[2023-03-15 20:34:26,740] [INFO] DFAST_QC pipeline started.
[2023-03-15 20:34:26,740] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 20:34:26,740] [INFO] DQC Reference Directory: /var/lib/cwl/stg3a3d26be-0de8-4b75-9b6e-d768695811da/dqc_reference
[2023-03-15 20:34:28,460] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 20:34:28,460] [INFO] Task started: Prodigal
[2023-03-15 20:34:28,460] [INFO] Running command: cat /var/lib/cwl/stgae41a977-8b0e-45ff-8c87-325bcfab916a/OceanDNA-b37839.fa | prodigal -d OceanDNA-b37839/cds.fna -a OceanDNA-b37839/protein.faa -g 11 -q > /dev/null
[2023-03-15 20:34:43,428] [INFO] Task succeeded: Prodigal
[2023-03-15 20:34:43,428] [INFO] Task started: HMMsearch
[2023-03-15 20:34:43,428] [INFO] Running command: hmmsearch --tblout OceanDNA-b37839/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3a3d26be-0de8-4b75-9b6e-d768695811da/dqc_reference/reference_markers.hmm OceanDNA-b37839/protein.faa > /dev/null
[2023-03-15 20:34:43,598] [INFO] Task succeeded: HMMsearch
[2023-03-15 20:34:43,598] [INFO] Found 6/6 markers.
[2023-03-15 20:34:43,615] [INFO] Query marker FASTA was written to OceanDNA-b37839/markers.fasta
[2023-03-15 20:34:43,616] [INFO] Task started: Blastn
[2023-03-15 20:34:43,616] [INFO] Running command: blastn -query OceanDNA-b37839/markers.fasta -db /var/lib/cwl/stg3a3d26be-0de8-4b75-9b6e-d768695811da/dqc_reference/reference_markers.fasta -out OceanDNA-b37839/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 20:34:44,148] [INFO] Task succeeded: Blastn
[2023-03-15 20:34:44,149] [INFO] Selected 30 target genomes.
[2023-03-15 20:34:44,149] [INFO] Target genome list was writen to OceanDNA-b37839/target_genomes.txt
[2023-03-15 20:34:44,165] [INFO] Task started: fastANI
[2023-03-15 20:34:44,165] [INFO] Running command: fastANI --query /var/lib/cwl/stgae41a977-8b0e-45ff-8c87-325bcfab916a/OceanDNA-b37839.fa --refList OceanDNA-b37839/target_genomes.txt --output OceanDNA-b37839/fastani_result.tsv --threads 1
[2023-03-15 20:35:03,592] [INFO] Task succeeded: fastANI
[2023-03-15 20:35:03,592] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3a3d26be-0de8-4b75-9b6e-d768695811da/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 20:35:03,592] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3a3d26be-0de8-4b75-9b6e-d768695811da/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 20:35:03,592] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 20:35:03,592] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 20:35:03,592] [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
--------------------------------------------------------------------------------
[2023-03-15 20:35:03,593] [INFO] DFAST Taxonomy check result was written to OceanDNA-b37839/tc_result.tsv
[2023-03-15 20:35:03,593] [INFO] ===== Taxonomy check completed =====
[2023-03-15 20:35:03,593] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 20:35:03,593] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3a3d26be-0de8-4b75-9b6e-d768695811da/dqc_reference/checkm_data
[2023-03-15 20:35:03,595] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 20:35:03,599] [INFO] Task started: CheckM
[2023-03-15 20:35:03,599] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b37839/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b37839/checkm_input OceanDNA-b37839/checkm_result
[2023-03-15 20:35:43,688] [INFO] Task succeeded: CheckM
[2023-03-15 20:35:43,689] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 20:35:43,691] [INFO] ===== Completeness check finished =====
[2023-03-15 20:35:43,691] [INFO] ===== Start GTDB Search =====
[2023-03-15 20:35:43,691] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b37839/markers.fasta)
[2023-03-15 20:35:43,691] [INFO] Task started: Blastn
[2023-03-15 20:35:43,691] [INFO] Running command: blastn -query OceanDNA-b37839/markers.fasta -db /var/lib/cwl/stg3a3d26be-0de8-4b75-9b6e-d768695811da/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b37839/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 20:35:44,455] [INFO] Task succeeded: Blastn
[2023-03-15 20:35:44,456] [INFO] Selected 19 target genomes.
[2023-03-15 20:35:44,456] [INFO] Target genome list was writen to OceanDNA-b37839/target_genomes_gtdb.txt
[2023-03-15 20:35:44,849] [INFO] Task started: fastANI
[2023-03-15 20:35:44,849] [INFO] Running command: fastANI --query /var/lib/cwl/stgae41a977-8b0e-45ff-8c87-325bcfab916a/OceanDNA-b37839.fa --refList OceanDNA-b37839/target_genomes_gtdb.txt --output OceanDNA-b37839/fastani_result_gtdb.tsv --threads 1
[2023-03-15 20:35:52,983] [INFO] Task succeeded: fastANI
[2023-03-15 20:35:52,988] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 20:35:52,988] [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	85.4207	527	817	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	84.615	559	817	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018666055.1	s__Luminiphilus sp018666055	84.4261	329	817	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016778085.1	s__Luminiphilus sp016778085	76.7732	67	817	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002377985.1	s__Luminiphilus sp002377985	76.5764	75	817	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016778045.1	s__Luminiphilus sp016778045	76.5304	72	817	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	76.2823	94	817	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	99.68	99.68	0.89	0.89	2	-
GCA_902623175.1	s__Luminiphilus sp902623175	76.2231	84	817	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 20:35:52,988] [INFO] GTDB search result was written to OceanDNA-b37839/result_gtdb.tsv
[2023-03-15 20:35:52,988] [INFO] ===== GTDB Search completed =====
[2023-03-15 20:35:52,989] [INFO] DFAST_QC result json was written to OceanDNA-b37839/dqc_result.json
[2023-03-15 20:35:52,989] [INFO] DFAST_QC completed!
[2023-03-15 20:35:52,989] [INFO] Total running time: 0h1m26s