[2024-01-24 11:26:26,283] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:26,286] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:26,286] [INFO] DQC Reference Directory: /var/lib/cwl/stg02a84e9a-41f3-417a-ada1-ac90f67ba3ba/dqc_reference
[2024-01-24 11:26:27,574] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:27,575] [INFO] Task started: Prodigal
[2024-01-24 11:26:27,575] [INFO] Running command: gunzip -c /var/lib/cwl/stg2f8548de-f096-44f1-a5eb-3ce537cb4ea7/GCF_900455835.1_51699_E01_genomic.fna.gz | prodigal -d GCF_900455835.1_51699_E01_genomic.fna/cds.fna -a GCF_900455835.1_51699_E01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:44,863] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:44,864] [INFO] Task started: HMMsearch
[2024-01-24 11:26:44,864] [INFO] Running command: hmmsearch --tblout GCF_900455835.1_51699_E01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg02a84e9a-41f3-417a-ada1-ac90f67ba3ba/dqc_reference/reference_markers.hmm GCF_900455835.1_51699_E01_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:45,255] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:45,256] [INFO] Found 6/6 markers.
[2024-01-24 11:26:45,295] [INFO] Query marker FASTA was written to GCF_900455835.1_51699_E01_genomic.fna/markers.fasta
[2024-01-24 11:26:45,296] [INFO] Task started: Blastn
[2024-01-24 11:26:45,296] [INFO] Running command: blastn -query GCF_900455835.1_51699_E01_genomic.fna/markers.fasta -db /var/lib/cwl/stg02a84e9a-41f3-417a-ada1-ac90f67ba3ba/dqc_reference/reference_markers.fasta -out GCF_900455835.1_51699_E01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:46,281] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:46,284] [INFO] Selected 10 target genomes.
[2024-01-24 11:26:46,285] [INFO] Target genome list was writen to GCF_900455835.1_51699_E01_genomic.fna/target_genomes.txt
[2024-01-24 11:26:46,289] [INFO] Task started: fastANI
[2024-01-24 11:26:46,289] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f8548de-f096-44f1-a5eb-3ce537cb4ea7/GCF_900455835.1_51699_E01_genomic.fna.gz --refList GCF_900455835.1_51699_E01_genomic.fna/target_genomes.txt --output GCF_900455835.1_51699_E01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:00,495] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:00,496] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg02a84e9a-41f3-417a-ada1-ac90f67ba3ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:00,496] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg02a84e9a-41f3-417a-ada1-ac90f67ba3ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:00,506] [INFO] Found 10 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 11:27:00,506] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:27:00,507] [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 pickettii	strain=NCTC11149	GCA_900455835.1	329	329	type	True	100.0	1596	1600	95	conclusive
Ralstonia pickettii	strain=FDAARGOS_1535	GCA_020341455.1	329	329	type	True	99.9993	1591	1600	95	conclusive
Ralstonia pickettii	strain=K-288	GCA_016466415.2	329	329	type	True	99.9902	1587	1600	95	conclusive
Ralstonia pickettii	strain=ATCC 27511	GCA_000743455.1	329	329	type	True	99.9785	1581	1600	95	conclusive
Ralstonia pickettii	strain=NBRC 102503	GCA_001544155.1	329	329	type	True	99.9771	1547	1600	95	conclusive
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_919586305.1	1310165	1310165	type	True	84.8148	1018	1600	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_024925465.1	1310165	1310165	type	True	84.7467	1060	1600	95	below_threshold
Burkholderia ubonensis	strain=LMG 20358	GCA_902833085.1	101571	101571	type	True	78.5246	530	1600	95	below_threshold
Burkholderia ubonensis		GCA_902499185.1	101571	101571	type	True	78.4237	520	1600	95	below_threshold
Paraburkholderia azotifigens	strain=NF 2-5-3	GCA_007995085.1	2057004	2057004	type	True	78.003	485	1600	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:00,508] [INFO] DFAST Taxonomy check result was written to GCF_900455835.1_51699_E01_genomic.fna/tc_result.tsv
[2024-01-24 11:27:00,509] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:00,509] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:00,509] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg02a84e9a-41f3-417a-ada1-ac90f67ba3ba/dqc_reference/checkm_data
[2024-01-24 11:27:00,510] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:00,558] [INFO] Task started: CheckM
[2024-01-24 11:27:00,559] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900455835.1_51699_E01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900455835.1_51699_E01_genomic.fna/checkm_input GCF_900455835.1_51699_E01_genomic.fna/checkm_result
[2024-01-24 11:27:57,087] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:57,089] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:57,109] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:57,109] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:57,110] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900455835.1_51699_E01_genomic.fna/markers.fasta)
[2024-01-24 11:27:57,110] [INFO] Task started: Blastn
[2024-01-24 11:27:57,110] [INFO] Running command: blastn -query GCF_900455835.1_51699_E01_genomic.fna/markers.fasta -db /var/lib/cwl/stg02a84e9a-41f3-417a-ada1-ac90f67ba3ba/dqc_reference/reference_markers_gtdb.fasta -out GCF_900455835.1_51699_E01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:58,941] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:58,960] [INFO] Selected 8 target genomes.
[2024-01-24 11:27:58,960] [INFO] Target genome list was writen to GCF_900455835.1_51699_E01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:58,968] [INFO] Task started: fastANI
[2024-01-24 11:27:58,968] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f8548de-f096-44f1-a5eb-3ce537cb4ea7/GCF_900455835.1_51699_E01_genomic.fna.gz --refList GCF_900455835.1_51699_E01_genomic.fna/target_genomes_gtdb.txt --output GCF_900455835.1_51699_E01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:28:09,587] [INFO] Task succeeded: fastANI
[2024-01-24 11:28:09,602] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:28:09,602] [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_016466415.1	s__Ralstonia pickettii	99.9902	1587	1600	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ralstonia	95.0	97.89	95.45	0.93	0.86	44	conclusive
GCF_000020205.1	s__Ralstonia pickettii_B	94.251	1395	1600	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ralstonia	95.0	98.08	96.31	0.87	0.83	22	-
GCF_000620465.1	s__Ralstonia sp000620465	92.9072	1372	1600	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ralstonia	95.0	96.59	96.59	0.94	0.94	2	-
GCF_007997035.1	s__Ralstonia sp007997035	92.2119	1278	1600	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ralstonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115545.1	s__Ralstonia sp900115545	91.6392	1378	1600	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ralstonia	95.0	98.84	98.84	0.97	0.97	2	-
GCF_000607165.1	s__Ralstonia pickettii_A	91.3854	1397	1600	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ralstonia	95.0	99.13	99.13	0.91	0.91	2	-
GCA_000955795.1	s__Ralstonia sp000955795	91.2561	1378	1600	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	87.0918	1247	1600	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ralstonia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:28:09,603] [INFO] GTDB search result was written to GCF_900455835.1_51699_E01_genomic.fna/result_gtdb.tsv
[2024-01-24 11:28:09,604] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:28:09,608] [INFO] DFAST_QC result json was written to GCF_900455835.1_51699_E01_genomic.fna/dqc_result.json
[2024-01-24 11:28:09,608] [INFO] DFAST_QC completed!
[2024-01-24 11:28:09,608] [INFO] Total running time: 0h1m43s