[2023-03-14 12:38:54,447] [INFO] DFAST_QC pipeline started.
[2023-03-14 12:38:54,447] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 12:38:54,448] [INFO] DQC Reference Directory: /var/lib/cwl/stgd5c34d04-8b7e-464c-8e1d-47888267857c/dqc_reference
[2023-03-14 12:38:57,160] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 12:38:57,160] [INFO] Task started: Prodigal
[2023-03-14 12:38:57,160] [INFO] Running command: cat /var/lib/cwl/stg7ed07a33-c067-46cc-bd08-49d57dca2b2c/OceanDNA-b40943.fa | prodigal -d OceanDNA-b40943/cds.fna -a OceanDNA-b40943/protein.faa -g 11 -q > /dev/null
[2023-03-14 12:39:18,605] [INFO] Task succeeded: Prodigal
[2023-03-14 12:39:18,605] [INFO] Task started: HMMsearch
[2023-03-14 12:39:18,605] [INFO] Running command: hmmsearch --tblout OceanDNA-b40943/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd5c34d04-8b7e-464c-8e1d-47888267857c/dqc_reference/reference_markers.hmm OceanDNA-b40943/protein.faa > /dev/null
[2023-03-14 12:39:18,808] [INFO] Task succeeded: HMMsearch
[2023-03-14 12:39:18,808] [INFO] Found 6/6 markers.
[2023-03-14 12:39:18,831] [INFO] Query marker FASTA was written to OceanDNA-b40943/markers.fasta
[2023-03-14 12:39:18,833] [INFO] Task started: Blastn
[2023-03-14 12:39:18,833] [INFO] Running command: blastn -query OceanDNA-b40943/markers.fasta -db /var/lib/cwl/stgd5c34d04-8b7e-464c-8e1d-47888267857c/dqc_reference/reference_markers.fasta -out OceanDNA-b40943/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:39:19,446] [INFO] Task succeeded: Blastn
[2023-03-14 12:39:19,449] [INFO] Selected 28 target genomes.
[2023-03-14 12:39:19,449] [INFO] Target genome list was writen to OceanDNA-b40943/target_genomes.txt
[2023-03-14 12:39:19,467] [INFO] Task started: fastANI
[2023-03-14 12:39:19,467] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ed07a33-c067-46cc-bd08-49d57dca2b2c/OceanDNA-b40943.fa --refList OceanDNA-b40943/target_genomes.txt --output OceanDNA-b40943/fastani_result.tsv --threads 1
[2023-03-14 12:39:39,693] [INFO] Task succeeded: fastANI
[2023-03-14 12:39:39,693] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd5c34d04-8b7e-464c-8e1d-47888267857c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 12:39:39,693] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd5c34d04-8b7e-464c-8e1d-47888267857c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 12:39:39,694] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 12:39:39,694] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 12:39:39,694] [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 12:39:39,695] [INFO] DFAST Taxonomy check result was written to OceanDNA-b40943/tc_result.tsv
[2023-03-14 12:39:39,695] [INFO] ===== Taxonomy check completed =====
[2023-03-14 12:39:39,695] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 12:39:39,695] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd5c34d04-8b7e-464c-8e1d-47888267857c/dqc_reference/checkm_data
[2023-03-14 12:39:39,699] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 12:39:39,733] [INFO] Task started: CheckM
[2023-03-14 12:39:39,734] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b40943/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b40943/checkm_input OceanDNA-b40943/checkm_result
[2023-03-14 12:40:22,273] [INFO] Task succeeded: CheckM
[2023-03-14 12:40:22,273] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 12:40:22,278] [INFO] ===== Completeness check finished =====
[2023-03-14 12:40:22,278] [INFO] ===== Start GTDB Search =====
[2023-03-14 12:40:22,278] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b40943/markers.fasta)
[2023-03-14 12:40:22,280] [INFO] Task started: Blastn
[2023-03-14 12:40:22,280] [INFO] Running command: blastn -query OceanDNA-b40943/markers.fasta -db /var/lib/cwl/stgd5c34d04-8b7e-464c-8e1d-47888267857c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b40943/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:40:23,953] [INFO] Task succeeded: Blastn
[2023-03-14 12:40:23,954] [INFO] Selected 21 target genomes.
[2023-03-14 12:40:23,954] [INFO] Target genome list was writen to OceanDNA-b40943/target_genomes_gtdb.txt
[2023-03-14 12:40:23,980] [INFO] Task started: fastANI
[2023-03-14 12:40:23,980] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ed07a33-c067-46cc-bd08-49d57dca2b2c/OceanDNA-b40943.fa --refList OceanDNA-b40943/target_genomes_gtdb.txt --output OceanDNA-b40943/fastani_result_gtdb.tsv --threads 1
[2023-03-14 12:40:41,560] [INFO] Task succeeded: fastANI
[2023-03-14 12:40:41,566] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 12:40:41,566] [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_905478195.1	s__UBA9145 sp003483155	99.61	791	898	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	99.23	98.96	0.87	0.81	6	conclusive
GCA_002401885.1	s__UBA9145 sp002401885	78.6294	359	898	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016762995.1	s__UBA9145 sp016762995	78.1801	266	898	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	96.79	96.79	0.78	0.78	2	-
GCA_016762975.1	s__UBA9145 sp016762975	77.8966	250	898	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018661465.1	s__UBA9145 sp018661465	77.1397	102	898	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	99.99	99.98	0.99	0.97	14	-
GCA_002402175.1	s__UBA9145 sp002402175	76.4222	85	898	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	76.4071	62	898	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	76.3961	60	898	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	98.95	97.46	0.90	0.76	11	-
GCA_002731775.1	s__UBA9145 sp002731775	76.1923	68	898	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	98.77	98.59	0.87	0.85	6	-
--------------------------------------------------------------------------------
[2023-03-14 12:40:41,567] [INFO] GTDB search result was written to OceanDNA-b40943/result_gtdb.tsv
[2023-03-14 12:40:41,567] [INFO] ===== GTDB Search completed =====
[2023-03-14 12:40:41,568] [INFO] DFAST_QC result json was written to OceanDNA-b40943/dqc_result.json
[2023-03-14 12:40:41,568] [INFO] DFAST_QC completed!
[2023-03-14 12:40:41,568] [INFO] Total running time: 0h1m47s