[2023-03-16 10:20:34,823] [INFO] DFAST_QC pipeline started.
[2023-03-16 10:20:34,823] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 10:20:34,823] [INFO] DQC Reference Directory: /var/lib/cwl/stgc6d4858d-bd27-402a-b6a5-1a4b0f05e642/dqc_reference
[2023-03-16 10:20:36,083] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 10:20:36,083] [INFO] Task started: Prodigal
[2023-03-16 10:20:36,083] [INFO] Running command: cat /var/lib/cwl/stgfb2f7c3d-23ce-4699-8325-b4f80ae0077c/OceanDNA-b36177.fa | prodigal -d OceanDNA-b36177/cds.fna -a OceanDNA-b36177/protein.faa -g 11 -q > /dev/null
[2023-03-16 10:20:42,068] [INFO] Task succeeded: Prodigal
[2023-03-16 10:20:42,068] [INFO] Task started: HMMsearch
[2023-03-16 10:20:42,068] [INFO] Running command: hmmsearch --tblout OceanDNA-b36177/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc6d4858d-bd27-402a-b6a5-1a4b0f05e642/dqc_reference/reference_markers.hmm OceanDNA-b36177/protein.faa > /dev/null
[2023-03-16 10:20:42,267] [INFO] Task succeeded: HMMsearch
[2023-03-16 10:20:42,267] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgfb2f7c3d-23ce-4699-8325-b4f80ae0077c/OceanDNA-b36177.fa]
[2023-03-16 10:20:42,277] [INFO] Query marker FASTA was written to OceanDNA-b36177/markers.fasta
[2023-03-16 10:20:42,277] [INFO] Task started: Blastn
[2023-03-16 10:20:42,277] [INFO] Running command: blastn -query OceanDNA-b36177/markers.fasta -db /var/lib/cwl/stgc6d4858d-bd27-402a-b6a5-1a4b0f05e642/dqc_reference/reference_markers.fasta -out OceanDNA-b36177/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:20:42,857] [INFO] Task succeeded: Blastn
[2023-03-16 10:20:42,858] [INFO] Selected 29 target genomes.
[2023-03-16 10:20:42,858] [INFO] Target genome list was writen to OceanDNA-b36177/target_genomes.txt
[2023-03-16 10:20:42,883] [INFO] Task started: fastANI
[2023-03-16 10:20:42,884] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb2f7c3d-23ce-4699-8325-b4f80ae0077c/OceanDNA-b36177.fa --refList OceanDNA-b36177/target_genomes.txt --output OceanDNA-b36177/fastani_result.tsv --threads 1
[2023-03-16 10:21:00,247] [INFO] Task succeeded: fastANI
[2023-03-16 10:21:00,247] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc6d4858d-bd27-402a-b6a5-1a4b0f05e642/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 10:21:00,247] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc6d4858d-bd27-402a-b6a5-1a4b0f05e642/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 10:21:00,248] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 10:21:00,248] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 10:21:00,248] [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
--------------------------------------------------------------------------------
[2023-03-16 10:21:00,248] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36177/tc_result.tsv
[2023-03-16 10:21:00,248] [INFO] ===== Taxonomy check completed =====
[2023-03-16 10:21:00,248] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 10:21:00,248] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc6d4858d-bd27-402a-b6a5-1a4b0f05e642/dqc_reference/checkm_data
[2023-03-16 10:21:00,251] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 10:21:00,254] [INFO] Task started: CheckM
[2023-03-16 10:21:00,255] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36177/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36177/checkm_input OceanDNA-b36177/checkm_result
[2023-03-16 10:21:21,454] [INFO] Task succeeded: CheckM
[2023-03-16 10:21:21,454] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 67.80%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 10:21:21,457] [INFO] ===== Completeness check finished =====
[2023-03-16 10:21:21,457] [INFO] ===== Start GTDB Search =====
[2023-03-16 10:21:21,457] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36177/markers.fasta)
[2023-03-16 10:21:21,458] [INFO] Task started: Blastn
[2023-03-16 10:21:21,458] [INFO] Running command: blastn -query OceanDNA-b36177/markers.fasta -db /var/lib/cwl/stgc6d4858d-bd27-402a-b6a5-1a4b0f05e642/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36177/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:21:22,352] [INFO] Task succeeded: Blastn
[2023-03-16 10:21:22,353] [INFO] Selected 17 target genomes.
[2023-03-16 10:21:22,353] [INFO] Target genome list was writen to OceanDNA-b36177/target_genomes_gtdb.txt
[2023-03-16 10:21:22,396] [INFO] Task started: fastANI
[2023-03-16 10:21:22,396] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb2f7c3d-23ce-4699-8325-b4f80ae0077c/OceanDNA-b36177.fa --refList OceanDNA-b36177/target_genomes_gtdb.txt --output OceanDNA-b36177/fastani_result_gtdb.tsv --threads 1
[2023-03-16 10:21:28,854] [INFO] Task succeeded: fastANI
[2023-03-16 10:21:28,859] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 10:21:28,859] [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_905181885.1	s__GCA-002733105 sp905181885	88.5563	364	375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018646825.1	s__GCA-002733105 sp018646825	77.1985	77	375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479985.1	s__GCA-002733105 sp905479985	77.1401	96	375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479075.1	s__GCA-002733105 sp905479075	76.8183	81	375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013215825.1	s__GCA-002733105 sp013215825	76.6206	50	375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013215775.1	s__GCA-002733105 sp013215775	76.4436	56	375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 10:21:28,859] [INFO] GTDB search result was written to OceanDNA-b36177/result_gtdb.tsv
[2023-03-16 10:21:28,860] [INFO] ===== GTDB Search completed =====
[2023-03-16 10:21:28,860] [INFO] DFAST_QC result json was written to OceanDNA-b36177/dqc_result.json
[2023-03-16 10:21:28,861] [INFO] DFAST_QC completed!
[2023-03-16 10:21:28,861] [INFO] Total running time: 0h0m54s