[2024-01-24 12:44:43,800] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:43,802] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:43,802] [INFO] DQC Reference Directory: /var/lib/cwl/stg8b84d794-6b63-4c8d-970d-9b71b5ed0850/dqc_reference
[2024-01-24 12:44:45,244] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:45,245] [INFO] Task started: Prodigal
[2024-01-24 12:44:45,245] [INFO] Running command: gunzip -c /var/lib/cwl/stg7f31dfa7-3337-4034-9c3d-2697729a1d29/GCF_023955645.1_ASM2395564v1_genomic.fna.gz | prodigal -d GCF_023955645.1_ASM2395564v1_genomic.fna/cds.fna -a GCF_023955645.1_ASM2395564v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:45:06,431] [INFO] Task succeeded: Prodigal
[2024-01-24 12:45:06,431] [INFO] Task started: HMMsearch
[2024-01-24 12:45:06,431] [INFO] Running command: hmmsearch --tblout GCF_023955645.1_ASM2395564v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8b84d794-6b63-4c8d-970d-9b71b5ed0850/dqc_reference/reference_markers.hmm GCF_023955645.1_ASM2395564v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:45:06,795] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:45:06,796] [INFO] Found 6/6 markers.
[2024-01-24 12:45:06,859] [INFO] Query marker FASTA was written to GCF_023955645.1_ASM2395564v1_genomic.fna/markers.fasta
[2024-01-24 12:45:06,860] [INFO] Task started: Blastn
[2024-01-24 12:45:06,860] [INFO] Running command: blastn -query GCF_023955645.1_ASM2395564v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8b84d794-6b63-4c8d-970d-9b71b5ed0850/dqc_reference/reference_markers.fasta -out GCF_023955645.1_ASM2395564v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:07,913] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:07,917] [INFO] Selected 11 target genomes.
[2024-01-24 12:45:07,917] [INFO] Target genome list was writen to GCF_023955645.1_ASM2395564v1_genomic.fna/target_genomes.txt
[2024-01-24 12:45:07,935] [INFO] Task started: fastANI
[2024-01-24 12:45:07,936] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f31dfa7-3337-4034-9c3d-2697729a1d29/GCF_023955645.1_ASM2395564v1_genomic.fna.gz --refList GCF_023955645.1_ASM2395564v1_genomic.fna/target_genomes.txt --output GCF_023955645.1_ASM2395564v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:23,162] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:23,163] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8b84d794-6b63-4c8d-970d-9b71b5ed0850/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:23,163] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8b84d794-6b63-4c8d-970d-9b71b5ed0850/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:23,173] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:45:23,173] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:45:23,174] [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=NBRC 102503	GCA_001544155.1	329	329	type	True	91.56	1358	1860	95	below_threshold
Ralstonia pickettii	strain=FDAARGOS_1535	GCA_020341455.1	329	329	type	True	91.49	1387	1860	95	below_threshold
Ralstonia pickettii	strain=K-288	GCA_016466415.2	329	329	type	True	91.4579	1389	1860	95	below_threshold
Ralstonia pickettii	strain=ATCC 27511	GCA_000743455.1	329	329	type	True	91.4577	1378	1860	95	below_threshold
Ralstonia pickettii	strain=NCTC11149	GCA_900455835.1	329	329	type	True	91.4442	1374	1860	95	below_threshold
Ralstonia insidiosa	strain=CCUG 46789	GCA_008801405.1	190721	190721	type	True	87.0123	1350	1860	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_919586305.1	1310165	1310165	type	True	84.6636	1066	1860	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_024925465.1	1310165	1310165	type	True	84.6139	1083	1860	95	below_threshold
Cupriavidus numazuensis	strain=LMG 26411	GCA_905397435.1	221992	221992	type	True	80.0071	673	1860	95	below_threshold
Burkholderia ubonensis	strain=LMG 20358	GCA_902833085.1	101571	101571	type	True	78.6635	523	1860	95	below_threshold
Burkholderia ubonensis		GCA_902499185.1	101571	101571	type	True	78.5724	513	1860	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:23,175] [INFO] DFAST Taxonomy check result was written to GCF_023955645.1_ASM2395564v1_genomic.fna/tc_result.tsv
[2024-01-24 12:45:23,176] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:23,176] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:23,177] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8b84d794-6b63-4c8d-970d-9b71b5ed0850/dqc_reference/checkm_data
[2024-01-24 12:45:23,179] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:23,236] [INFO] Task started: CheckM
[2024-01-24 12:45:23,237] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_023955645.1_ASM2395564v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_023955645.1_ASM2395564v1_genomic.fna/checkm_input GCF_023955645.1_ASM2395564v1_genomic.fna/checkm_result
[2024-01-24 12:46:29,270] [INFO] Task succeeded: CheckM
[2024-01-24 12:46:29,272] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:46:29,305] [INFO] ===== Completeness check finished =====
[2024-01-24 12:46:29,305] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:46:29,306] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_023955645.1_ASM2395564v1_genomic.fna/markers.fasta)
[2024-01-24 12:46:29,306] [INFO] Task started: Blastn
[2024-01-24 12:46:29,307] [INFO] Running command: blastn -query GCF_023955645.1_ASM2395564v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8b84d794-6b63-4c8d-970d-9b71b5ed0850/dqc_reference/reference_markers_gtdb.fasta -out GCF_023955645.1_ASM2395564v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:46:31,164] [INFO] Task succeeded: Blastn
[2024-01-24 12:46:31,169] [INFO] Selected 7 target genomes.
[2024-01-24 12:46:31,169] [INFO] Target genome list was writen to GCF_023955645.1_ASM2395564v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:46:31,198] [INFO] Task started: fastANI
[2024-01-24 12:46:31,198] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f31dfa7-3337-4034-9c3d-2697729a1d29/GCF_023955645.1_ASM2395564v1_genomic.fna.gz --refList GCF_023955645.1_ASM2395564v1_genomic.fna/target_genomes_gtdb.txt --output GCF_023955645.1_ASM2395564v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:46:40,898] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:40,909] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:46:40,909] [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_900115545.1	s__Ralstonia sp900115545	95.6109	1648	1860	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ralstonia	95.0	98.84	98.84	0.97	0.97	2	conclusive
GCA_000955795.1	s__Ralstonia sp000955795	94.1463	1572	1860	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	93.5749	1532	1860	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ralstonia	95.0	99.13	99.13	0.91	0.91	2	-
GCF_000620465.1	s__Ralstonia sp000620465	91.9584	1543	1860	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	91.8527	1470	1860	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ralstonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016466415.1	s__Ralstonia pickettii	91.4579	1389	1860	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ralstonia	95.0	97.89	95.45	0.93	0.86	44	-
GCF_000020205.1	s__Ralstonia pickettii_B	91.4258	1365	1860	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ralstonia	95.0	98.08	96.31	0.87	0.83	22	-
--------------------------------------------------------------------------------
[2024-01-24 12:46:40,911] [INFO] GTDB search result was written to GCF_023955645.1_ASM2395564v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:46:40,912] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:46:40,915] [INFO] DFAST_QC result json was written to GCF_023955645.1_ASM2395564v1_genomic.fna/dqc_result.json
[2024-01-24 12:46:40,915] [INFO] DFAST_QC completed!
[2024-01-24 12:46:40,915] [INFO] Total running time: 0h1m57s