[2023-06-05 00:14:32,692] [INFO] DFAST_QC pipeline started.
[2023-06-05 00:14:32,694] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 00:14:32,694] [INFO] DQC Reference Directory: /var/lib/cwl/stgcdd9fa88-baea-4073-8cbf-7c8e8b61fdc3/dqc_reference
[2023-06-05 00:14:33,925] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 00:14:33,926] [INFO] Task started: Prodigal
[2023-06-05 00:14:33,927] [INFO] Running command: gunzip -c /var/lib/cwl/stga299e58e-ff5c-4236-8137-475215c56f4e/GCA_902524645.1_AG-895-L02_genomic.fna.gz | prodigal -d GCA_902524645.1_AG-895-L02_genomic.fna/cds.fna -a GCA_902524645.1_AG-895-L02_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 00:14:36,086] [INFO] Task succeeded: Prodigal
[2023-06-05 00:14:36,086] [INFO] Task started: HMMsearch
[2023-06-05 00:14:36,087] [INFO] Running command: hmmsearch --tblout GCA_902524645.1_AG-895-L02_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcdd9fa88-baea-4073-8cbf-7c8e8b61fdc3/dqc_reference/reference_markers.hmm GCA_902524645.1_AG-895-L02_genomic.fna/protein.faa > /dev/null
[2023-06-05 00:14:36,313] [INFO] Task succeeded: HMMsearch
[2023-06-05 00:14:36,314] [WARNING] Found 5/6 markers. [/var/lib/cwl/stga299e58e-ff5c-4236-8137-475215c56f4e/GCA_902524645.1_AG-895-L02_genomic.fna.gz]
[2023-06-05 00:14:36,336] [INFO] Query marker FASTA was written to GCA_902524645.1_AG-895-L02_genomic.fna/markers.fasta
[2023-06-05 00:14:36,336] [INFO] Task started: Blastn
[2023-06-05 00:14:36,337] [INFO] Running command: blastn -query GCA_902524645.1_AG-895-L02_genomic.fna/markers.fasta -db /var/lib/cwl/stgcdd9fa88-baea-4073-8cbf-7c8e8b61fdc3/dqc_reference/reference_markers.fasta -out GCA_902524645.1_AG-895-L02_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 00:14:36,917] [INFO] Task succeeded: Blastn
[2023-06-05 00:14:37,229] [INFO] Selected 11 target genomes.
[2023-06-05 00:14:37,229] [INFO] Target genome list was writen to GCA_902524645.1_AG-895-L02_genomic.fna/target_genomes.txt
[2023-06-05 00:14:37,231] [INFO] Task started: fastANI
[2023-06-05 00:14:37,232] [INFO] Running command: fastANI --query /var/lib/cwl/stga299e58e-ff5c-4236-8137-475215c56f4e/GCA_902524645.1_AG-895-L02_genomic.fna.gz --refList GCA_902524645.1_AG-895-L02_genomic.fna/target_genomes.txt --output GCA_902524645.1_AG-895-L02_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 00:14:41,460] [INFO] Task succeeded: fastANI
[2023-06-05 00:14:41,461] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcdd9fa88-baea-4073-8cbf-7c8e8b61fdc3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 00:14:41,461] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcdd9fa88-baea-4073-8cbf-7c8e8b61fdc3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 00:14:41,463] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 00:14:41,464] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 00:14:41,464] [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
--------------------------------------------------------------------------------
[2023-06-05 00:14:41,466] [INFO] DFAST Taxonomy check result was written to GCA_902524645.1_AG-895-L02_genomic.fna/tc_result.tsv
[2023-06-05 00:14:41,467] [INFO] ===== Taxonomy check completed =====
[2023-06-05 00:14:41,467] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 00:14:41,467] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcdd9fa88-baea-4073-8cbf-7c8e8b61fdc3/dqc_reference/checkm_data
[2023-06-05 00:14:41,471] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 00:14:41,487] [INFO] Task started: CheckM
[2023-06-05 00:14:41,487] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902524645.1_AG-895-L02_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902524645.1_AG-895-L02_genomic.fna/checkm_input GCA_902524645.1_AG-895-L02_genomic.fna/checkm_result
[2023-06-05 00:14:56,182] [INFO] Task succeeded: CheckM
[2023-06-05 00:14:56,183] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 00:14:56,202] [INFO] ===== Completeness check finished =====
[2023-06-05 00:14:56,203] [INFO] ===== Start GTDB Search =====
[2023-06-05 00:14:56,203] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902524645.1_AG-895-L02_genomic.fna/markers.fasta)
[2023-06-05 00:14:56,203] [INFO] Task started: Blastn
[2023-06-05 00:14:56,204] [INFO] Running command: blastn -query GCA_902524645.1_AG-895-L02_genomic.fna/markers.fasta -db /var/lib/cwl/stgcdd9fa88-baea-4073-8cbf-7c8e8b61fdc3/dqc_reference/reference_markers_gtdb.fasta -out GCA_902524645.1_AG-895-L02_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 00:14:57,077] [INFO] Task succeeded: Blastn
[2023-06-05 00:14:57,081] [INFO] Selected 8 target genomes.
[2023-06-05 00:14:57,081] [INFO] Target genome list was writen to GCA_902524645.1_AG-895-L02_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 00:14:57,087] [INFO] Task started: fastANI
[2023-06-05 00:14:57,087] [INFO] Running command: fastANI --query /var/lib/cwl/stga299e58e-ff5c-4236-8137-475215c56f4e/GCA_902524645.1_AG-895-L02_genomic.fna.gz --refList GCA_902524645.1_AG-895-L02_genomic.fna/target_genomes_gtdb.txt --output GCA_902524645.1_AG-895-L02_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 00:14:58,986] [INFO] Task succeeded: fastANI
[2023-06-05 00:14:59,000] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 00:14:59,000] [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_902570035.1	s__CACNYO01 sp902570035	97.3519	307	371	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__CACNYO01	95.0	96.39	95.41	0.82	0.78	11	conclusive
GCA_902594855.1	s__CACNYO01 sp902594855	93.8521	316	371	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__CACNYO01	95.0	96.60	95.51	0.88	0.82	11	-
GCA_902578495.1	s__CACNYO01 sp902578495	93.6683	298	371	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__CACNYO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902596665.1	s__CACNYO01 sp902596665	93.3308	325	371	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__CACNYO01	95.0	95.60	95.38	0.89	0.88	7	-
GCA_902589965.1	s__CACNYO01 sp902589965	92.2465	270	371	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__CACNYO01	95.0	95.54	95.01	0.78	0.76	10	-
GCA_902526045.1	s__CACNYO01 sp902526045	87.5818	305	371	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__CACNYO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902624765.1	s__CACNYO01 sp902624765	87.4393	207	371	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__CACNYO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902528485.1	s__CACNYO01 sp902528485	87.4105	177	371	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__CACNYO01	95.0	95.61	95.61	0.68	0.68	2	-
--------------------------------------------------------------------------------
[2023-06-05 00:14:59,002] [INFO] GTDB search result was written to GCA_902524645.1_AG-895-L02_genomic.fna/result_gtdb.tsv
[2023-06-05 00:14:59,002] [INFO] ===== GTDB Search completed =====
[2023-06-05 00:14:59,005] [INFO] DFAST_QC result json was written to GCA_902524645.1_AG-895-L02_genomic.fna/dqc_result.json
[2023-06-05 00:14:59,005] [INFO] DFAST_QC completed!
[2023-06-05 00:14:59,005] [INFO] Total running time: 0h0m26s