[2024-01-24 15:10:20,215] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:20,220] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:20,220] [INFO] DQC Reference Directory: /var/lib/cwl/stg835c2691-343c-430a-8d17-5bd69fa19695/dqc_reference
[2024-01-24 15:10:22,721] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:22,722] [INFO] Task started: Prodigal
[2024-01-24 15:10:22,723] [INFO] Running command: gunzip -c /var/lib/cwl/stg2f3e4c81-bd43-450b-91bf-cf26daab29e9/GCF_004216695.1_ASM421669v1_genomic.fna.gz | prodigal -d GCF_004216695.1_ASM421669v1_genomic.fna/cds.fna -a GCF_004216695.1_ASM421669v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:10:41,896] [INFO] Task succeeded: Prodigal
[2024-01-24 15:10:41,897] [INFO] Task started: HMMsearch
[2024-01-24 15:10:41,897] [INFO] Running command: hmmsearch --tblout GCF_004216695.1_ASM421669v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg835c2691-343c-430a-8d17-5bd69fa19695/dqc_reference/reference_markers.hmm GCF_004216695.1_ASM421669v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:10:42,229] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:10:42,230] [INFO] Found 6/6 markers.
[2024-01-24 15:10:42,285] [INFO] Query marker FASTA was written to GCF_004216695.1_ASM421669v1_genomic.fna/markers.fasta
[2024-01-24 15:10:42,286] [INFO] Task started: Blastn
[2024-01-24 15:10:42,286] [INFO] Running command: blastn -query GCF_004216695.1_ASM421669v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg835c2691-343c-430a-8d17-5bd69fa19695/dqc_reference/reference_markers.fasta -out GCF_004216695.1_ASM421669v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:10:43,396] [INFO] Task succeeded: Blastn
[2024-01-24 15:10:43,400] [INFO] Selected 24 target genomes.
[2024-01-24 15:10:43,400] [INFO] Target genome list was writen to GCF_004216695.1_ASM421669v1_genomic.fna/target_genomes.txt
[2024-01-24 15:10:43,410] [INFO] Task started: fastANI
[2024-01-24 15:10:43,410] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f3e4c81-bd43-450b-91bf-cf26daab29e9/GCF_004216695.1_ASM421669v1_genomic.fna.gz --refList GCF_004216695.1_ASM421669v1_genomic.fna/target_genomes.txt --output GCF_004216695.1_ASM421669v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:11:14,110] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:14,110] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg835c2691-343c-430a-8d17-5bd69fa19695/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:11:14,110] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg835c2691-343c-430a-8d17-5bd69fa19695/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:11:14,128] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:11:14,128] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:11:14,129] [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
Pigmentiphaga kullae	strain=K24	GCA_004216695.1	151784	151784	type	True	100.0	2071	2071	95	conclusive
Achromobacter ruhlandii	strain=LMG 1866	GCA_902859695.1	72557	72557	type	True	79.6383	735	2071	95	below_threshold
Achromobacter xylosoxidans	strain=NCTC10807	GCA_001457475.1	85698	85698	type	True	79.5379	734	2071	95	below_threshold
Achromobacter xylosoxidans	strain=FDAARGOS_789	GCA_013343135.1	85698	85698	type	True	79.5336	740	2071	95	below_threshold
Achromobacter xylosoxidans	strain=PartM-Axylosoxidans-RM8376	GCA_022870085.1	85698	85698	type	True	79.5169	741	2071	95	below_threshold
Achromobacter xylosoxidans	strain=NBRC 15126	GCA_001598595.1	85698	85698	type	True	79.4793	744	2071	95	below_threshold
Pigmentiphaga litoralis	strain=KCTC 22165	GCA_014651835.1	516702	516702	type	True	79.396	740	2071	95	below_threshold
Castellaniella defragrans	strain=CCUG 39790	GCA_008801975.1	75697	75697	type	True	79.1983	474	2071	95	below_threshold
Bordetella pertussis	strain=FDAARGOS_1543	GCA_020736265.1	520	520	type	True	79.189	578	2071	95	below_threshold
Bordetella pertussis	strain=18323	GCA_000306945.1	520	520	type	True	79.1853	575	2071	95	below_threshold
Achromobacter insuavis	strain=LMG 26845	GCA_902859645.1	1287735	1287735	type	True	79.1801	723	2071	95	below_threshold
Achromobacter dolens	strain=LMG 26840	GCA_902859745.1	1287738	1287738	type	True	79.0468	693	2071	95	below_threshold
Bordetella parapertussis	strain=FDAARGOS_1541	GCA_020735925.1	519	519	suspected-type	True	79.0153	629	2071	95	below_threshold
Castellaniella defragrans	strain=DSM 12141	GCA_014203015.1	75697	75697	type	True	78.9494	523	2071	95	below_threshold
Bordetella bronchiseptica	strain=CCUG 219	GCA_021391275.1	518	518	suspected-type	True	78.8995	615	2071	95	below_threshold
Bordetella bronchiseptica	strain=NBRC 13691	GCA_001598655.1	518	518	suspected-type	True	78.8394	633	2071	95	below_threshold
Achromobacter denitrificans	strain=LMG 1231	GCA_902859715.1	32002	32002	type	True	78.7411	702	2071	95	below_threshold
Achromobacter denitrificans	strain=NCTC8582	GCA_900444675.1	32002	32002	type	True	78.682	713	2071	95	below_threshold
Achromobacter denitrificans	strain=FDAARGOS_786	GCA_013267395.1	32002	32002	type	True	78.6714	714	2071	95	below_threshold
Achromobacter insolitus	strain=NCTC 13520	GCA_024168865.1	217204	217204	type	True	78.6316	563	2071	95	below_threshold
Achromobacter denitrificans	strain=NBRC 15125	GCA_001571365.1	32002	32002	type	True	78.5896	713	2071	95	below_threshold
Verticiella sediminum	strain=DSM 27279	GCA_007558815.1	1247510	1247510	type	True	78.5604	601	2071	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_919586305.1	1310165	1310165	type	True	77.9602	444	2071	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_024925465.1	1310165	1310165	type	True	77.9382	449	2071	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:11:14,130] [INFO] DFAST Taxonomy check result was written to GCF_004216695.1_ASM421669v1_genomic.fna/tc_result.tsv
[2024-01-24 15:11:14,131] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:11:14,131] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:11:14,131] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg835c2691-343c-430a-8d17-5bd69fa19695/dqc_reference/checkm_data
[2024-01-24 15:11:14,132] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:11:14,196] [INFO] Task started: CheckM
[2024-01-24 15:11:14,196] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004216695.1_ASM421669v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004216695.1_ASM421669v1_genomic.fna/checkm_input GCF_004216695.1_ASM421669v1_genomic.fna/checkm_result
[2024-01-24 15:12:18,940] [INFO] Task succeeded: CheckM
[2024-01-24 15:12:18,942] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:12:18,966] [INFO] ===== Completeness check finished =====
[2024-01-24 15:12:18,967] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:12:18,967] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004216695.1_ASM421669v1_genomic.fna/markers.fasta)
[2024-01-24 15:12:18,968] [INFO] Task started: Blastn
[2024-01-24 15:12:18,968] [INFO] Running command: blastn -query GCF_004216695.1_ASM421669v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg835c2691-343c-430a-8d17-5bd69fa19695/dqc_reference/reference_markers_gtdb.fasta -out GCF_004216695.1_ASM421669v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:12:21,156] [INFO] Task succeeded: Blastn
[2024-01-24 15:12:21,160] [INFO] Selected 5 target genomes.
[2024-01-24 15:12:21,161] [INFO] Target genome list was writen to GCF_004216695.1_ASM421669v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:12:21,165] [INFO] Task started: fastANI
[2024-01-24 15:12:21,166] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f3e4c81-bd43-450b-91bf-cf26daab29e9/GCF_004216695.1_ASM421669v1_genomic.fna.gz --refList GCF_004216695.1_ASM421669v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004216695.1_ASM421669v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:12:31,120] [INFO] Task succeeded: fastANI
[2024-01-24 15:12:31,131] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:12:31,131] [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_004216695.1	s__Pigmentiphaga kullae	100.0	2071	2071	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pigmentiphaga	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003854895.1	s__Pigmentiphaga sp003854895	94.3218	1740	2071	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pigmentiphaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898625.1	s__Pigmentiphaga sp001898625	93.9952	1753	2071	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pigmentiphaga	95.0	99.98	99.98	0.96	0.93	3	-
GCF_002188635.1	s__Pigmentiphaga sp002188635	93.2547	1643	2071	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pigmentiphaga	95.0	99.65	99.31	0.97	0.93	3	-
GCA_009360345.1	s__Pigmentiphaga sp009360345	92.0196	1570	2071	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pigmentiphaga	95.0	99.85	99.84	0.97	0.96	3	-
--------------------------------------------------------------------------------
[2024-01-24 15:12:31,133] [INFO] GTDB search result was written to GCF_004216695.1_ASM421669v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:12:31,134] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:12:31,141] [INFO] DFAST_QC result json was written to GCF_004216695.1_ASM421669v1_genomic.fna/dqc_result.json
[2024-01-24 15:12:31,141] [INFO] DFAST_QC completed!
[2024-01-24 15:12:31,141] [INFO] Total running time: 0h2m11s