[2024-01-24 10:47:40,959] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:40,965] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:40,965] [INFO] DQC Reference Directory: /var/lib/cwl/stg3c6a456f-7e6b-4831-adcd-f226a1f7b96e/dqc_reference
[2024-01-24 10:47:44,786] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:44,789] [INFO] Task started: Prodigal
[2024-01-24 10:47:44,789] [INFO] Running command: gunzip -c /var/lib/cwl/stgfd65fcef-a3d6-412e-be95-4c15a1f1c75b/GCF_905397375.1_LMG_6866_genomic.fna.gz | prodigal -d GCF_905397375.1_LMG_6866_genomic.fna/cds.fna -a GCF_905397375.1_LMG_6866_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:48:01,283] [INFO] Task succeeded: Prodigal
[2024-01-24 10:48:01,284] [INFO] Task started: HMMsearch
[2024-01-24 10:48:01,284] [INFO] Running command: hmmsearch --tblout GCF_905397375.1_LMG_6866_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3c6a456f-7e6b-4831-adcd-f226a1f7b96e/dqc_reference/reference_markers.hmm GCF_905397375.1_LMG_6866_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:48:01,594] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:48:01,596] [INFO] Found 6/6 markers.
[2024-01-24 10:48:01,642] [INFO] Query marker FASTA was written to GCF_905397375.1_LMG_6866_genomic.fna/markers.fasta
[2024-01-24 10:48:01,643] [INFO] Task started: Blastn
[2024-01-24 10:48:01,643] [INFO] Running command: blastn -query GCF_905397375.1_LMG_6866_genomic.fna/markers.fasta -db /var/lib/cwl/stg3c6a456f-7e6b-4831-adcd-f226a1f7b96e/dqc_reference/reference_markers.fasta -out GCF_905397375.1_LMG_6866_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:02,708] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:02,712] [INFO] Selected 13 target genomes.
[2024-01-24 10:48:02,712] [INFO] Target genome list was writen to GCF_905397375.1_LMG_6866_genomic.fna/target_genomes.txt
[2024-01-24 10:48:02,717] [INFO] Task started: fastANI
[2024-01-24 10:48:02,717] [INFO] Running command: fastANI --query /var/lib/cwl/stgfd65fcef-a3d6-412e-be95-4c15a1f1c75b/GCF_905397375.1_LMG_6866_genomic.fna.gz --refList GCF_905397375.1_LMG_6866_genomic.fna/target_genomes.txt --output GCF_905397375.1_LMG_6866_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:18,079] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:18,080] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3c6a456f-7e6b-4831-adcd-f226a1f7b96e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:18,080] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3c6a456f-7e6b-4831-adcd-f226a1f7b96e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:18,091] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:48:18,091] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:48:18,091] [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 mannitolilytica	strain=LMG 6866	GCA_905397375.1	105219	105219	type	True	100.0	1588	1591	95	conclusive
Ralstonia pickettii	strain=NCTC11149	GCA_900455835.1	329	329	type	True	87.7446	1224	1591	95	below_threshold
Ralstonia pickettii	strain=NBRC 102503	GCA_001544155.1	329	329	type	True	87.6906	1217	1591	95	below_threshold
Ralstonia pickettii	strain=FDAARGOS_1535	GCA_020341455.1	329	329	type	True	87.6404	1250	1591	95	below_threshold
Ralstonia pickettii	strain=ATCC 27511	GCA_000743455.1	329	329	type	True	87.6287	1244	1591	95	below_threshold
Ralstonia insidiosa	strain=CCUG 46789	GCA_008801405.1	190721	190721	type	True	86.7223	1251	1591	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_919586305.1	1310165	1310165	type	True	85.6227	1036	1591	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_024925465.1	1310165	1310165	type	True	85.5431	1062	1591	95	below_threshold
Ralstonia solanacearum	strain=NCPPB 325	GCA_015910705.1	305	305	type	True	85.3007	1076	1591	95	below_threshold
Ralstonia solanacearum	strain=K60	GCA_002251695.1	305	305	type	True	85.206	1081	1591	95	below_threshold
Burkholderia ubonensis		GCA_902499185.1	101571	101571	type	True	78.8612	603	1591	95	below_threshold
Burkholderia ubonensis	strain=LMG 20358	GCA_902833085.1	101571	101571	type	True	78.8036	623	1591	95	below_threshold
Paraburkholderia azotifigens	strain=NF 2-5-3	GCA_007995085.1	2057004	2057004	type	True	77.9849	518	1591	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:18,093] [INFO] DFAST Taxonomy check result was written to GCF_905397375.1_LMG_6866_genomic.fna/tc_result.tsv
[2024-01-24 10:48:18,093] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:18,093] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:18,093] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3c6a456f-7e6b-4831-adcd-f226a1f7b96e/dqc_reference/checkm_data
[2024-01-24 10:48:18,094] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:18,145] [INFO] Task started: CheckM
[2024-01-24 10:48:18,145] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_905397375.1_LMG_6866_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_905397375.1_LMG_6866_genomic.fna/checkm_input GCF_905397375.1_LMG_6866_genomic.fna/checkm_result
[2024-01-24 10:49:15,160] [INFO] Task succeeded: CheckM
[2024-01-24 10:49:15,161] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:49:15,180] [INFO] ===== Completeness check finished =====
[2024-01-24 10:49:15,180] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:49:15,181] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_905397375.1_LMG_6866_genomic.fna/markers.fasta)
[2024-01-24 10:49:15,181] [INFO] Task started: Blastn
[2024-01-24 10:49:15,181] [INFO] Running command: blastn -query GCF_905397375.1_LMG_6866_genomic.fna/markers.fasta -db /var/lib/cwl/stg3c6a456f-7e6b-4831-adcd-f226a1f7b96e/dqc_reference/reference_markers_gtdb.fasta -out GCF_905397375.1_LMG_6866_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:49:17,267] [INFO] Task succeeded: Blastn
[2024-01-24 10:49:17,270] [INFO] Selected 16 target genomes.
[2024-01-24 10:49:17,270] [INFO] Target genome list was writen to GCF_905397375.1_LMG_6866_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:49:17,283] [INFO] Task started: fastANI
[2024-01-24 10:49:17,283] [INFO] Running command: fastANI --query /var/lib/cwl/stgfd65fcef-a3d6-412e-be95-4c15a1f1c75b/GCF_905397375.1_LMG_6866_genomic.fna.gz --refList GCF_905397375.1_LMG_6866_genomic.fna/target_genomes_gtdb.txt --output GCF_905397375.1_LMG_6866_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:49:37,081] [INFO] Task succeeded: fastANI
[2024-01-24 10:49:37,099] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:49:37,099] [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_905397375.1	s__Ralstonia mannitolilytica	100.0	1588	1591	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ralstonia	95.0	98.68	96.05	0.93	0.87	14	conclusive
GCF_000620465.1	s__Ralstonia sp000620465	88.9321	1307	1591	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	88.5042	1234	1591	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ralstonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000020205.1	s__Ralstonia pickettii_B	88.0035	1243	1591	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ralstonia	95.0	98.08	96.31	0.87	0.83	22	-
GCF_900115545.1	s__Ralstonia sp900115545	87.6979	1276	1591	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ralstonia	95.0	98.84	98.84	0.97	0.97	2	-
GCF_016466415.1	s__Ralstonia pickettii	87.6901	1235	1591	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ralstonia	95.0	97.89	95.45	0.93	0.86	44	-
GCF_000607165.1	s__Ralstonia pickettii_A	87.3984	1290	1591	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	87.3708	1272	1591	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ralstonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002298975.1	s__Ralstonia sp002298975	86.8395	1147	1591	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	86.7717	1167	1591	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	86.7464	1228	1591	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ralstonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001078575.1	s__Ralstonia sp001078575	86.7402	1263	1591	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ralstonia	95.0	99.81	99.41	0.97	0.93	9	-
GCF_008801405.1	s__Ralstonia insidiosa	86.7047	1253	1591	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ralstonia	95.0	97.92	96.99	0.90	0.85	9	-
GCF_016429285.1	s__Ralstonia sp016429285	86.4192	1127	1591	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ralstonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003999715.1	s__Ralstonia pseudosolanacearum	85.3989	1099	1591	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ralstonia	95.0	98.86	95.79	0.91	0.82	165	-
GCF_002251695.1	s__Ralstonia solanacearum	85.2217	1079	1591	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ralstonia	95.0	96.27	95.49	0.87	0.78	131	-
--------------------------------------------------------------------------------
[2024-01-24 10:49:37,100] [INFO] GTDB search result was written to GCF_905397375.1_LMG_6866_genomic.fna/result_gtdb.tsv
[2024-01-24 10:49:37,101] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:49:37,104] [INFO] DFAST_QC result json was written to GCF_905397375.1_LMG_6866_genomic.fna/dqc_result.json
[2024-01-24 10:49:37,104] [INFO] DFAST_QC completed!
[2024-01-24 10:49:37,104] [INFO] Total running time: 0h1m56s