[2023-06-19 10:30:22,873] [INFO] DFAST_QC pipeline started.
[2023-06-19 10:30:22,877] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 10:30:22,877] [INFO] DQC Reference Directory: /var/lib/cwl/stg29803796-94ea-462b-93b4-5747bc51da3c/dqc_reference
[2023-06-19 10:30:24,376] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 10:30:24,377] [INFO] Task started: Prodigal
[2023-06-19 10:30:24,377] [INFO] Running command: gunzip -c /var/lib/cwl/stge09354b6-b61f-445b-9ef7-818a7937299a/GCA_018607845.1_ASM1860784v1_genomic.fna.gz | prodigal -d GCA_018607845.1_ASM1860784v1_genomic.fna/cds.fna -a GCA_018607845.1_ASM1860784v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 10:30:33,337] [INFO] Task succeeded: Prodigal
[2023-06-19 10:30:33,337] [INFO] Task started: HMMsearch
[2023-06-19 10:30:33,337] [INFO] Running command: hmmsearch --tblout GCA_018607845.1_ASM1860784v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg29803796-94ea-462b-93b4-5747bc51da3c/dqc_reference/reference_markers.hmm GCA_018607845.1_ASM1860784v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 10:30:33,617] [INFO] Task succeeded: HMMsearch
[2023-06-19 10:30:33,618] [WARNING] Found 4/6 markers. [/var/lib/cwl/stge09354b6-b61f-445b-9ef7-818a7937299a/GCA_018607845.1_ASM1860784v1_genomic.fna.gz]
[2023-06-19 10:30:33,656] [INFO] Query marker FASTA was written to GCA_018607845.1_ASM1860784v1_genomic.fna/markers.fasta
[2023-06-19 10:30:33,656] [INFO] Task started: Blastn
[2023-06-19 10:30:33,657] [INFO] Running command: blastn -query GCA_018607845.1_ASM1860784v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg29803796-94ea-462b-93b4-5747bc51da3c/dqc_reference/reference_markers.fasta -out GCA_018607845.1_ASM1860784v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 10:30:34,567] [INFO] Task succeeded: Blastn
[2023-06-19 10:30:34,578] [INFO] Selected 12 target genomes.
[2023-06-19 10:30:34,579] [INFO] Target genome list was writen to GCA_018607845.1_ASM1860784v1_genomic.fna/target_genomes.txt
[2023-06-19 10:30:34,581] [INFO] Task started: fastANI
[2023-06-19 10:30:34,581] [INFO] Running command: fastANI --query /var/lib/cwl/stge09354b6-b61f-445b-9ef7-818a7937299a/GCA_018607845.1_ASM1860784v1_genomic.fna.gz --refList GCA_018607845.1_ASM1860784v1_genomic.fna/target_genomes.txt --output GCA_018607845.1_ASM1860784v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 10:30:48,550] [INFO] Task succeeded: fastANI
[2023-06-19 10:30:48,551] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg29803796-94ea-462b-93b4-5747bc51da3c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 10:30:48,551] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg29803796-94ea-462b-93b4-5747bc51da3c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 10:30:48,562] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2023-06-19 10:30:48,562] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-19 10:30:48,562] [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
Achromobacter insuavis	strain=LMG 26845	GCA_902859645.1	1287735	1287735	type	True	98.7708	773	825	95	conclusive
Achromobacter dolens	strain=LMG 26840	GCA_902859745.1	1287738	1287738	type	True	93.9473	730	825	95	below_threshold
Achromobacter ruhlandii	strain=LMG 1866	GCA_902859695.1	72557	72557	type	True	93.1462	729	825	95	below_threshold
Achromobacter xylosoxidans	strain=FDAARGOS_789	GCA_013343135.1	85698	85698	type	True	92.3851	728	825	95	below_threshold
Achromobacter xylosoxidans	strain=NCTC10807	GCA_001457475.1	85698	85698	type	True	92.3754	727	825	95	below_threshold
Achromobacter xylosoxidans	strain=PartM-Axylosoxidans-RM8376	GCA_022870085.1	85698	85698	type	True	92.3528	737	825	95	below_threshold
Achromobacter xylosoxidans	strain=NBRC 15126	GCA_001598595.1	85698	85698	type	True	92.2366	734	825	95	below_threshold
Achromobacter pulmonis	strain=LMG 26696	GCA_902859765.1	1389932	1389932	type	True	90.7374	690	825	95	below_threshold
Achromobacter insolitus	strain=NCTC 13520	GCA_024168865.1	217204	217204	type	True	85.8487	630	825	95	below_threshold
Bordetella bronchiseptica	strain=CCUG 219	GCA_021391275.1	518	518	suspected-type	True	83.3342	478	825	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_919586305.1	1310165	1310165	type	True	78.6068	263	825	95	below_threshold
Cupriavidus numazuensis	strain=LMG 26411	GCA_905397435.1	221992	221992	type	True	78.3713	270	825	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 10:30:48,564] [INFO] DFAST Taxonomy check result was written to GCA_018607845.1_ASM1860784v1_genomic.fna/tc_result.tsv
[2023-06-19 10:30:48,565] [INFO] ===== Taxonomy check completed =====
[2023-06-19 10:30:48,565] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 10:30:48,565] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg29803796-94ea-462b-93b4-5747bc51da3c/dqc_reference/checkm_data
[2023-06-19 10:30:48,566] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 10:30:48,609] [INFO] Task started: CheckM
[2023-06-19 10:30:48,609] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018607845.1_ASM1860784v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018607845.1_ASM1860784v1_genomic.fna/checkm_input GCA_018607845.1_ASM1860784v1_genomic.fna/checkm_result
[2023-06-19 10:31:18,573] [INFO] Task succeeded: CheckM
[2023-06-19 10:31:18,574] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 10:31:18,597] [INFO] ===== Completeness check finished =====
[2023-06-19 10:31:18,597] [INFO] ===== Start GTDB Search =====
[2023-06-19 10:31:18,598] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018607845.1_ASM1860784v1_genomic.fna/markers.fasta)
[2023-06-19 10:31:18,598] [INFO] Task started: Blastn
[2023-06-19 10:31:18,599] [INFO] Running command: blastn -query GCA_018607845.1_ASM1860784v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg29803796-94ea-462b-93b4-5747bc51da3c/dqc_reference/reference_markers_gtdb.fasta -out GCA_018607845.1_ASM1860784v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 10:31:20,121] [INFO] Task succeeded: Blastn
[2023-06-19 10:31:20,126] [INFO] Selected 6 target genomes.
[2023-06-19 10:31:20,126] [INFO] Target genome list was writen to GCA_018607845.1_ASM1860784v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 10:31:20,133] [INFO] Task started: fastANI
[2023-06-19 10:31:20,133] [INFO] Running command: fastANI --query /var/lib/cwl/stge09354b6-b61f-445b-9ef7-818a7937299a/GCA_018607845.1_ASM1860784v1_genomic.fna.gz --refList GCA_018607845.1_ASM1860784v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018607845.1_ASM1860784v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 10:31:27,398] [INFO] Task succeeded: fastANI
[2023-06-19 10:31:27,405] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 10:31:27,405] [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_902859645.1	s__Achromobacter insuavis	98.7708	773	825	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.6014	99.48	98.86	0.95	0.90	7	conclusive
GCF_016127315.1	s__Achromobacter insuavis_A	95.5858	762	825	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.6014	97.14	97.13	0.90	0.90	4	-
GCF_902859745.1	s__Achromobacter dolens	93.9473	730	825	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0063	99.05	99.03	0.93	0.90	8	-
GCF_902859695.1	s__Achromobacter ruhlandii	93.1702	728	825	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0063	98.29	97.95	0.91	0.85	19	-
GCF_001457475.1	s__Achromobacter xylosoxidans	92.4667	723	825	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	98.72	96.70	0.93	0.87	75	-
GCF_902859765.1	s__Achromobacter pulmonis	90.7842	688	825	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	99.40	99.40	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2023-06-19 10:31:27,407] [INFO] GTDB search result was written to GCA_018607845.1_ASM1860784v1_genomic.fna/result_gtdb.tsv
[2023-06-19 10:31:27,407] [INFO] ===== GTDB Search completed =====
[2023-06-19 10:31:27,411] [INFO] DFAST_QC result json was written to GCA_018607845.1_ASM1860784v1_genomic.fna/dqc_result.json
[2023-06-19 10:31:27,411] [INFO] DFAST_QC completed!
[2023-06-19 10:31:27,411] [INFO] Total running time: 0h1m5s