[2023-03-17 05:16:57,862] [INFO] DFAST_QC pipeline started.
[2023-03-17 05:16:57,862] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 05:16:57,862] [INFO] DQC Reference Directory: /var/lib/cwl/stgc708a4a4-044f-4a44-afac-86e46284274a/dqc_reference
[2023-03-17 05:16:59,367] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 05:16:59,367] [INFO] Task started: Prodigal
[2023-03-17 05:16:59,367] [INFO] Running command: cat /var/lib/cwl/stgaad69c4b-c96e-432e-b297-51b7ac10d10f/OceanDNA-b40162.fa | prodigal -d OceanDNA-b40162/cds.fna -a OceanDNA-b40162/protein.faa -g 11 -q > /dev/null
[2023-03-17 05:17:16,239] [INFO] Task succeeded: Prodigal
[2023-03-17 05:17:16,240] [INFO] Task started: HMMsearch
[2023-03-17 05:17:16,240] [INFO] Running command: hmmsearch --tblout OceanDNA-b40162/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc708a4a4-044f-4a44-afac-86e46284274a/dqc_reference/reference_markers.hmm OceanDNA-b40162/protein.faa > /dev/null
[2023-03-17 05:17:16,429] [INFO] Task succeeded: HMMsearch
[2023-03-17 05:17:16,429] [INFO] Found 6/6 markers.
[2023-03-17 05:17:16,446] [INFO] Query marker FASTA was written to OceanDNA-b40162/markers.fasta
[2023-03-17 05:17:16,447] [INFO] Task started: Blastn
[2023-03-17 05:17:16,447] [INFO] Running command: blastn -query OceanDNA-b40162/markers.fasta -db /var/lib/cwl/stgc708a4a4-044f-4a44-afac-86e46284274a/dqc_reference/reference_markers.fasta -out OceanDNA-b40162/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:17:17,069] [INFO] Task succeeded: Blastn
[2023-03-17 05:17:17,070] [INFO] Selected 27 target genomes.
[2023-03-17 05:17:17,070] [INFO] Target genome list was writen to OceanDNA-b40162/target_genomes.txt
[2023-03-17 05:17:17,297] [INFO] Task started: fastANI
[2023-03-17 05:17:17,297] [INFO] Running command: fastANI --query /var/lib/cwl/stgaad69c4b-c96e-432e-b297-51b7ac10d10f/OceanDNA-b40162.fa --refList OceanDNA-b40162/target_genomes.txt --output OceanDNA-b40162/fastani_result.tsv --threads 1
[2023-03-17 05:17:33,964] [INFO] Task succeeded: fastANI
[2023-03-17 05:17:33,965] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc708a4a4-044f-4a44-afac-86e46284274a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 05:17:33,965] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc708a4a4-044f-4a44-afac-86e46284274a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 05:17:33,968] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 05:17:33,968] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 05:17:33,968] [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
Porticoccus hydrocarbonoclasticus	strain=MCTG13d	GCA_000744735.1	1073414	1073414	type	True	94.7306	762	907	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 05:17:33,968] [INFO] DFAST Taxonomy check result was written to OceanDNA-b40162/tc_result.tsv
[2023-03-17 05:17:33,968] [INFO] ===== Taxonomy check completed =====
[2023-03-17 05:17:33,969] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 05:17:33,969] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc708a4a4-044f-4a44-afac-86e46284274a/dqc_reference/checkm_data
[2023-03-17 05:17:33,969] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 05:17:33,974] [INFO] Task started: CheckM
[2023-03-17 05:17:33,974] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b40162/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b40162/checkm_input OceanDNA-b40162/checkm_result
[2023-03-17 05:18:18,171] [INFO] Task succeeded: CheckM
[2023-03-17 05:18:18,171] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 05:18:18,174] [INFO] ===== Completeness check finished =====
[2023-03-17 05:18:18,174] [INFO] ===== Start GTDB Search =====
[2023-03-17 05:18:18,175] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b40162/markers.fasta)
[2023-03-17 05:18:18,176] [INFO] Task started: Blastn
[2023-03-17 05:18:18,176] [INFO] Running command: blastn -query OceanDNA-b40162/markers.fasta -db /var/lib/cwl/stgc708a4a4-044f-4a44-afac-86e46284274a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b40162/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:18:19,223] [INFO] Task succeeded: Blastn
[2023-03-17 05:18:19,224] [INFO] Selected 11 target genomes.
[2023-03-17 05:18:19,225] [INFO] Target genome list was writen to OceanDNA-b40162/target_genomes_gtdb.txt
[2023-03-17 05:18:19,262] [INFO] Task started: fastANI
[2023-03-17 05:18:19,262] [INFO] Running command: fastANI --query /var/lib/cwl/stgaad69c4b-c96e-432e-b297-51b7ac10d10f/OceanDNA-b40162.fa --refList OceanDNA-b40162/target_genomes_gtdb.txt --output OceanDNA-b40162/fastani_result_gtdb.tsv --threads 1
[2023-03-17 05:18:24,679] [INFO] Task succeeded: fastANI
[2023-03-17 05:18:24,685] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 05:18:24,685] [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_002707685.1	s__Porticoccus sp002707685	99.6695	875	907	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__Porticoccus	95.0	99.58	99.58	0.96	0.96	2	conclusive
GCF_000744735.1	s__Porticoccus hydrocarbonoclasticus	94.7306	762	907	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__Porticoccus	95.0	99.20	98.73	0.89	0.78	4	-
GCA_002341315.1	s__Porticoccus sp002341315	94.2016	718	907	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__Porticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733125.1	s__Porticoccus sp002733125	93.1157	631	907	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__Porticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006226995.1	s__Porticoccus sp006226995	77.1431	88	907	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__Porticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002390285.1	s__Porticoccus sp002390285	76.998	66	907	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__Porticoccus	95.0	99.85	99.48	0.95	0.89	6	-
GCA_006227015.1	s__Porticoccus sp006227015	76.9669	91	907	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__Porticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002746985.1	s__Porticoccus sp002746985	76.901	69	907	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__Porticoccus	95.0	97.07	97.07	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2023-03-17 05:18:24,687] [INFO] GTDB search result was written to OceanDNA-b40162/result_gtdb.tsv
[2023-03-17 05:18:24,688] [INFO] ===== GTDB Search completed =====
[2023-03-17 05:18:24,690] [INFO] DFAST_QC result json was written to OceanDNA-b40162/dqc_result.json
[2023-03-17 05:18:24,690] [INFO] DFAST_QC completed!
[2023-03-17 05:18:24,690] [INFO] Total running time: 0h1m27s