[2023-03-17 06:30:51,177] [INFO] DFAST_QC pipeline started.
[2023-03-17 06:30:51,177] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 06:30:51,177] [INFO] DQC Reference Directory: /var/lib/cwl/stga3f288e3-fd8b-47bb-bc7f-64908b173f39/dqc_reference
[2023-03-17 06:30:52,296] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 06:30:52,296] [INFO] Task started: Prodigal
[2023-03-17 06:30:52,296] [INFO] Running command: cat /var/lib/cwl/stg0781d9eb-088a-49f2-8cda-3c69ba684f7b/OceanDNA-b37833.fa | prodigal -d OceanDNA-b37833/cds.fna -a OceanDNA-b37833/protein.faa -g 11 -q > /dev/null
[2023-03-17 06:31:08,620] [INFO] Task succeeded: Prodigal
[2023-03-17 06:31:08,620] [INFO] Task started: HMMsearch
[2023-03-17 06:31:08,620] [INFO] Running command: hmmsearch --tblout OceanDNA-b37833/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga3f288e3-fd8b-47bb-bc7f-64908b173f39/dqc_reference/reference_markers.hmm OceanDNA-b37833/protein.faa > /dev/null
[2023-03-17 06:31:08,830] [INFO] Task succeeded: HMMsearch
[2023-03-17 06:31:08,831] [INFO] Found 6/6 markers.
[2023-03-17 06:31:08,849] [INFO] Query marker FASTA was written to OceanDNA-b37833/markers.fasta
[2023-03-17 06:31:08,850] [INFO] Task started: Blastn
[2023-03-17 06:31:08,850] [INFO] Running command: blastn -query OceanDNA-b37833/markers.fasta -db /var/lib/cwl/stga3f288e3-fd8b-47bb-bc7f-64908b173f39/dqc_reference/reference_markers.fasta -out OceanDNA-b37833/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 06:31:09,457] [INFO] Task succeeded: Blastn
[2023-03-17 06:31:09,458] [INFO] Selected 28 target genomes.
[2023-03-17 06:31:09,459] [INFO] Target genome list was writen to OceanDNA-b37833/target_genomes.txt
[2023-03-17 06:31:09,472] [INFO] Task started: fastANI
[2023-03-17 06:31:09,473] [INFO] Running command: fastANI --query /var/lib/cwl/stg0781d9eb-088a-49f2-8cda-3c69ba684f7b/OceanDNA-b37833.fa --refList OceanDNA-b37833/target_genomes.txt --output OceanDNA-b37833/fastani_result.tsv --threads 1
[2023-03-17 06:31:26,503] [INFO] Task succeeded: fastANI
[2023-03-17 06:31:26,504] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga3f288e3-fd8b-47bb-bc7f-64908b173f39/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 06:31:26,504] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga3f288e3-fd8b-47bb-bc7f-64908b173f39/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 06:31:26,504] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 06:31:26,504] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 06:31:26,504] [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 06:31:26,504] [INFO] DFAST Taxonomy check result was written to OceanDNA-b37833/tc_result.tsv
[2023-03-17 06:31:26,504] [INFO] ===== Taxonomy check completed =====
[2023-03-17 06:31:26,505] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 06:31:26,505] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga3f288e3-fd8b-47bb-bc7f-64908b173f39/dqc_reference/checkm_data
[2023-03-17 06:31:26,507] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 06:31:26,512] [INFO] Task started: CheckM
[2023-03-17 06:31:26,512] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b37833/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b37833/checkm_input OceanDNA-b37833/checkm_result
[2023-03-17 06:32:10,403] [INFO] Task succeeded: CheckM
[2023-03-17 06:32:10,404] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 06:32:10,406] [INFO] ===== Completeness check finished =====
[2023-03-17 06:32:10,406] [INFO] ===== Start GTDB Search =====
[2023-03-17 06:32:10,407] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b37833/markers.fasta)
[2023-03-17 06:32:10,407] [INFO] Task started: Blastn
[2023-03-17 06:32:10,407] [INFO] Running command: blastn -query OceanDNA-b37833/markers.fasta -db /var/lib/cwl/stga3f288e3-fd8b-47bb-bc7f-64908b173f39/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b37833/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 06:32:11,379] [INFO] Task succeeded: Blastn
[2023-03-17 06:32:11,380] [INFO] Selected 21 target genomes.
[2023-03-17 06:32:11,380] [INFO] Target genome list was writen to OceanDNA-b37833/target_genomes_gtdb.txt
[2023-03-17 06:32:11,748] [INFO] Task started: fastANI
[2023-03-17 06:32:11,748] [INFO] Running command: fastANI --query /var/lib/cwl/stg0781d9eb-088a-49f2-8cda-3c69ba684f7b/OceanDNA-b37833.fa --refList OceanDNA-b37833/target_genomes_gtdb.txt --output OceanDNA-b37833/fastani_result_gtdb.tsv --threads 1
[2023-03-17 06:32:22,743] [INFO] Task succeeded: fastANI
[2023-03-17 06:32:22,749] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 06:32:22,749] [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_905182485.1	s__Luminiphilus sp905182485	98.9277	625	890	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018666055.1	s__Luminiphilus sp018666055	88.8752	339	890	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905478845.1	s__Luminiphilus sp905478845	86.0136	599	890	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002683335.1	s__Luminiphilus sp002683335	78.5539	76	890	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	98.43	98.43	0.60	0.60	2	-
GCA_016779445.1	s__Luminiphilus sp016779445	76.8228	66	890	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	98.89	98.12	0.82	0.77	3	-
GCA_002683395.1	s__Luminiphilus sp002683395	76.6414	85	890	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	98.62	98.62	0.87	0.87	2	-
GCA_016778045.1	s__Luminiphilus sp016778045	76.3062	72	890	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002721785.1	s__Luminiphilus sp002721785	76.1926	73	890	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	99.68	99.68	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2023-03-17 06:32:22,749] [INFO] GTDB search result was written to OceanDNA-b37833/result_gtdb.tsv
[2023-03-17 06:32:22,749] [INFO] ===== GTDB Search completed =====
[2023-03-17 06:32:22,750] [INFO] DFAST_QC result json was written to OceanDNA-b37833/dqc_result.json
[2023-03-17 06:32:22,750] [INFO] DFAST_QC completed!
[2023-03-17 06:32:22,750] [INFO] Total running time: 0h1m32s