[2023-03-16 17:08:13,819] [INFO] DFAST_QC pipeline started.
[2023-03-16 17:08:13,819] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 17:08:13,820] [INFO] DQC Reference Directory: /var/lib/cwl/stg4cbdd19b-e173-4c2a-98cd-97fcb678ed8b/dqc_reference
[2023-03-16 17:08:16,715] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 17:08:16,716] [INFO] Task started: Prodigal
[2023-03-16 17:08:16,716] [INFO] Running command: cat /var/lib/cwl/stg6794e6e9-8962-47ce-ad37-9d6ad5ca3eb6/OceanDNA-b37351.fa | prodigal -d OceanDNA-b37351/cds.fna -a OceanDNA-b37351/protein.faa -g 11 -q > /dev/null
[2023-03-16 17:08:36,766] [INFO] Task succeeded: Prodigal
[2023-03-16 17:08:36,766] [INFO] Task started: HMMsearch
[2023-03-16 17:08:36,766] [INFO] Running command: hmmsearch --tblout OceanDNA-b37351/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4cbdd19b-e173-4c2a-98cd-97fcb678ed8b/dqc_reference/reference_markers.hmm OceanDNA-b37351/protein.faa > /dev/null
[2023-03-16 17:08:36,987] [INFO] Task succeeded: HMMsearch
[2023-03-16 17:08:36,988] [INFO] Found 6/6 markers.
[2023-03-16 17:08:37,014] [INFO] Query marker FASTA was written to OceanDNA-b37351/markers.fasta
[2023-03-16 17:08:37,015] [INFO] Task started: Blastn
[2023-03-16 17:08:37,015] [INFO] Running command: blastn -query OceanDNA-b37351/markers.fasta -db /var/lib/cwl/stg4cbdd19b-e173-4c2a-98cd-97fcb678ed8b/dqc_reference/reference_markers.fasta -out OceanDNA-b37351/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:08:37,613] [INFO] Task succeeded: Blastn
[2023-03-16 17:08:37,614] [INFO] Selected 23 target genomes.
[2023-03-16 17:08:37,614] [INFO] Target genome list was writen to OceanDNA-b37351/target_genomes.txt
[2023-03-16 17:08:37,766] [INFO] Task started: fastANI
[2023-03-16 17:08:37,766] [INFO] Running command: fastANI --query /var/lib/cwl/stg6794e6e9-8962-47ce-ad37-9d6ad5ca3eb6/OceanDNA-b37351.fa --refList OceanDNA-b37351/target_genomes.txt --output OceanDNA-b37351/fastani_result.tsv --threads 1
[2023-03-16 17:08:52,680] [INFO] Task succeeded: fastANI
[2023-03-16 17:08:52,680] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4cbdd19b-e173-4c2a-98cd-97fcb678ed8b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 17:08:52,680] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4cbdd19b-e173-4c2a-98cd-97fcb678ed8b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 17:08:52,680] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 17:08:52,680] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 17:08:52,680] [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 17:08:52,681] [INFO] DFAST Taxonomy check result was written to OceanDNA-b37351/tc_result.tsv
[2023-03-16 17:08:52,681] [INFO] ===== Taxonomy check completed =====
[2023-03-16 17:08:52,681] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 17:08:52,681] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4cbdd19b-e173-4c2a-98cd-97fcb678ed8b/dqc_reference/checkm_data
[2023-03-16 17:08:52,684] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 17:08:52,691] [INFO] Task started: CheckM
[2023-03-16 17:08:52,691] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b37351/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b37351/checkm_input OceanDNA-b37351/checkm_result
[2023-03-16 17:09:59,386] [INFO] Task succeeded: CheckM
[2023-03-16 17:09:59,387] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 17:09:59,396] [INFO] ===== Completeness check finished =====
[2023-03-16 17:09:59,396] [INFO] ===== Start GTDB Search =====
[2023-03-16 17:09:59,396] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b37351/markers.fasta)
[2023-03-16 17:09:59,398] [INFO] Task started: Blastn
[2023-03-16 17:09:59,398] [INFO] Running command: blastn -query OceanDNA-b37351/markers.fasta -db /var/lib/cwl/stg4cbdd19b-e173-4c2a-98cd-97fcb678ed8b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b37351/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:10:01,775] [INFO] Task succeeded: Blastn
[2023-03-16 17:10:01,777] [INFO] Selected 31 target genomes.
[2023-03-16 17:10:01,777] [INFO] Target genome list was writen to OceanDNA-b37351/target_genomes_gtdb.txt
[2023-03-16 17:10:01,924] [INFO] Task started: fastANI
[2023-03-16 17:10:01,925] [INFO] Running command: fastANI --query /var/lib/cwl/stg6794e6e9-8962-47ce-ad37-9d6ad5ca3eb6/OceanDNA-b37351.fa --refList OceanDNA-b37351/target_genomes_gtdb.txt --output OceanDNA-b37351/fastani_result_gtdb.tsv --threads 1
[2023-03-16 17:10:32,677] [INFO] Task succeeded: fastANI
[2023-03-16 17:10:32,682] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 17:10:32,682] [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_012961165.1	s__UBA9659 sp012961165	77.3888	110	1115	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA9659	95.0	99.55	99.55	0.89	0.89	2	-
GCA_018665025.1	s__UBA9659 sp018665025	76.7672	80	1115	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA9659	95.0	99.67	99.61	0.89	0.86	14	-
GCA_018656865.1	s__UBA9659 sp018656865	76.4848	56	1115	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA9659	95.0	99.73	99.68	0.90	0.90	3	-
GCA_016779585.1	s__UBA9659 sp016779585	76.2386	80	1115	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA9659	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012960755.1	s__UBA4582 sp012960755	76.0576	51	1115	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA4582	95.0	99.81	99.81	0.87	0.87	2	-
GCA_017642855.1	s__UBA9659 sp017642855	75.982	75	1115	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA9659	95.0	99.28	99.09	0.95	0.93	7	-
GCA_018607685.1	s__UBA9659 sp018607685	75.8916	61	1115	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA9659	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 17:10:32,683] [INFO] GTDB search result was written to OceanDNA-b37351/result_gtdb.tsv
[2023-03-16 17:10:32,684] [INFO] ===== GTDB Search completed =====
[2023-03-16 17:10:32,685] [INFO] DFAST_QC result json was written to OceanDNA-b37351/dqc_result.json
[2023-03-16 17:10:32,685] [INFO] DFAST_QC completed!
[2023-03-16 17:10:32,685] [INFO] Total running time: 0h2m19s