[2024-01-24 11:52:49,734] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:52:49,736] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:52:49,736] [INFO] DQC Reference Directory: /var/lib/cwl/stgbc9e5b10-07d9-4f28-812b-6ef494815e37/dqc_reference
[2024-01-24 11:52:50,925] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:52:50,926] [INFO] Task started: Prodigal
[2024-01-24 11:52:50,926] [INFO] Running command: gunzip -c /var/lib/cwl/stg0c013e6b-8b9d-4ffd-9ce6-28d77e889e7e/GCF_016466415.2_ASM1646641v2_genomic.fna.gz | prodigal -d GCF_016466415.2_ASM1646641v2_genomic.fna/cds.fna -a GCF_016466415.2_ASM1646641v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:53:07,749] [INFO] Task succeeded: Prodigal
[2024-01-24 11:53:07,750] [INFO] Task started: HMMsearch
[2024-01-24 11:53:07,750] [INFO] Running command: hmmsearch --tblout GCF_016466415.2_ASM1646641v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbc9e5b10-07d9-4f28-812b-6ef494815e37/dqc_reference/reference_markers.hmm GCF_016466415.2_ASM1646641v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:53:08,047] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:53:08,049] [INFO] Found 6/6 markers.
[2024-01-24 11:53:08,091] [INFO] Query marker FASTA was written to GCF_016466415.2_ASM1646641v2_genomic.fna/markers.fasta
[2024-01-24 11:53:08,092] [INFO] Task started: Blastn
[2024-01-24 11:53:08,092] [INFO] Running command: blastn -query GCF_016466415.2_ASM1646641v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgbc9e5b10-07d9-4f28-812b-6ef494815e37/dqc_reference/reference_markers.fasta -out GCF_016466415.2_ASM1646641v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:53:09,044] [INFO] Task succeeded: Blastn
[2024-01-24 11:53:09,048] [INFO] Selected 10 target genomes.
[2024-01-24 11:53:09,049] [INFO] Target genome list was writen to GCF_016466415.2_ASM1646641v2_genomic.fna/target_genomes.txt
[2024-01-24 11:53:09,053] [INFO] Task started: fastANI
[2024-01-24 11:53:09,053] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c013e6b-8b9d-4ffd-9ce6-28d77e889e7e/GCF_016466415.2_ASM1646641v2_genomic.fna.gz --refList GCF_016466415.2_ASM1646641v2_genomic.fna/target_genomes.txt --output GCF_016466415.2_ASM1646641v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:53:20,821] [INFO] Task succeeded: fastANI
[2024-01-24 11:53:20,822] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbc9e5b10-07d9-4f28-812b-6ef494815e37/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:53:20,822] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbc9e5b10-07d9-4f28-812b-6ef494815e37/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:53:20,835] [INFO] Found 10 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 11:53:20,835] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:53:20,835] [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=K-288	GCA_016466415.2	329	329	type	True	100.0	1609	1609	95	conclusive
Ralstonia pickettii	strain=FDAARGOS_1535	GCA_020341455.1	329	329	type	True	99.9877	1604	1609	95	conclusive
Ralstonia pickettii	strain=NCTC11149	GCA_900455835.1	329	329	type	True	99.9839	1589	1609	95	conclusive
Ralstonia pickettii	strain=ATCC 27511	GCA_000743455.1	329	329	type	True	99.9723	1581	1609	95	conclusive
Ralstonia pickettii	strain=NBRC 102503	GCA_001544155.1	329	329	type	True	99.9687	1544	1609	95	conclusive
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_024925465.1	1310165	1310165	type	True	84.8603	1039	1609	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_919586305.1	1310165	1310165	type	True	84.8546	1017	1609	95	below_threshold
Burkholderia ubonensis	strain=LMG 20358	GCA_902833085.1	101571	101571	type	True	78.517	542	1609	95	below_threshold
Burkholderia ubonensis		GCA_902499185.1	101571	101571	type	True	78.4569	526	1609	95	below_threshold
Paraburkholderia azotifigens	strain=NF 2-5-3	GCA_007995085.1	2057004	2057004	type	True	78.1635	473	1609	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:53:20,837] [INFO] DFAST Taxonomy check result was written to GCF_016466415.2_ASM1646641v2_genomic.fna/tc_result.tsv
[2024-01-24 11:53:20,837] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:53:20,837] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:53:20,837] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbc9e5b10-07d9-4f28-812b-6ef494815e37/dqc_reference/checkm_data
[2024-01-24 11:53:20,838] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:53:20,883] [INFO] Task started: CheckM
[2024-01-24 11:53:20,884] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016466415.2_ASM1646641v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016466415.2_ASM1646641v2_genomic.fna/checkm_input GCF_016466415.2_ASM1646641v2_genomic.fna/checkm_result
[2024-01-24 11:54:18,115] [INFO] Task succeeded: CheckM
[2024-01-24 11:54:18,117] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:54:18,138] [INFO] ===== Completeness check finished =====
[2024-01-24 11:54:18,138] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:54:18,139] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016466415.2_ASM1646641v2_genomic.fna/markers.fasta)
[2024-01-24 11:54:18,139] [INFO] Task started: Blastn
[2024-01-24 11:54:18,139] [INFO] Running command: blastn -query GCF_016466415.2_ASM1646641v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgbc9e5b10-07d9-4f28-812b-6ef494815e37/dqc_reference/reference_markers_gtdb.fasta -out GCF_016466415.2_ASM1646641v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:54:19,969] [INFO] Task succeeded: Blastn
[2024-01-24 11:54:19,973] [INFO] Selected 8 target genomes.
[2024-01-24 11:54:19,973] [INFO] Target genome list was writen to GCF_016466415.2_ASM1646641v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:54:19,985] [INFO] Task started: fastANI
[2024-01-24 11:54:19,986] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c013e6b-8b9d-4ffd-9ce6-28d77e889e7e/GCF_016466415.2_ASM1646641v2_genomic.fna.gz --refList GCF_016466415.2_ASM1646641v2_genomic.fna/target_genomes_gtdb.txt --output GCF_016466415.2_ASM1646641v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:54:31,027] [INFO] Task succeeded: fastANI
[2024-01-24 11:54:31,040] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:54:31,041] [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	99.9999	1608	1609	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	94.3217	1403	1609	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	92.8374	1374	1609	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	92.218	1271	1609	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	91.5419	1381	1609	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	91.3769	1393	1609	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	91.2017	1379	1609	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	87.0599	1260	1609	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 11:54:31,043] [INFO] GTDB search result was written to GCF_016466415.2_ASM1646641v2_genomic.fna/result_gtdb.tsv
[2024-01-24 11:54:31,044] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:54:31,046] [INFO] DFAST_QC result json was written to GCF_016466415.2_ASM1646641v2_genomic.fna/dqc_result.json
[2024-01-24 11:54:31,047] [INFO] DFAST_QC completed!
[2024-01-24 11:54:31,047] [INFO] Total running time: 0h1m41s