[2023-03-18 23:32:58,547] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:32:58,548] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:32:58,548] [INFO] DQC Reference Directory: /var/lib/cwl/stgdfff9e3e-385b-4915-b91f-934432b7d15a/dqc_reference
[2023-03-18 23:32:59,886] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:32:59,887] [INFO] Task started: Prodigal
[2023-03-18 23:32:59,887] [INFO] Running command: cat /var/lib/cwl/stg737cf912-6ef7-44aa-b037-11810aedc1af/OceanDNA-b38658.fa | prodigal -d OceanDNA-b38658/cds.fna -a OceanDNA-b38658/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:33:12,156] [INFO] Task succeeded: Prodigal
[2023-03-18 23:33:12,156] [INFO] Task started: HMMsearch
[2023-03-18 23:33:12,156] [INFO] Running command: hmmsearch --tblout OceanDNA-b38658/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdfff9e3e-385b-4915-b91f-934432b7d15a/dqc_reference/reference_markers.hmm OceanDNA-b38658/protein.faa > /dev/null
[2023-03-18 23:33:12,339] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:33:12,339] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg737cf912-6ef7-44aa-b037-11810aedc1af/OceanDNA-b38658.fa]
[2023-03-18 23:33:12,356] [INFO] Query marker FASTA was written to OceanDNA-b38658/markers.fasta
[2023-03-18 23:33:12,357] [INFO] Task started: Blastn
[2023-03-18 23:33:12,357] [INFO] Running command: blastn -query OceanDNA-b38658/markers.fasta -db /var/lib/cwl/stgdfff9e3e-385b-4915-b91f-934432b7d15a/dqc_reference/reference_markers.fasta -out OceanDNA-b38658/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:33:12,896] [INFO] Task succeeded: Blastn
[2023-03-18 23:33:12,896] [INFO] Selected 27 target genomes.
[2023-03-18 23:33:12,897] [INFO] Target genome list was writen to OceanDNA-b38658/target_genomes.txt
[2023-03-18 23:33:12,914] [INFO] Task started: fastANI
[2023-03-18 23:33:12,914] [INFO] Running command: fastANI --query /var/lib/cwl/stg737cf912-6ef7-44aa-b037-11810aedc1af/OceanDNA-b38658.fa --refList OceanDNA-b38658/target_genomes.txt --output OceanDNA-b38658/fastani_result.tsv --threads 1
[2023-03-18 23:33:28,023] [INFO] Task succeeded: fastANI
[2023-03-18 23:33:28,023] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdfff9e3e-385b-4915-b91f-934432b7d15a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:33:28,024] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdfff9e3e-385b-4915-b91f-934432b7d15a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:33:28,024] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:33:28,024] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 23:33:28,024] [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 23:33:28,024] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38658/tc_result.tsv
[2023-03-18 23:33:28,024] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:33:28,024] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:33:28,024] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdfff9e3e-385b-4915-b91f-934432b7d15a/dqc_reference/checkm_data
[2023-03-18 23:33:28,027] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:33:28,031] [INFO] Task started: CheckM
[2023-03-18 23:33:28,031] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38658/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38658/checkm_input OceanDNA-b38658/checkm_result
[2023-03-18 23:34:02,448] [INFO] Task succeeded: CheckM
[2023-03-18 23:34:02,448] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 23:34:02,467] [INFO] ===== Completeness check finished =====
[2023-03-18 23:34:02,467] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:34:02,467] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38658/markers.fasta)
[2023-03-18 23:34:02,468] [INFO] Task started: Blastn
[2023-03-18 23:34:02,468] [INFO] Running command: blastn -query OceanDNA-b38658/markers.fasta -db /var/lib/cwl/stgdfff9e3e-385b-4915-b91f-934432b7d15a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38658/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:34:03,201] [INFO] Task succeeded: Blastn
[2023-03-18 23:34:03,203] [INFO] Selected 25 target genomes.
[2023-03-18 23:34:03,203] [INFO] Target genome list was writen to OceanDNA-b38658/target_genomes_gtdb.txt
[2023-03-18 23:34:03,228] [INFO] Task started: fastANI
[2023-03-18 23:34:03,229] [INFO] Running command: fastANI --query /var/lib/cwl/stg737cf912-6ef7-44aa-b037-11810aedc1af/OceanDNA-b38658.fa --refList OceanDNA-b38658/target_genomes_gtdb.txt --output OceanDNA-b38658/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:34:17,476] [INFO] Task succeeded: fastANI
[2023-03-18 23:34:17,481] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 23:34:17,481] [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_003521845.1	s__ASP10-02a sp003521845	85.4432	548	688	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__ASP10-02a	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016845445.1	s__ASP10-02a sp016845445	78.6361	184	688	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__ASP10-02a	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002686055.1	s__ASP10-02a sp002686055	77.2212	79	688	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__ASP10-02a	95.0	99.76	99.76	0.70	0.70	2	-
GCA_003497765.1	s__ASP10-02a sp003497765	77.17	67	688	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__ASP10-02a	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003523085.1	s__ASP10-02a sp003523085	76.8948	98	688	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__ASP10-02a	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018647765.1	s__ASP10-02a sp018647765	76.6268	89	688	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__ASP10-02a	95.0	99.86	99.85	0.95	0.93	3	-
GCA_905182035.1	s__ASP10-02a sp905182035	75.9752	56	688	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__ASP10-02a	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 23:34:17,482] [INFO] GTDB search result was written to OceanDNA-b38658/result_gtdb.tsv
[2023-03-18 23:34:17,486] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:34:17,490] [INFO] DFAST_QC result json was written to OceanDNA-b38658/dqc_result.json
[2023-03-18 23:34:17,490] [INFO] DFAST_QC completed!
[2023-03-18 23:34:17,490] [INFO] Total running time: 0h1m19s