[2023-03-14 14:05:20,209] [INFO] DFAST_QC pipeline started.
[2023-03-14 14:05:20,209] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 14:05:20,209] [INFO] DQC Reference Directory: /var/lib/cwl/stgb069f382-01a0-446a-b578-0c8c7eb3f3e0/dqc_reference
[2023-03-14 14:05:21,285] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 14:05:21,285] [INFO] Task started: Prodigal
[2023-03-14 14:05:21,285] [INFO] Running command: cat /var/lib/cwl/stgdeb04dbf-5ecc-4d17-b68d-5523e0d490e3/OceanDNA-b37293.fa | prodigal -d OceanDNA-b37293/cds.fna -a OceanDNA-b37293/protein.faa -g 11 -q > /dev/null
[2023-03-14 14:05:44,073] [INFO] Task succeeded: Prodigal
[2023-03-14 14:05:44,074] [INFO] Task started: HMMsearch
[2023-03-14 14:05:44,074] [INFO] Running command: hmmsearch --tblout OceanDNA-b37293/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb069f382-01a0-446a-b578-0c8c7eb3f3e0/dqc_reference/reference_markers.hmm OceanDNA-b37293/protein.faa > /dev/null
[2023-03-14 14:05:44,284] [INFO] Task succeeded: HMMsearch
[2023-03-14 14:05:44,284] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgdeb04dbf-5ecc-4d17-b68d-5523e0d490e3/OceanDNA-b37293.fa]
[2023-03-14 14:05:44,309] [INFO] Query marker FASTA was written to OceanDNA-b37293/markers.fasta
[2023-03-14 14:05:44,310] [INFO] Task started: Blastn
[2023-03-14 14:05:44,310] [INFO] Running command: blastn -query OceanDNA-b37293/markers.fasta -db /var/lib/cwl/stgb069f382-01a0-446a-b578-0c8c7eb3f3e0/dqc_reference/reference_markers.fasta -out OceanDNA-b37293/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 14:05:44,883] [INFO] Task succeeded: Blastn
[2023-03-14 14:05:44,884] [INFO] Selected 25 target genomes.
[2023-03-14 14:05:44,884] [INFO] Target genome list was writen to OceanDNA-b37293/target_genomes.txt
[2023-03-14 14:05:44,894] [INFO] Task started: fastANI
[2023-03-14 14:05:44,895] [INFO] Running command: fastANI --query /var/lib/cwl/stgdeb04dbf-5ecc-4d17-b68d-5523e0d490e3/OceanDNA-b37293.fa --refList OceanDNA-b37293/target_genomes.txt --output OceanDNA-b37293/fastani_result.tsv --threads 1
[2023-03-14 14:06:06,076] [INFO] Task succeeded: fastANI
[2023-03-14 14:06:06,077] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb069f382-01a0-446a-b578-0c8c7eb3f3e0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 14:06:06,077] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb069f382-01a0-446a-b578-0c8c7eb3f3e0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 14:06:06,077] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 14:06:06,077] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 14:06:06,077] [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
--------------------------------------------------------------------------------
[2023-03-14 14:06:06,077] [INFO] DFAST Taxonomy check result was written to OceanDNA-b37293/tc_result.tsv
[2023-03-14 14:06:06,078] [INFO] ===== Taxonomy check completed =====
[2023-03-14 14:06:06,078] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 14:06:06,078] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb069f382-01a0-446a-b578-0c8c7eb3f3e0/dqc_reference/checkm_data
[2023-03-14 14:06:06,086] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 14:06:06,092] [INFO] Task started: CheckM
[2023-03-14 14:06:06,092] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b37293/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b37293/checkm_input OceanDNA-b37293/checkm_result
[2023-03-14 14:07:19,697] [INFO] Task succeeded: CheckM
[2023-03-14 14:07:19,697] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 14:07:19,701] [INFO] ===== Completeness check finished =====
[2023-03-14 14:07:19,701] [INFO] ===== Start GTDB Search =====
[2023-03-14 14:07:19,701] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b37293/markers.fasta)
[2023-03-14 14:07:19,702] [INFO] Task started: Blastn
[2023-03-14 14:07:19,702] [INFO] Running command: blastn -query OceanDNA-b37293/markers.fasta -db /var/lib/cwl/stgb069f382-01a0-446a-b578-0c8c7eb3f3e0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b37293/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 14:07:20,609] [INFO] Task succeeded: Blastn
[2023-03-14 14:07:20,610] [INFO] Selected 14 target genomes.
[2023-03-14 14:07:20,610] [INFO] Target genome list was writen to OceanDNA-b37293/target_genomes_gtdb.txt
[2023-03-14 14:07:20,625] [INFO] Task started: fastANI
[2023-03-14 14:07:20,625] [INFO] Running command: fastANI --query /var/lib/cwl/stgdeb04dbf-5ecc-4d17-b68d-5523e0d490e3/OceanDNA-b37293.fa --refList OceanDNA-b37293/target_genomes_gtdb.txt --output OceanDNA-b37293/fastani_result_gtdb.tsv --threads 1
[2023-03-14 14:07:29,896] [INFO] Task succeeded: fastANI
[2023-03-14 14:07:29,901] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 14:07:29,901] [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_018667205.1	s__UBA9659 sp018667205	97.6836	660	1308	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA9659	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_012961165.1	s__UBA9659 sp012961165	85.088	891	1308	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	84.3192	822	1308	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA9659	95.0	99.67	99.61	0.89	0.86	14	-
GCA_018645845.1	s__UBA9659 sp018645845	81.6833	592	1308	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA9659	95.0	98.73	98.60	0.77	0.73	4	-
GCA_018607685.1	s__UBA9659 sp018607685	79.4967	503	1308	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA9659	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016779585.1	s__UBA9659 sp016779585	76.0629	57	1308	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA9659	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017642855.1	s__UBA9659 sp017642855	76.0535	61	1308	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA9659	95.0	99.28	99.09	0.95	0.93	7	-
--------------------------------------------------------------------------------
[2023-03-14 14:07:29,901] [INFO] GTDB search result was written to OceanDNA-b37293/result_gtdb.tsv
[2023-03-14 14:07:29,901] [INFO] ===== GTDB Search completed =====
[2023-03-14 14:07:29,902] [INFO] DFAST_QC result json was written to OceanDNA-b37293/dqc_result.json
[2023-03-14 14:07:29,902] [INFO] DFAST_QC completed!
[2023-03-14 14:07:29,903] [INFO] Total running time: 0h2m10s