[2023-03-18 03:28:30,759] [INFO] DFAST_QC pipeline started.
[2023-03-18 03:28:30,759] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 03:28:30,759] [INFO] DQC Reference Directory: /var/lib/cwl/stgaa486cb5-8e65-4d56-8eb1-52da742cc00e/dqc_reference
[2023-03-18 03:28:31,872] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 03:28:31,872] [INFO] Task started: Prodigal
[2023-03-18 03:28:31,872] [INFO] Running command: cat /var/lib/cwl/stg6bc1ec53-6fc4-4454-a931-37702291e0de/OceanDNA-b36287.fa | prodigal -d OceanDNA-b36287/cds.fna -a OceanDNA-b36287/protein.faa -g 11 -q > /dev/null
[2023-03-18 03:28:38,203] [INFO] Task succeeded: Prodigal
[2023-03-18 03:28:38,203] [INFO] Task started: HMMsearch
[2023-03-18 03:28:38,203] [INFO] Running command: hmmsearch --tblout OceanDNA-b36287/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaa486cb5-8e65-4d56-8eb1-52da742cc00e/dqc_reference/reference_markers.hmm OceanDNA-b36287/protein.faa > /dev/null
[2023-03-18 03:28:38,363] [INFO] Task succeeded: HMMsearch
[2023-03-18 03:28:38,364] [INFO] Found 6/6 markers.
[2023-03-18 03:28:38,377] [INFO] Query marker FASTA was written to OceanDNA-b36287/markers.fasta
[2023-03-18 03:28:38,377] [INFO] Task started: Blastn
[2023-03-18 03:28:38,377] [INFO] Running command: blastn -query OceanDNA-b36287/markers.fasta -db /var/lib/cwl/stgaa486cb5-8e65-4d56-8eb1-52da742cc00e/dqc_reference/reference_markers.fasta -out OceanDNA-b36287/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:28:38,953] [INFO] Task succeeded: Blastn
[2023-03-18 03:28:38,954] [INFO] Selected 25 target genomes.
[2023-03-18 03:28:38,954] [INFO] Target genome list was writen to OceanDNA-b36287/target_genomes.txt
[2023-03-18 03:28:38,967] [INFO] Task started: fastANI
[2023-03-18 03:28:38,968] [INFO] Running command: fastANI --query /var/lib/cwl/stg6bc1ec53-6fc4-4454-a931-37702291e0de/OceanDNA-b36287.fa --refList OceanDNA-b36287/target_genomes.txt --output OceanDNA-b36287/fastani_result.tsv --threads 1
[2023-03-18 03:28:50,386] [INFO] Task succeeded: fastANI
[2023-03-18 03:28:50,387] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaa486cb5-8e65-4d56-8eb1-52da742cc00e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 03:28:50,387] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaa486cb5-8e65-4d56-8eb1-52da742cc00e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 03:28:50,387] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 03:28:50,387] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 03:28:50,387] [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
--------------------------------------------------------------------------------
[2023-03-18 03:28:50,387] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36287/tc_result.tsv
[2023-03-18 03:28:50,388] [INFO] ===== Taxonomy check completed =====
[2023-03-18 03:28:50,388] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 03:28:50,388] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaa486cb5-8e65-4d56-8eb1-52da742cc00e/dqc_reference/checkm_data
[2023-03-18 03:28:50,390] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 03:28:50,393] [INFO] Task started: CheckM
[2023-03-18 03:28:50,393] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36287/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36287/checkm_input OceanDNA-b36287/checkm_result
[2023-03-18 03:29:11,992] [INFO] Task succeeded: CheckM
[2023-03-18 03:29:11,992] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 03:29:11,994] [INFO] ===== Completeness check finished =====
[2023-03-18 03:29:11,995] [INFO] ===== Start GTDB Search =====
[2023-03-18 03:29:11,995] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36287/markers.fasta)
[2023-03-18 03:29:11,995] [INFO] Task started: Blastn
[2023-03-18 03:29:11,995] [INFO] Running command: blastn -query OceanDNA-b36287/markers.fasta -db /var/lib/cwl/stgaa486cb5-8e65-4d56-8eb1-52da742cc00e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36287/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:29:12,936] [INFO] Task succeeded: Blastn
[2023-03-18 03:29:12,937] [INFO] Selected 15 target genomes.
[2023-03-18 03:29:12,937] [INFO] Target genome list was writen to OceanDNA-b36287/target_genomes_gtdb.txt
[2023-03-18 03:29:12,954] [INFO] Task started: fastANI
[2023-03-18 03:29:12,954] [INFO] Running command: fastANI --query /var/lib/cwl/stg6bc1ec53-6fc4-4454-a931-37702291e0de/OceanDNA-b36287.fa --refList OceanDNA-b36287/target_genomes_gtdb.txt --output OceanDNA-b36287/fastani_result_gtdb.tsv --threads 1
[2023-03-18 03:29:18,415] [INFO] Task succeeded: fastANI
[2023-03-18 03:29:18,424] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 03:29:18,424] [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_013215775.1	s__GCA-002733105 sp013215775	99.8261	354	358	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002733105.1	s__GCA-002733105 sp002733105	81.0323	133	358	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_003645385.1	s__GCA-002733105 sp003645385	78.0803	108	358	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	98.88	98.88	0.61	0.61	2	-
GCA_002733335.1	s__GCA-002733105 sp002733335	77.8895	92	358	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	77.7763	138	358	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_002163085.1	s__41-12-T18 sp002163085	77.7227	99	358	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__41-12-T18	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014859375.1	s__GCA-002733105 sp014859375	77.7133	77	358	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_013139345.1	s__GCA-002733105 sp013139345	77.5551	86	358	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_002402245.1	s__GCA-002733105 sp002402245	77.4246	85	358	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_002733715.2	s__GCA-002733105 sp002733715	77.4165	106	358	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_002733505.1	s__GCA-002733105 sp002733505	77.3397	90	358	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	77.1868	54	358	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_011053005.1	s__GCA-002733105 sp011053005	76.7961	88	358	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	76.7597	71	358	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 03:29:18,424] [INFO] GTDB search result was written to OceanDNA-b36287/result_gtdb.tsv
[2023-03-18 03:29:18,424] [INFO] ===== GTDB Search completed =====
[2023-03-18 03:29:18,425] [INFO] DFAST_QC result json was written to OceanDNA-b36287/dqc_result.json
[2023-03-18 03:29:18,425] [INFO] DFAST_QC completed!
[2023-03-18 03:29:18,425] [INFO] Total running time: 0h0m48s