[2023-03-16 09:15:41,451] [INFO] DFAST_QC pipeline started.
[2023-03-16 09:15:41,451] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 09:15:41,451] [INFO] DQC Reference Directory: /var/lib/cwl/stg4ef50d87-e33c-41b3-ad0f-c6973c658cea/dqc_reference
[2023-03-16 09:15:42,555] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 09:15:42,555] [INFO] Task started: Prodigal
[2023-03-16 09:15:42,555] [INFO] Running command: cat /var/lib/cwl/stg96b5d4eb-44af-4d49-8f41-0da04e2b4bcf/OceanDNA-b33510.fa | prodigal -d OceanDNA-b33510/cds.fna -a OceanDNA-b33510/protein.faa -g 11 -q > /dev/null
[2023-03-16 09:15:52,805] [INFO] Task succeeded: Prodigal
[2023-03-16 09:15:52,805] [INFO] Task started: HMMsearch
[2023-03-16 09:15:52,805] [INFO] Running command: hmmsearch --tblout OceanDNA-b33510/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4ef50d87-e33c-41b3-ad0f-c6973c658cea/dqc_reference/reference_markers.hmm OceanDNA-b33510/protein.faa > /dev/null
[2023-03-16 09:15:52,957] [INFO] Task succeeded: HMMsearch
[2023-03-16 09:15:52,957] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg96b5d4eb-44af-4d49-8f41-0da04e2b4bcf/OceanDNA-b33510.fa]
[2023-03-16 09:15:52,980] [INFO] Query marker FASTA was written to OceanDNA-b33510/markers.fasta
[2023-03-16 09:15:52,981] [INFO] Task started: Blastn
[2023-03-16 09:15:52,981] [INFO] Running command: blastn -query OceanDNA-b33510/markers.fasta -db /var/lib/cwl/stg4ef50d87-e33c-41b3-ad0f-c6973c658cea/dqc_reference/reference_markers.fasta -out OceanDNA-b33510/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:15:53,516] [INFO] Task succeeded: Blastn
[2023-03-16 09:15:53,517] [INFO] Selected 10 target genomes.
[2023-03-16 09:15:53,517] [INFO] Target genome list was writen to OceanDNA-b33510/target_genomes.txt
[2023-03-16 09:15:53,523] [INFO] Task started: fastANI
[2023-03-16 09:15:53,524] [INFO] Running command: fastANI --query /var/lib/cwl/stg96b5d4eb-44af-4d49-8f41-0da04e2b4bcf/OceanDNA-b33510.fa --refList OceanDNA-b33510/target_genomes.txt --output OceanDNA-b33510/fastani_result.tsv --threads 1
[2023-03-16 09:16:01,905] [INFO] Task succeeded: fastANI
[2023-03-16 09:16:01,905] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4ef50d87-e33c-41b3-ad0f-c6973c658cea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 09:16:01,905] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4ef50d87-e33c-41b3-ad0f-c6973c658cea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 09:16:01,912] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2023-03-16 09:16:01,912] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-16 09:16:01,912] [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
Ralstonia insidiosa	strain=CCUG 46789	GCA_008801405.1	190721	190721	type	True	97.1909	172	190	95	conclusive
Ralstonia pickettii	strain=FDAARGOS_1535	GCA_020341455.1	329	329	type	True	86.2281	158	190	95	below_threshold
Ralstonia pickettii	strain=ATCC 27511	GCA_000743455.1	329	329	type	True	85.7791	153	190	95	below_threshold
Ralstonia pickettii	strain=NBRC 102503	GCA_001544155.1	329	329	type	True	85.7431	152	190	95	below_threshold
Ralstonia mannitolilytica	strain=LMG 6866	GCA_905397375.1	105219	105219	type	True	85.5242	146	190	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_024925465.1	1310165	1310165	type	True	83.3829	131	190	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_919586305.1	1310165	1310165	type	True	83.3377	129	190	95	below_threshold
Cupriavidus numazuensis	strain=LMG 26411	GCA_905397435.1	221992	221992	type	True	79.2839	75	190	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 09:16:01,912] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33510/tc_result.tsv
[2023-03-16 09:16:01,912] [INFO] ===== Taxonomy check completed =====
[2023-03-16 09:16:01,912] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 09:16:01,912] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4ef50d87-e33c-41b3-ad0f-c6973c658cea/dqc_reference/checkm_data
[2023-03-16 09:16:01,913] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 09:16:01,917] [INFO] Task started: CheckM
[2023-03-16 09:16:01,917] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33510/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33510/checkm_input OceanDNA-b33510/checkm_result
[2023-03-16 09:16:32,351] [INFO] Task succeeded: CheckM
[2023-03-16 09:16:32,351] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 56.21%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 09:16:32,354] [INFO] ===== Completeness check finished =====
[2023-03-16 09:16:32,354] [INFO] ===== Start GTDB Search =====
[2023-03-16 09:16:32,354] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33510/markers.fasta)
[2023-03-16 09:16:32,355] [INFO] Task started: Blastn
[2023-03-16 09:16:32,355] [INFO] Running command: blastn -query OceanDNA-b33510/markers.fasta -db /var/lib/cwl/stg4ef50d87-e33c-41b3-ad0f-c6973c658cea/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33510/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:16:33,111] [INFO] Task succeeded: Blastn
[2023-03-16 09:16:33,112] [INFO] Selected 8 target genomes.
[2023-03-16 09:16:33,112] [INFO] Target genome list was writen to OceanDNA-b33510/target_genomes_gtdb.txt
[2023-03-16 09:16:33,125] [INFO] Task started: fastANI
[2023-03-16 09:16:33,125] [INFO] Running command: fastANI --query /var/lib/cwl/stg96b5d4eb-44af-4d49-8f41-0da04e2b4bcf/OceanDNA-b33510.fa --refList OceanDNA-b33510/target_genomes_gtdb.txt --output OceanDNA-b33510/fastani_result_gtdb.tsv --threads 1
[2023-03-16 09:16:39,682] [INFO] Task succeeded: fastANI
[2023-03-16 09:16:39,688] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 09:16:39,688] [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
GCF_008801405.1	s__Ralstonia insidiosa	97.1909	172	190	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ralstonia	95.0	97.92	96.99	0.90	0.85	9	conclusive
GCF_001078575.1	s__Ralstonia sp001078575	93.0073	168	190	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ralstonia	95.0	99.81	99.41	0.97	0.93	9	-
GCF_016429285.1	s__Ralstonia sp016429285	91.2481	159	190	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ralstonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000801955.1	s__Ralstonia sp000801955	90.0419	160	190	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ralstonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000607165.1	s__Ralstonia pickettii_A	86.7759	153	190	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ralstonia	95.0	99.13	99.13	0.91	0.91	2	-
GCA_002298975.1	s__Ralstonia sp002298975	86.495	146	190	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ralstonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003851545.1	s__Ralstonia sp003851545	86.1998	143	190	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ralstonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007997035.1	s__Ralstonia sp007997035	85.9881	141	190	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ralstonia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 09:16:39,688] [INFO] GTDB search result was written to OceanDNA-b33510/result_gtdb.tsv
[2023-03-16 09:16:39,688] [INFO] ===== GTDB Search completed =====
[2023-03-16 09:16:39,689] [INFO] DFAST_QC result json was written to OceanDNA-b33510/dqc_result.json
[2023-03-16 09:16:39,689] [INFO] DFAST_QC completed!
[2023-03-16 09:16:39,689] [INFO] Total running time: 0h0m58s