[2023-03-19 03:22:59,885] [INFO] DFAST_QC pipeline started.
[2023-03-19 03:22:59,887] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 03:22:59,887] [INFO] DQC Reference Directory: /var/lib/cwl/stg10fc97e4-3e78-46ce-9865-3dc743fb43d8/dqc_reference
[2023-03-19 03:23:00,967] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 03:23:00,967] [INFO] Task started: Prodigal
[2023-03-19 03:23:00,968] [INFO] Running command: cat /var/lib/cwl/stg8461b7cc-27b0-4a72-a04f-876216f133fa/OceanDNA-b40777.fa | prodigal -d OceanDNA-b40777/cds.fna -a OceanDNA-b40777/protein.faa -g 11 -q > /dev/null
[2023-03-19 03:23:19,813] [INFO] Task succeeded: Prodigal
[2023-03-19 03:23:19,813] [INFO] Task started: HMMsearch
[2023-03-19 03:23:19,813] [INFO] Running command: hmmsearch --tblout OceanDNA-b40777/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg10fc97e4-3e78-46ce-9865-3dc743fb43d8/dqc_reference/reference_markers.hmm OceanDNA-b40777/protein.faa > /dev/null
[2023-03-19 03:23:20,020] [INFO] Task succeeded: HMMsearch
[2023-03-19 03:23:20,021] [INFO] Found 6/6 markers.
[2023-03-19 03:23:20,076] [INFO] Query marker FASTA was written to OceanDNA-b40777/markers.fasta
[2023-03-19 03:23:20,076] [INFO] Task started: Blastn
[2023-03-19 03:23:20,076] [INFO] Running command: blastn -query OceanDNA-b40777/markers.fasta -db /var/lib/cwl/stg10fc97e4-3e78-46ce-9865-3dc743fb43d8/dqc_reference/reference_markers.fasta -out OceanDNA-b40777/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:23:20,688] [INFO] Task succeeded: Blastn
[2023-03-19 03:23:20,710] [INFO] Selected 34 target genomes.
[2023-03-19 03:23:20,710] [INFO] Target genome list was writen to OceanDNA-b40777/target_genomes.txt
[2023-03-19 03:23:20,729] [INFO] Task started: fastANI
[2023-03-19 03:23:20,729] [INFO] Running command: fastANI --query /var/lib/cwl/stg8461b7cc-27b0-4a72-a04f-876216f133fa/OceanDNA-b40777.fa --refList OceanDNA-b40777/target_genomes.txt --output OceanDNA-b40777/fastani_result.tsv --threads 1
[2023-03-19 03:23:43,757] [INFO] Task succeeded: fastANI
[2023-03-19 03:23:43,757] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg10fc97e4-3e78-46ce-9865-3dc743fb43d8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 03:23:43,758] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg10fc97e4-3e78-46ce-9865-3dc743fb43d8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 03:23:43,758] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 03:23:43,758] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 03:23:43,758] [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
--------------------------------------------------------------------------------
[2023-03-19 03:23:43,761] [INFO] DFAST Taxonomy check result was written to OceanDNA-b40777/tc_result.tsv
[2023-03-19 03:23:43,764] [INFO] ===== Taxonomy check completed =====
[2023-03-19 03:23:43,764] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 03:23:43,764] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg10fc97e4-3e78-46ce-9865-3dc743fb43d8/dqc_reference/checkm_data
[2023-03-19 03:23:43,767] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 03:23:43,774] [INFO] Task started: CheckM
[2023-03-19 03:23:43,774] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b40777/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b40777/checkm_input OceanDNA-b40777/checkm_result
[2023-03-19 03:24:32,043] [INFO] Task succeeded: CheckM
[2023-03-19 03:24:32,044] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 03:24:32,138] [INFO] ===== Completeness check finished =====
[2023-03-19 03:24:32,138] [INFO] ===== Start GTDB Search =====
[2023-03-19 03:24:32,138] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b40777/markers.fasta)
[2023-03-19 03:24:32,139] [INFO] Task started: Blastn
[2023-03-19 03:24:32,139] [INFO] Running command: blastn -query OceanDNA-b40777/markers.fasta -db /var/lib/cwl/stg10fc97e4-3e78-46ce-9865-3dc743fb43d8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b40777/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:24:33,159] [INFO] Task succeeded: Blastn
[2023-03-19 03:24:33,165] [INFO] Selected 20 target genomes.
[2023-03-19 03:24:33,165] [INFO] Target genome list was writen to OceanDNA-b40777/target_genomes_gtdb.txt
[2023-03-19 03:24:33,362] [INFO] Task started: fastANI
[2023-03-19 03:24:33,363] [INFO] Running command: fastANI --query /var/lib/cwl/stg8461b7cc-27b0-4a72-a04f-876216f133fa/OceanDNA-b40777.fa --refList OceanDNA-b40777/target_genomes_gtdb.txt --output OceanDNA-b40777/fastani_result_gtdb.tsv --threads 1
[2023-03-19 03:24:45,246] [INFO] Task succeeded: fastANI
[2023-03-19 03:24:45,252] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 03:24:45,252] [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_002477465.1	s__UBA9145 sp002477465	99.7831	992	1044	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	98.95	97.46	0.90	0.76	11	conclusive
GCA_002684935.1	s__UBA9145 sp002684935	91.4737	836	1044	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	98.47	98.41	0.83	0.81	3	-
GCA_002729315.1	s__UBA9145 sp002729315	76.9102	80	1044	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008081045.1	s__UBA9145 sp008081045	76.6492	129	1044	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	98.92	98.40	0.89	0.82	4	-
GCA_902597095.1	s__UBA9145 sp902597095	76.6132	102	1044	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012103535.1	s__UBA9145 sp012103535	76.2375	71	1044	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	76.0223	61	1044	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	99.99	99.98	0.99	0.97	14	-
GCA_002730035.1	s__UBA9145 sp002730035	75.9715	73	1044	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	99.69	99.69	0.91	0.91	2	-
GCA_009692305.1	s__UBA9145 sp009692305	75.6885	63	1044	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 03:24:45,262] [INFO] GTDB search result was written to OceanDNA-b40777/result_gtdb.tsv
[2023-03-19 03:24:45,283] [INFO] ===== GTDB Search completed =====
[2023-03-19 03:24:45,296] [INFO] DFAST_QC result json was written to OceanDNA-b40777/dqc_result.json
[2023-03-19 03:24:45,296] [INFO] DFAST_QC completed!
[2023-03-19 03:24:45,296] [INFO] Total running time: 0h1m45s