[2024-01-24 12:36:57,771] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:36:57,773] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:36:57,773] [INFO] DQC Reference Directory: /var/lib/cwl/stg7670f68f-a44e-44c0-9a0e-75cf7200aeef/dqc_reference
[2024-01-24 12:36:59,126] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:36:59,127] [INFO] Task started: Prodigal
[2024-01-24 12:36:59,127] [INFO] Running command: gunzip -c /var/lib/cwl/stg9c95eb34-9b22-4be4-a1de-09273422c471/GCF_902859645.1_LMG_26845_genomic.fna.gz | prodigal -d GCF_902859645.1_LMG_26845_genomic.fna/cds.fna -a GCF_902859645.1_LMG_26845_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:20,106] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:20,106] [INFO] Task started: HMMsearch
[2024-01-24 12:37:20,107] [INFO] Running command: hmmsearch --tblout GCF_902859645.1_LMG_26845_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7670f68f-a44e-44c0-9a0e-75cf7200aeef/dqc_reference/reference_markers.hmm GCF_902859645.1_LMG_26845_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:20,589] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:20,591] [INFO] Found 6/6 markers.
[2024-01-24 12:37:20,644] [INFO] Query marker FASTA was written to GCF_902859645.1_LMG_26845_genomic.fna/markers.fasta
[2024-01-24 12:37:20,645] [INFO] Task started: Blastn
[2024-01-24 12:37:20,645] [INFO] Running command: blastn -query GCF_902859645.1_LMG_26845_genomic.fna/markers.fasta -db /var/lib/cwl/stg7670f68f-a44e-44c0-9a0e-75cf7200aeef/dqc_reference/reference_markers.fasta -out GCF_902859645.1_LMG_26845_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:21,767] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:21,770] [INFO] Selected 11 target genomes.
[2024-01-24 12:37:21,771] [INFO] Target genome list was writen to GCF_902859645.1_LMG_26845_genomic.fna/target_genomes.txt
[2024-01-24 12:37:21,775] [INFO] Task started: fastANI
[2024-01-24 12:37:21,775] [INFO] Running command: fastANI --query /var/lib/cwl/stg9c95eb34-9b22-4be4-a1de-09273422c471/GCF_902859645.1_LMG_26845_genomic.fna.gz --refList GCF_902859645.1_LMG_26845_genomic.fna/target_genomes.txt --output GCF_902859645.1_LMG_26845_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:37:42,847] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:42,848] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7670f68f-a44e-44c0-9a0e-75cf7200aeef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:37:42,848] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7670f68f-a44e-44c0-9a0e-75cf7200aeef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:37:42,858] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:37:42,859] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:37:42,859] [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	100.0	2169	2179	95	conclusive
Achromobacter dolens	strain=LMG 26840	GCA_902859745.1	1287738	1287738	type	True	94.3051	1765	2179	95	below_threshold
Achromobacter ruhlandii	strain=LMG 1866	GCA_902859695.1	72557	72557	type	True	93.3032	1775	2179	95	below_threshold
Achromobacter xylosoxidans	strain=NBRC 15126	GCA_001598595.1	85698	85698	type	True	92.3835	1770	2179	95	below_threshold
Achromobacter xylosoxidans	strain=FDAARGOS_789	GCA_013343135.1	85698	85698	type	True	92.3775	1790	2179	95	below_threshold
Achromobacter xylosoxidans	strain=NCTC10807	GCA_001457475.1	85698	85698	type	True	92.3759	1781	2179	95	below_threshold
Achromobacter xylosoxidans	strain=PartM-Axylosoxidans-RM8376	GCA_022870085.1	85698	85698	type	True	92.3499	1797	2179	95	below_threshold
Achromobacter insolitus	strain=NCTC 13520	GCA_024168865.1	217204	217204	type	True	85.2944	1394	2179	95	below_threshold
Bordetella bronchiseptica	strain=CCUG 219	GCA_021391275.1	518	518	suspected-type	True	83.0097	912	2179	95	below_threshold
Eoetvoesia caeni	strain=PB3-7B	GCA_022688825.1	645616	645616	type	True	78.1957	369	2179	95	below_threshold
Cupriavidus numazuensis	strain=LMG 26411	GCA_905397435.1	221992	221992	type	True	77.8278	597	2179	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:37:42,860] [INFO] DFAST Taxonomy check result was written to GCF_902859645.1_LMG_26845_genomic.fna/tc_result.tsv
[2024-01-24 12:37:42,861] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:37:42,861] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:37:42,861] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7670f68f-a44e-44c0-9a0e-75cf7200aeef/dqc_reference/checkm_data
[2024-01-24 12:37:42,862] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:37:42,936] [INFO] Task started: CheckM
[2024-01-24 12:37:42,936] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902859645.1_LMG_26845_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902859645.1_LMG_26845_genomic.fna/checkm_input GCF_902859645.1_LMG_26845_genomic.fna/checkm_result
[2024-01-24 12:38:47,696] [INFO] Task succeeded: CheckM
[2024-01-24 12:38:47,697] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:38:47,720] [INFO] ===== Completeness check finished =====
[2024-01-24 12:38:47,721] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:38:47,721] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902859645.1_LMG_26845_genomic.fna/markers.fasta)
[2024-01-24 12:38:47,722] [INFO] Task started: Blastn
[2024-01-24 12:38:47,722] [INFO] Running command: blastn -query GCF_902859645.1_LMG_26845_genomic.fna/markers.fasta -db /var/lib/cwl/stg7670f68f-a44e-44c0-9a0e-75cf7200aeef/dqc_reference/reference_markers_gtdb.fasta -out GCF_902859645.1_LMG_26845_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:38:49,981] [INFO] Task succeeded: Blastn
[2024-01-24 12:38:49,985] [INFO] Selected 6 target genomes.
[2024-01-24 12:38:49,986] [INFO] Target genome list was writen to GCF_902859645.1_LMG_26845_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:38:49,993] [INFO] Task started: fastANI
[2024-01-24 12:38:49,993] [INFO] Running command: fastANI --query /var/lib/cwl/stg9c95eb34-9b22-4be4-a1de-09273422c471/GCF_902859645.1_LMG_26845_genomic.fna.gz --refList GCF_902859645.1_LMG_26845_genomic.fna/target_genomes_gtdb.txt --output GCF_902859645.1_LMG_26845_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:39:01,957] [INFO] Task succeeded: fastANI
[2024-01-24 12:39:01,969] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:39:01,969] [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	100.0	2169	2179	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	95.6002	1962	2179	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	94.2937	1766	2179	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	93.2986	1776	2179	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	92.3657	1782	2179	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	91.0021	1548	2179	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	99.40	99.40	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:39:01,971] [INFO] GTDB search result was written to GCF_902859645.1_LMG_26845_genomic.fna/result_gtdb.tsv
[2024-01-24 12:39:01,971] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:39:01,975] [INFO] DFAST_QC result json was written to GCF_902859645.1_LMG_26845_genomic.fna/dqc_result.json
[2024-01-24 12:39:01,975] [INFO] DFAST_QC completed!
[2024-01-24 12:39:01,975] [INFO] Total running time: 0h2m4s