[2023-03-17 06:30:49,080] [INFO] DFAST_QC pipeline started.
[2023-03-17 06:30:49,081] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 06:30:49,081] [INFO] DQC Reference Directory: /var/lib/cwl/stg72297c95-ec6e-49c1-a778-2dd457c9e7fd/dqc_reference
[2023-03-17 06:30:50,270] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 06:30:50,293] [INFO] Task started: Prodigal
[2023-03-17 06:30:50,293] [INFO] Running command: cat /var/lib/cwl/stgb8ab4f4c-e8c9-430c-901b-3e38ff99e347/OceanDNA-b40171.fa | prodigal -d OceanDNA-b40171/cds.fna -a OceanDNA-b40171/protein.faa -g 11 -q > /dev/null
[2023-03-17 06:30:56,849] [INFO] Task succeeded: Prodigal
[2023-03-17 06:30:56,850] [INFO] Task started: HMMsearch
[2023-03-17 06:30:56,850] [INFO] Running command: hmmsearch --tblout OceanDNA-b40171/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg72297c95-ec6e-49c1-a778-2dd457c9e7fd/dqc_reference/reference_markers.hmm OceanDNA-b40171/protein.faa > /dev/null
[2023-03-17 06:30:57,024] [INFO] Task succeeded: HMMsearch
[2023-03-17 06:30:57,024] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgb8ab4f4c-e8c9-430c-901b-3e38ff99e347/OceanDNA-b40171.fa]
[2023-03-17 06:30:57,036] [INFO] Query marker FASTA was written to OceanDNA-b40171/markers.fasta
[2023-03-17 06:30:57,037] [INFO] Task started: Blastn
[2023-03-17 06:30:57,037] [INFO] Running command: blastn -query OceanDNA-b40171/markers.fasta -db /var/lib/cwl/stg72297c95-ec6e-49c1-a778-2dd457c9e7fd/dqc_reference/reference_markers.fasta -out OceanDNA-b40171/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 06:30:57,609] [INFO] Task succeeded: Blastn
[2023-03-17 06:30:57,610] [INFO] Selected 15 target genomes.
[2023-03-17 06:30:57,610] [INFO] Target genome list was writen to OceanDNA-b40171/target_genomes.txt
[2023-03-17 06:30:57,618] [INFO] Task started: fastANI
[2023-03-17 06:30:57,618] [INFO] Running command: fastANI --query /var/lib/cwl/stgb8ab4f4c-e8c9-430c-901b-3e38ff99e347/OceanDNA-b40171.fa --refList OceanDNA-b40171/target_genomes.txt --output OceanDNA-b40171/fastani_result.tsv --threads 1
[2023-03-17 06:31:05,379] [INFO] Task succeeded: fastANI
[2023-03-17 06:31:05,379] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg72297c95-ec6e-49c1-a778-2dd457c9e7fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 06:31:05,379] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg72297c95-ec6e-49c1-a778-2dd457c9e7fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 06:31:05,379] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 06:31:05,379] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 06:31:05,380] [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 06:31:05,380] [INFO] DFAST Taxonomy check result was written to OceanDNA-b40171/tc_result.tsv
[2023-03-17 06:31:05,380] [INFO] ===== Taxonomy check completed =====
[2023-03-17 06:31:05,380] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 06:31:05,380] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg72297c95-ec6e-49c1-a778-2dd457c9e7fd/dqc_reference/checkm_data
[2023-03-17 06:31:05,382] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 06:31:05,386] [INFO] Task started: CheckM
[2023-03-17 06:31:05,386] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b40171/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b40171/checkm_input OceanDNA-b40171/checkm_result
[2023-03-17 06:31:27,631] [INFO] Task succeeded: CheckM
[2023-03-17 06:31:27,631] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.19%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 06:31:27,633] [INFO] ===== Completeness check finished =====
[2023-03-17 06:31:27,633] [INFO] ===== Start GTDB Search =====
[2023-03-17 06:31:27,633] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b40171/markers.fasta)
[2023-03-17 06:31:27,633] [INFO] Task started: Blastn
[2023-03-17 06:31:27,633] [INFO] Running command: blastn -query OceanDNA-b40171/markers.fasta -db /var/lib/cwl/stg72297c95-ec6e-49c1-a778-2dd457c9e7fd/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b40171/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 06:31:28,513] [INFO] Task succeeded: Blastn
[2023-03-17 06:31:28,513] [INFO] Selected 15 target genomes.
[2023-03-17 06:31:28,513] [INFO] Target genome list was writen to OceanDNA-b40171/target_genomes_gtdb.txt
[2023-03-17 06:31:28,779] [INFO] Task started: fastANI
[2023-03-17 06:31:28,779] [INFO] Running command: fastANI --query /var/lib/cwl/stgb8ab4f4c-e8c9-430c-901b-3e38ff99e347/OceanDNA-b40171.fa --refList OceanDNA-b40171/target_genomes_gtdb.txt --output OceanDNA-b40171/fastani_result_gtdb.tsv --threads 1
[2023-03-17 06:31:36,962] [INFO] Task succeeded: fastANI
[2023-03-17 06:31:36,966] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 06:31:36,966] [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_902557735.1	s__TMED48 sp902557735	97.5007	227	332	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__TMED48	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002692165.1	s__TMED48 sp002692165	81.8484	173	332	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__TMED48	95.0	100.00	100.00	0.99	0.99	2	-
GCA_002701765.1	s__TMED48 sp002701765	80.3051	187	332	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__TMED48	95.0	97.58	97.58	0.65	0.65	2	-
GCA_002591625.1	s__TMED48 sp002591625	79.5108	183	332	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__TMED48	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 06:31:36,966] [INFO] GTDB search result was written to OceanDNA-b40171/result_gtdb.tsv
[2023-03-17 06:31:36,966] [INFO] ===== GTDB Search completed =====
[2023-03-17 06:31:36,967] [INFO] DFAST_QC result json was written to OceanDNA-b40171/dqc_result.json
[2023-03-17 06:31:36,967] [INFO] DFAST_QC completed!
[2023-03-17 06:31:36,967] [INFO] Total running time: 0h0m48s