[2023-03-15 04:30:16,423] [INFO] DFAST_QC pipeline started.
[2023-03-15 04:30:16,424] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 04:30:16,424] [INFO] DQC Reference Directory: /var/lib/cwl/stgabb31cda-9563-48ea-a99e-9cc6461d1662/dqc_reference
[2023-03-15 04:30:19,822] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 04:30:19,823] [INFO] Task started: Prodigal
[2023-03-15 04:30:19,823] [INFO] Running command: cat /var/lib/cwl/stgedeed694-8dcd-45e9-8999-3e9cfdd36db3/OceanDNA-b40920.fa | prodigal -d OceanDNA-b40920/cds.fna -a OceanDNA-b40920/protein.faa -g 11 -q > /dev/null
[2023-03-15 04:30:38,786] [INFO] Task succeeded: Prodigal
[2023-03-15 04:30:38,786] [INFO] Task started: HMMsearch
[2023-03-15 04:30:38,786] [INFO] Running command: hmmsearch --tblout OceanDNA-b40920/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgabb31cda-9563-48ea-a99e-9cc6461d1662/dqc_reference/reference_markers.hmm OceanDNA-b40920/protein.faa > /dev/null
[2023-03-15 04:30:39,006] [INFO] Task succeeded: HMMsearch
[2023-03-15 04:30:39,006] [INFO] Found 6/6 markers.
[2023-03-15 04:30:39,040] [INFO] Query marker FASTA was written to OceanDNA-b40920/markers.fasta
[2023-03-15 04:30:39,041] [INFO] Task started: Blastn
[2023-03-15 04:30:39,042] [INFO] Running command: blastn -query OceanDNA-b40920/markers.fasta -db /var/lib/cwl/stgabb31cda-9563-48ea-a99e-9cc6461d1662/dqc_reference/reference_markers.fasta -out OceanDNA-b40920/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 04:30:39,648] [INFO] Task succeeded: Blastn
[2023-03-15 04:30:39,656] [INFO] Selected 28 target genomes.
[2023-03-15 04:30:39,656] [INFO] Target genome list was writen to OceanDNA-b40920/target_genomes.txt
[2023-03-15 04:30:39,673] [INFO] Task started: fastANI
[2023-03-15 04:30:39,673] [INFO] Running command: fastANI --query /var/lib/cwl/stgedeed694-8dcd-45e9-8999-3e9cfdd36db3/OceanDNA-b40920.fa --refList OceanDNA-b40920/target_genomes.txt --output OceanDNA-b40920/fastani_result.tsv --threads 1
[2023-03-15 04:30:56,810] [INFO] Task succeeded: fastANI
[2023-03-15 04:30:56,810] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgabb31cda-9563-48ea-a99e-9cc6461d1662/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 04:30:56,810] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgabb31cda-9563-48ea-a99e-9cc6461d1662/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 04:30:56,810] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 04:30:56,811] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 04:30:56,811] [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 04:30:56,811] [INFO] DFAST Taxonomy check result was written to OceanDNA-b40920/tc_result.tsv
[2023-03-15 04:30:56,812] [INFO] ===== Taxonomy check completed =====
[2023-03-15 04:30:56,812] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 04:30:56,812] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgabb31cda-9563-48ea-a99e-9cc6461d1662/dqc_reference/checkm_data
[2023-03-15 04:30:56,815] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 04:30:56,822] [INFO] Task started: CheckM
[2023-03-15 04:30:56,822] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b40920/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b40920/checkm_input OceanDNA-b40920/checkm_result
[2023-03-15 04:31:45,728] [INFO] Task succeeded: CheckM
[2023-03-15 04:31:45,728] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 04:31:45,755] [INFO] ===== Completeness check finished =====
[2023-03-15 04:31:45,755] [INFO] ===== Start GTDB Search =====
[2023-03-15 04:31:45,755] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b40920/markers.fasta)
[2023-03-15 04:31:45,757] [INFO] Task started: Blastn
[2023-03-15 04:31:45,757] [INFO] Running command: blastn -query OceanDNA-b40920/markers.fasta -db /var/lib/cwl/stgabb31cda-9563-48ea-a99e-9cc6461d1662/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b40920/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 04:31:46,785] [INFO] Task succeeded: Blastn
[2023-03-15 04:31:46,787] [INFO] Selected 25 target genomes.
[2023-03-15 04:31:46,787] [INFO] Target genome list was writen to OceanDNA-b40920/target_genomes_gtdb.txt
[2023-03-15 04:31:46,871] [INFO] Task started: fastANI
[2023-03-15 04:31:46,871] [INFO] Running command: fastANI --query /var/lib/cwl/stgedeed694-8dcd-45e9-8999-3e9cfdd36db3/OceanDNA-b40920.fa --refList OceanDNA-b40920/target_genomes_gtdb.txt --output OceanDNA-b40920/fastani_result_gtdb.tsv --threads 1
[2023-03-15 04:32:01,367] [INFO] Task succeeded: fastANI
[2023-03-15 04:32:01,373] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 04:32:01,373] [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_002731775.1	s__UBA9145 sp002731775	98.4065	892	1052	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	98.77	98.59	0.87	0.85	6	conclusive
GCA_002402175.1	s__UBA9145 sp002402175	76.8543	61	1052	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002401885.1	s__UBA9145 sp002401885	76.7009	72	1052	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013204155.1	s__UBA9145 sp013204155	76.6869	108	1052	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003451715.1	s__UBA9145 sp003451715	76.685	88	1052	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905478195.1	s__UBA9145 sp003483155	76.4938	92	1052	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	99.23	98.96	0.87	0.81	6	-
GCA_016762975.1	s__UBA9145 sp016762975	76.1777	63	1052	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009692305.1	s__UBA9145 sp009692305	76.0161	94	1052	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002477465.1	s__UBA9145 sp002477465	75.7441	72	1052	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	98.95	97.46	0.90	0.76	11	-
--------------------------------------------------------------------------------
[2023-03-15 04:32:01,374] [INFO] GTDB search result was written to OceanDNA-b40920/result_gtdb.tsv
[2023-03-15 04:32:01,374] [INFO] ===== GTDB Search completed =====
[2023-03-15 04:32:01,375] [INFO] DFAST_QC result json was written to OceanDNA-b40920/dqc_result.json
[2023-03-15 04:32:01,375] [INFO] DFAST_QC completed!
[2023-03-15 04:32:01,376] [INFO] Total running time: 0h1m45s