[2024-01-24 12:14:34,695] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:34,697] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:34,697] [INFO] DQC Reference Directory: /var/lib/cwl/stgf672a4a8-41a9-48b1-8797-97b143b3c3df/dqc_reference
[2024-01-24 12:14:36,118] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:36,119] [INFO] Task started: Prodigal
[2024-01-24 12:14:36,119] [INFO] Running command: gunzip -c /var/lib/cwl/stg255761bc-a505-43f0-af69-f70822d0acef/GCF_014199165.1_ASM1419916v1_genomic.fna.gz | prodigal -d GCF_014199165.1_ASM1419916v1_genomic.fna/cds.fna -a GCF_014199165.1_ASM1419916v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:43,444] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:43,444] [INFO] Task started: HMMsearch
[2024-01-24 12:14:43,444] [INFO] Running command: hmmsearch --tblout GCF_014199165.1_ASM1419916v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf672a4a8-41a9-48b1-8797-97b143b3c3df/dqc_reference/reference_markers.hmm GCF_014199165.1_ASM1419916v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:43,690] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:43,692] [INFO] Found 6/6 markers.
[2024-01-24 12:14:43,718] [INFO] Query marker FASTA was written to GCF_014199165.1_ASM1419916v1_genomic.fna/markers.fasta
[2024-01-24 12:14:43,719] [INFO] Task started: Blastn
[2024-01-24 12:14:43,719] [INFO] Running command: blastn -query GCF_014199165.1_ASM1419916v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf672a4a8-41a9-48b1-8797-97b143b3c3df/dqc_reference/reference_markers.fasta -out GCF_014199165.1_ASM1419916v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:44,655] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:44,659] [INFO] Selected 17 target genomes.
[2024-01-24 12:14:44,659] [INFO] Target genome list was writen to GCF_014199165.1_ASM1419916v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:44,671] [INFO] Task started: fastANI
[2024-01-24 12:14:44,671] [INFO] Running command: fastANI --query /var/lib/cwl/stg255761bc-a505-43f0-af69-f70822d0acef/GCF_014199165.1_ASM1419916v1_genomic.fna.gz --refList GCF_014199165.1_ASM1419916v1_genomic.fna/target_genomes.txt --output GCF_014199165.1_ASM1419916v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:55,964] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:55,964] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf672a4a8-41a9-48b1-8797-97b143b3c3df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:55,964] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf672a4a8-41a9-48b1-8797-97b143b3c3df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:55,978] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:14:55,978] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:14:55,979] [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
Brevundimonas halotolerans	strain=DSM 24448	GCA_014199165.1	69670	69670	type	True	100.0	835	836	95	conclusive
Brevundimonas halotolerans	strain=MCS24	GCA_003730275.1	69670	69670	type	True	99.9972	835	836	95	conclusive
Brevundimonas basaltis	strain=DSM 25335	GCA_014202075.1	472166	472166	type	True	81.3082	534	836	95	below_threshold
Brevundimonas albigilva	strain=KEME 9005-016	GCA_023503965.1	1312364	1312364	type	True	80.9652	497	836	95	below_threshold
Brevundimonas lenta	strain=DSM 23960	GCA_014196335.1	424796	424796	type	True	80.7285	539	836	95	below_threshold
Brevundimonas bullata	strain=HAMBI_262	GCA_003350205.1	13160	13160	type	True	80.6833	489	836	95	below_threshold
Brevundimonas pondensis	strain=LVF1	GCA_017487345.1	2774189	2774189	type	True	80.6191	523	836	95	below_threshold
Brevundimonas diminuta	strain=ATCC 11568	GCA_000204035.1	293	293	type	True	80.6057	502	836	95	below_threshold
Brevundimonas aurantiaca	strain=DSM 4731	GCA_014199955.1	74316	74316	type	True	80.5804	496	836	95	below_threshold
Brevundimonas goettingensis	strain=LVF2	GCA_017487405.1	2774190	2774190	type	True	80.5656	536	836	95	below_threshold
Brevundimonas guildfordensis	strain=Sa3CVA3	GCA_014836405.1	2762241	2762241	type	True	80.5606	479	836	95	below_threshold
Brevundimonas vitisensis	strain=GR-TSA-9	GCA_016656965.1	2800818	2800818	type	True	80.5052	508	836	95	below_threshold
Brevundimonas fluminis	strain=LA-55	GCA_003934285.1	2487274	2487274	type	True	80.4663	531	836	95	below_threshold
Brevundimonas viscosa	strain=CGMCC 1.10683	GCA_900116065.1	871741	871741	type	True	80.4319	529	836	95	below_threshold
Brevundimonas naejangsanensis	strain=DSM 23858	GCA_000421705.1	588932	588932	type	True	80.3746	486	836	95	below_threshold
Paracoccus mutanolyticus	strain=RSP-02	GCA_003285265.1	1499308	1499308	type	True	76.6656	114	836	95	below_threshold
Methylobacterium mesophilicum	strain=NBRC 15688	GCA_022179445.1	39956	39956	type	True	76.4837	125	836	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:55,980] [INFO] DFAST Taxonomy check result was written to GCF_014199165.1_ASM1419916v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:55,981] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:55,981] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:55,981] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf672a4a8-41a9-48b1-8797-97b143b3c3df/dqc_reference/checkm_data
[2024-01-24 12:14:55,982] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:56,011] [INFO] Task started: CheckM
[2024-01-24 12:14:56,011] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014199165.1_ASM1419916v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014199165.1_ASM1419916v1_genomic.fna/checkm_input GCF_014199165.1_ASM1419916v1_genomic.fna/checkm_result
[2024-01-24 12:15:22,937] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:22,938] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:22,958] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:22,958] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:22,958] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014199165.1_ASM1419916v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:22,959] [INFO] Task started: Blastn
[2024-01-24 12:15:22,959] [INFO] Running command: blastn -query GCF_014199165.1_ASM1419916v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf672a4a8-41a9-48b1-8797-97b143b3c3df/dqc_reference/reference_markers_gtdb.fasta -out GCF_014199165.1_ASM1419916v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:24,791] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:24,796] [INFO] Selected 14 target genomes.
[2024-01-24 12:15:24,797] [INFO] Target genome list was writen to GCF_014199165.1_ASM1419916v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:24,807] [INFO] Task started: fastANI
[2024-01-24 12:15:24,808] [INFO] Running command: fastANI --query /var/lib/cwl/stg255761bc-a505-43f0-af69-f70822d0acef/GCF_014199165.1_ASM1419916v1_genomic.fna.gz --refList GCF_014199165.1_ASM1419916v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014199165.1_ASM1419916v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:34,017] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:34,029] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:15:34,029] [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_003730275.1	s__Brevundimonas halotolerans	99.9972	835	836	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	97.75	97.09	0.92	0.85	7	conclusive
GCA_018826885.1	s__Brevundimonas sp018826885	91.449	607	836	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016742135.1	s__Brevundimonas sp016742135	89.0524	721	836	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017744255.1	s__Brevundimonas sp017744255	86.7042	720	836	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014202075.1	s__Brevundimonas basaltis	81.3213	533	836	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018820275.1	s__Brevundimonas sp018820275	81.2085	554	836	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	99.93	99.85	0.97	0.95	5	-
GCA_016183935.1	s__Brevundimonas sp016183935	80.8761	501	836	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002157625.1	s__Brevundimonas sp002157625	80.7781	508	836	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013912005.1	s__Brevundimonas sp013912005	80.7214	508	836	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001794825.1	s__Brevundimonas sp001794825	80.6092	503	836	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017487345.1	s__Brevundimonas sp017487345	80.5923	525	836	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013823285.1	s__Brevundimonas sp013823285	80.4157	434	836	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000466985.1	s__Brevundimonas abyssalis	80.3671	459	836	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	99.78	99.71	0.94	0.89	3	-
GCA_002387245.1	s__Brevundimonas sp002387245	80.1882	484	836	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:15:34,031] [INFO] GTDB search result was written to GCF_014199165.1_ASM1419916v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:34,031] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:34,035] [INFO] DFAST_QC result json was written to GCF_014199165.1_ASM1419916v1_genomic.fna/dqc_result.json
[2024-01-24 12:15:34,035] [INFO] DFAST_QC completed!
[2024-01-24 12:15:34,035] [INFO] Total running time: 0h0m59s