tc_result.tsv
[2023-03-14 12:29:09,108] [INFO] ===== Taxonomy check completed =====
[2023-03-14 12:29:09,109] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 12:29:09,109] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8aca440f-a4f5-463a-82ea-800f770cdf16/dqc_reference/checkm_data
[2023-03-14 12:29:09,109] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 12:29:09,280] [INFO] Task started: CheckM
[2023-03-14 12:29:09,280] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b4102/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b4102/checkm_input OceanDNA-b4102/checkm_result
[2023-03-14 12:30:19,647] [INFO] Task succeeded: CheckM
[2023-03-14 12:30:19,648] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 56.63%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 12:30:19,652] [INFO] ===== Completeness check finished =====
[2023-03-14 12:30:19,652] [INFO] ===== Start GTDB Search =====
[2023-03-14 12:30:19,652] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b4102/markers.fasta)
[2023-03-14 12:30:19,654] [INFO] Task started: Blastn
[2023-03-14 12:30:19,654] [INFO] Running command: blastn -query OceanDNA-b4102/markers.fasta -db /var/lib/cwl/stg8aca440f-a4f5-463a-82ea-800f770cdf16/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b4102/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:30:20,382] [INFO] Task succeeded: Blastn
[2023-03-14 12:30:20,384] [INFO] Selected 19 target genomes.
[2023-03-14 12:30:20,384] [INFO] Target genome list was writen to OceanDNA-b4102/target_genomes_gtdb.txt
[2023-03-14 12:30:20,421] [INFO] Task started: fastANI
[2023-03-14 12:30:20,421] [INFO] Running command: fastANI --query /var/lib/cwl/stga156df69-9f16-49a9-86e4-edbee1e4bf71/OceanDNA-b4102.fa --refList OceanDNA-b4102/target_genomes_gtdb.txt --output OceanDNA-b4102/fastani_result_gtdb.tsv --threads 1
[2023-03-14 12:30:34,291] [INFO] Task succeeded: fastANI
[2023-03-14 12:30:34,296] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 12:30:34,296] [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
GCF_016757215.1	s__Fulvivirga sp016757215	78.0708	336	1384	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fulvivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009711405.1	s__Fulvivirga kasyanovii	76.3012	76	1384	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fulvivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016775155.1	s__Fulvivirga sp016775155	76.2652	105	1384	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fulvivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000331535.1	s__Fulvivirga imtechensis	76.189	88	1384	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fulvivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009711525.1	s__Fulvivirga lutimaris	75.9545	61	1384	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fulvivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017068455.1	s__Fulvivirga sp017068455	75.4636	58	1384	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fulvivirga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 12:30:34,296] [INFO] GTDB search result was written to OceanDNA-b4102/result_gtdb.tsv
[2023-03-14 12:30:34,296] [INFO] ===== GTDB Search completed =====
[2023-03-14 12:30:34,299] [INFO] DFAST_QC result json was written to OceanDNA-b4102/dqc_result.json
[2023-03-14 12:30:34,299] [INFO] DFAST_QC completed!
[2023-03-14 12:30:34,299] [INFO] Total running time: 0h2m11s