[2024-01-24 14:22:01,473] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:01,475] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:01,475] [INFO] DQC Reference Directory: /var/lib/cwl/stg8e2031db-ef23-47a4-91c0-39afc63e75d9/dqc_reference
[2024-01-24 14:22:02,717] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:02,718] [INFO] Task started: Prodigal
[2024-01-24 14:22:02,718] [INFO] Running command: gunzip -c /var/lib/cwl/stg55f78806-aa64-441f-ad29-dd2614781e63/GCF_001544155.1_ASM154415v1_genomic.fna.gz | prodigal -d GCF_001544155.1_ASM154415v1_genomic.fna/cds.fna -a GCF_001544155.1_ASM154415v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:18,936] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:18,936] [INFO] Task started: HMMsearch
[2024-01-24 14:22:18,936] [INFO] Running command: hmmsearch --tblout GCF_001544155.1_ASM154415v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8e2031db-ef23-47a4-91c0-39afc63e75d9/dqc_reference/reference_markers.hmm GCF_001544155.1_ASM154415v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:19,220] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:19,222] [INFO] Found 6/6 markers.
[2024-01-24 14:22:19,263] [INFO] Query marker FASTA was written to GCF_001544155.1_ASM154415v1_genomic.fna/markers.fasta
[2024-01-24 14:22:19,263] [INFO] Task started: Blastn
[2024-01-24 14:22:19,264] [INFO] Running command: blastn -query GCF_001544155.1_ASM154415v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8e2031db-ef23-47a4-91c0-39afc63e75d9/dqc_reference/reference_markers.fasta -out GCF_001544155.1_ASM154415v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:20,233] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:20,237] [INFO] Selected 10 target genomes.
[2024-01-24 14:22:20,237] [INFO] Target genome list was writen to GCF_001544155.1_ASM154415v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:20,241] [INFO] Task started: fastANI
[2024-01-24 14:22:20,241] [INFO] Running command: fastANI --query /var/lib/cwl/stg55f78806-aa64-441f-ad29-dd2614781e63/GCF_001544155.1_ASM154415v1_genomic.fna.gz --refList GCF_001544155.1_ASM154415v1_genomic.fna/target_genomes.txt --output GCF_001544155.1_ASM154415v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:22:32,679] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:32,680] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8e2031db-ef23-47a4-91c0-39afc63e75d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:22:32,680] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8e2031db-ef23-47a4-91c0-39afc63e75d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:22:32,692] [INFO] Found 10 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 14:22:32,692] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:22:32,692] [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	100.0	1546	1548	95	conclusive
Ralstonia pickettii	strain=ATCC 27511	GCA_000743455.1	329	329	type	True	99.9983	1548	1548	95	conclusive
Ralstonia pickettii	strain=FDAARGOS_1535	GCA_020341455.1	329	329	type	True	99.9976	1548	1548	95	conclusive
Ralstonia pickettii	strain=NCTC11149	GCA_900455835.1	329	329	type	True	99.9971	1547	1548	95	conclusive
Ralstonia pickettii	strain=K-288	GCA_016466415.2	329	329	type	True	99.993	1546	1548	95	conclusive
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_919586305.1	1310165	1310165	type	True	84.6893	1003	1548	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_024925465.1	1310165	1310165	type	True	84.6435	1037	1548	95	below_threshold
Burkholderia ubonensis	strain=LMG 20358	GCA_902833085.1	101571	101571	type	True	78.3653	533	1548	95	below_threshold
Burkholderia ubonensis		GCA_902499185.1	101571	101571	type	True	78.3142	529	1548	95	below_threshold
Paraburkholderia azotifigens	strain=NF 2-5-3	GCA_007995085.1	2057004	2057004	type	True	77.9098	473	1548	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:22:32,694] [INFO] DFAST Taxonomy check result was written to GCF_001544155.1_ASM154415v1_genomic.fna/tc_result.tsv
[2024-01-24 14:22:32,694] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:22:32,695] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:22:32,695] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8e2031db-ef23-47a4-91c0-39afc63e75d9/dqc_reference/checkm_data
[2024-01-24 14:22:32,696] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:22:32,742] [INFO] Task started: CheckM
[2024-01-24 14:22:32,742] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001544155.1_ASM154415v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001544155.1_ASM154415v1_genomic.fna/checkm_input GCF_001544155.1_ASM154415v1_genomic.fna/checkm_result
[2024-01-24 14:23:23,080] [INFO] Task succeeded: CheckM
[2024-01-24 14:23:23,081] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:23:23,102] [INFO] ===== Completeness check finished =====
[2024-01-24 14:23:23,102] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:23:23,103] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001544155.1_ASM154415v1_genomic.fna/markers.fasta)
[2024-01-24 14:23:23,103] [INFO] Task started: Blastn
[2024-01-24 14:23:23,103] [INFO] Running command: blastn -query GCF_001544155.1_ASM154415v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8e2031db-ef23-47a4-91c0-39afc63e75d9/dqc_reference/reference_markers_gtdb.fasta -out GCF_001544155.1_ASM154415v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:24,839] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:24,842] [INFO] Selected 8 target genomes.
[2024-01-24 14:23:24,843] [INFO] Target genome list was writen to GCF_001544155.1_ASM154415v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:23:24,849] [INFO] Task started: fastANI
[2024-01-24 14:23:24,849] [INFO] Running command: fastANI --query /var/lib/cwl/stg55f78806-aa64-441f-ad29-dd2614781e63/GCF_001544155.1_ASM154415v1_genomic.fna.gz --refList GCF_001544155.1_ASM154415v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001544155.1_ASM154415v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:23:35,479] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:35,487] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:23:35,487] [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	99.993	1546	1548	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	94.2552	1363	1548	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	92.8575	1354	1548	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	92.2339	1270	1548	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	91.6163	1357	1548	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	91.431	1370	1548	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	91.2714	1354	1548	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	87.0588	1243	1548	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 14:23:35,490] [INFO] GTDB search result was written to GCF_001544155.1_ASM154415v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:23:35,490] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:23:35,493] [INFO] DFAST_QC result json was written to GCF_001544155.1_ASM154415v1_genomic.fna/dqc_result.json
[2024-01-24 14:23:35,493] [INFO] DFAST_QC completed!
[2024-01-24 14:23:35,493] [INFO] Total running time: 0h1m34s