[2023-03-16 15:11:23,404] [INFO] DFAST_QC pipeline started.
[2023-03-16 15:11:23,404] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 15:11:23,404] [INFO] DQC Reference Directory: /var/lib/cwl/stgdea5088e-1734-465d-b588-f03995bc690e/dqc_reference
[2023-03-16 15:11:24,899] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 15:11:24,899] [INFO] Task started: Prodigal
[2023-03-16 15:11:24,899] [INFO] Running command: cat /var/lib/cwl/stgdf84fe9a-87c7-4437-82dd-af19858b8669/OceanDNA-b39458.fa | prodigal -d OceanDNA-b39458/cds.fna -a OceanDNA-b39458/protein.faa -g 11 -q > /dev/null
[2023-03-16 15:11:36,962] [INFO] Task succeeded: Prodigal
[2023-03-16 15:11:36,962] [INFO] Task started: HMMsearch
[2023-03-16 15:11:36,962] [INFO] Running command: hmmsearch --tblout OceanDNA-b39458/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdea5088e-1734-465d-b588-f03995bc690e/dqc_reference/reference_markers.hmm OceanDNA-b39458/protein.faa > /dev/null
[2023-03-16 15:11:37,155] [INFO] Task succeeded: HMMsearch
[2023-03-16 15:11:37,155] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgdf84fe9a-87c7-4437-82dd-af19858b8669/OceanDNA-b39458.fa]
[2023-03-16 15:11:37,169] [INFO] Query marker FASTA was written to OceanDNA-b39458/markers.fasta
[2023-03-16 15:11:37,170] [INFO] Task started: Blastn
[2023-03-16 15:11:37,170] [INFO] Running command: blastn -query OceanDNA-b39458/markers.fasta -db /var/lib/cwl/stgdea5088e-1734-465d-b588-f03995bc690e/dqc_reference/reference_markers.fasta -out OceanDNA-b39458/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 15:11:37,719] [INFO] Task succeeded: Blastn
[2023-03-16 15:11:37,719] [INFO] Selected 25 target genomes.
[2023-03-16 15:11:37,720] [INFO] Target genome list was writen to OceanDNA-b39458/target_genomes.txt
[2023-03-16 15:11:37,735] [INFO] Task started: fastANI
[2023-03-16 15:11:37,735] [INFO] Running command: fastANI --query /var/lib/cwl/stgdf84fe9a-87c7-4437-82dd-af19858b8669/OceanDNA-b39458.fa --refList OceanDNA-b39458/target_genomes.txt --output OceanDNA-b39458/fastani_result.tsv --threads 1
[2023-03-16 15:11:55,852] [INFO] Task succeeded: fastANI
[2023-03-16 15:11:55,852] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdea5088e-1734-465d-b588-f03995bc690e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 15:11:55,852] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdea5088e-1734-465d-b588-f03995bc690e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 15:11:55,852] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 15:11:55,852] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 15:11:55,853] [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
--------------------------------------------------------------------------------
[2023-03-16 15:11:55,853] [INFO] DFAST Taxonomy check result was written to OceanDNA-b39458/tc_result.tsv
[2023-03-16 15:11:55,853] [INFO] ===== Taxonomy check completed =====
[2023-03-16 15:11:55,853] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 15:11:55,853] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdea5088e-1734-465d-b588-f03995bc690e/dqc_reference/checkm_data
[2023-03-16 15:11:55,856] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 15:11:55,860] [INFO] Task started: CheckM
[2023-03-16 15:11:55,860] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b39458/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b39458/checkm_input OceanDNA-b39458/checkm_result
[2023-03-16 15:12:40,047] [INFO] Task succeeded: CheckM
[2023-03-16 15:12:40,048] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 15:12:40,050] [INFO] ===== Completeness check finished =====
[2023-03-16 15:12:40,050] [INFO] ===== Start GTDB Search =====
[2023-03-16 15:12:40,051] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b39458/markers.fasta)
[2023-03-16 15:12:40,052] [INFO] Task started: Blastn
[2023-03-16 15:12:40,052] [INFO] Running command: blastn -query OceanDNA-b39458/markers.fasta -db /var/lib/cwl/stgdea5088e-1734-465d-b588-f03995bc690e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b39458/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 15:12:40,946] [INFO] Task succeeded: Blastn
[2023-03-16 15:12:40,947] [INFO] Selected 20 target genomes.
[2023-03-16 15:12:40,947] [INFO] Target genome list was writen to OceanDNA-b39458/target_genomes_gtdb.txt
[2023-03-16 15:12:41,705] [INFO] Task started: fastANI
[2023-03-16 15:12:41,705] [INFO] Running command: fastANI --query /var/lib/cwl/stgdf84fe9a-87c7-4437-82dd-af19858b8669/OceanDNA-b39458.fa --refList OceanDNA-b39458/target_genomes_gtdb.txt --output OceanDNA-b39458/fastani_result_gtdb.tsv --threads 1
[2023-03-16 15:12:58,544] [INFO] Task succeeded: fastANI
[2023-03-16 15:12:58,550] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 15:12:58,550] [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_002685715.1	s__HTCC2207 sp002685715	93.6012	508	702	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004211905.1	s__HTCC2207 sp004211905	78.0651	59	702	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	98.48	98.48	0.76	0.76	2	-
GCA_018663035.1	s__HTCC2207 sp018663035	77.814	131	702	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.88	99.88	0.90	0.90	2	-
GCA_018664075.1	s__HTCC2207 sp018664075	77.8063	219	702	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.59	99.59	0.81	0.81	2	-
GCA_002334915.1	s__HTCC2207 sp002334915	77.8044	172	702	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.52	99.52	0.87	0.87	2	-
GCA_002378645.1	s__HTCC2207 sp002378645	77.7062	163	702	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.56	99.15	0.89	0.85	12	-
GCA_905182265.1	s__HTCC2207 sp905182265	77.4311	162	702	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182855.1	s__HTCC2207 sp905182855	77.0498	71	702	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001438605.1	s__HTCC2207 sp001438605	76.7247	71	702	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.34	98.71	0.91	0.87	10	-
--------------------------------------------------------------------------------
[2023-03-16 15:12:58,551] [INFO] GTDB search result was written to OceanDNA-b39458/result_gtdb.tsv
[2023-03-16 15:12:58,551] [INFO] ===== GTDB Search completed =====
[2023-03-16 15:12:58,552] [INFO] DFAST_QC result json was written to OceanDNA-b39458/dqc_result.json
[2023-03-16 15:12:58,552] [INFO] DFAST_QC completed!
[2023-03-16 15:12:58,552] [INFO] Total running time: 0h1m35s