[2024-01-24 11:48:21,279] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:48:21,280] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:48:21,281] [INFO] DQC Reference Directory: /var/lib/cwl/stgbb7c9216-af83-47a8-bdef-858bace43a31/dqc_reference
[2024-01-24 11:48:24,564] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:48:24,566] [INFO] Task started: Prodigal
[2024-01-24 11:48:24,566] [INFO] Running command: gunzip -c /var/lib/cwl/stg8a290928-4424-4a02-a830-bec0cff293a8/GCF_017487345.1_ASM1748734v1_genomic.fna.gz | prodigal -d GCF_017487345.1_ASM1748734v1_genomic.fna/cds.fna -a GCF_017487345.1_ASM1748734v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:48:33,911] [INFO] Task succeeded: Prodigal
[2024-01-24 11:48:33,912] [INFO] Task started: HMMsearch
[2024-01-24 11:48:33,912] [INFO] Running command: hmmsearch --tblout GCF_017487345.1_ASM1748734v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbb7c9216-af83-47a8-bdef-858bace43a31/dqc_reference/reference_markers.hmm GCF_017487345.1_ASM1748734v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:48:34,175] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:48:34,177] [INFO] Found 6/6 markers.
[2024-01-24 11:48:34,208] [INFO] Query marker FASTA was written to GCF_017487345.1_ASM1748734v1_genomic.fna/markers.fasta
[2024-01-24 11:48:34,209] [INFO] Task started: Blastn
[2024-01-24 11:48:34,209] [INFO] Running command: blastn -query GCF_017487345.1_ASM1748734v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb7c9216-af83-47a8-bdef-858bace43a31/dqc_reference/reference_markers.fasta -out GCF_017487345.1_ASM1748734v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:48:35,100] [INFO] Task succeeded: Blastn
[2024-01-24 11:48:35,104] [INFO] Selected 12 target genomes.
[2024-01-24 11:48:35,104] [INFO] Target genome list was writen to GCF_017487345.1_ASM1748734v1_genomic.fna/target_genomes.txt
[2024-01-24 11:48:35,129] [INFO] Task started: fastANI
[2024-01-24 11:48:35,129] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a290928-4424-4a02-a830-bec0cff293a8/GCF_017487345.1_ASM1748734v1_genomic.fna.gz --refList GCF_017487345.1_ASM1748734v1_genomic.fna/target_genomes.txt --output GCF_017487345.1_ASM1748734v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:48:44,529] [INFO] Task succeeded: fastANI
[2024-01-24 11:48:44,530] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbb7c9216-af83-47a8-bdef-858bace43a31/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:48:44,531] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbb7c9216-af83-47a8-bdef-858bace43a31/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:48:44,545] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:48:44,545] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:48:44,545] [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 pondensis	strain=LVF1	GCA_017487345.1	2774189	2774189	type	True	100.0	1182	1183	95	conclusive
Brevundimonas bullata	strain=HAMBI_262	GCA_003350205.1	13160	13160	type	True	89.5404	864	1183	95	below_threshold
Brevundimonas diminuta	strain=NCTC8545	GCA_900445995.1	293	293	type	True	87.0051	825	1183	95	below_threshold
Brevundimonas diminuta	strain=ATCC 11568	GCA_000204035.1	293	293	type	True	86.9536	819	1183	95	below_threshold
Brevundimonas naejangsanensis	strain=DSM 23858	GCA_000421705.1	588932	588932	type	True	85.9545	748	1183	95	below_threshold
Brevundimonas guildfordensis	strain=Sa3CVA3	GCA_014836405.1	2762241	2762241	type	True	85.9368	737	1183	95	below_threshold
Brevundimonas nasdae	strain=JCM 11415	GCA_016654005.1	172043	172043	type	True	83.0519	689	1183	95	below_threshold
Brevundimonas albigilva	strain=KEME 9005-016	GCA_023503965.1	1312364	1312364	type	True	82.8768	705	1183	95	below_threshold
Brevundimonas vesicularis	strain=NBRC 12165	GCA_001592205.1	41276	41276	suspected-type	True	82.1441	648	1183	95	below_threshold
Brevundimonas vitisensis	strain=GR-TSA-9	GCA_016656965.1	2800818	2800818	type	True	80.4064	544	1183	95	below_threshold
Brevundimonas pishanensis	strain=CHPC 1.3453	GCA_022750635.1	2896315	2896315	type	True	80.1098	493	1183	95	below_threshold
Phenylobacterium aquaticum	strain=KACC 18306	GCA_022695515.1	1763816	1763816	type	True	78.1307	410	1183	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:48:44,547] [INFO] DFAST Taxonomy check result was written to GCF_017487345.1_ASM1748734v1_genomic.fna/tc_result.tsv
[2024-01-24 11:48:44,547] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:48:44,547] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:48:44,547] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbb7c9216-af83-47a8-bdef-858bace43a31/dqc_reference/checkm_data
[2024-01-24 11:48:44,549] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:48:44,584] [INFO] Task started: CheckM
[2024-01-24 11:48:44,585] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017487345.1_ASM1748734v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017487345.1_ASM1748734v1_genomic.fna/checkm_input GCF_017487345.1_ASM1748734v1_genomic.fna/checkm_result
[2024-01-24 11:49:16,033] [INFO] Task succeeded: CheckM
[2024-01-24 11:49:16,034] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:49:16,061] [INFO] ===== Completeness check finished =====
[2024-01-24 11:49:16,063] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:49:16,064] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017487345.1_ASM1748734v1_genomic.fna/markers.fasta)
[2024-01-24 11:49:16,064] [INFO] Task started: Blastn
[2024-01-24 11:49:16,065] [INFO] Running command: blastn -query GCF_017487345.1_ASM1748734v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb7c9216-af83-47a8-bdef-858bace43a31/dqc_reference/reference_markers_gtdb.fasta -out GCF_017487345.1_ASM1748734v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:49:17,701] [INFO] Task succeeded: Blastn
[2024-01-24 11:49:17,704] [INFO] Selected 11 target genomes.
[2024-01-24 11:49:17,704] [INFO] Target genome list was writen to GCF_017487345.1_ASM1748734v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:49:17,714] [INFO] Task started: fastANI
[2024-01-24 11:49:17,715] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a290928-4424-4a02-a830-bec0cff293a8/GCF_017487345.1_ASM1748734v1_genomic.fna.gz --refList GCF_017487345.1_ASM1748734v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017487345.1_ASM1748734v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:49:26,948] [INFO] Task succeeded: fastANI
[2024-01-24 11:49:26,959] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:49:26,960] [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_017487345.1	s__Brevundimonas sp017487345	100.0	1182	1183	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002979535.1	s__Brevundimonas sp002979535	90.8717	870	1183	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	100.00	100.00	0.99	0.98	5	-
GCA_002479495.1	s__Brevundimonas sp002479495	90.6135	839	1183	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014207965.1	s__Brevundimonas bullata_A	89.6637	878	1183	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003350205.1	s__Brevundimonas bullata	89.5661	863	1183	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	96.07	95.78	0.81	0.78	3	-
GCA_002387245.1	s__Brevundimonas sp002387245	89.029	836	1183	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003627995.1	s__Brevundimonas naejangsanensis_B	86.8527	777	1183	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002386585.1	s__Brevundimonas sp002386585	86.8403	664	1183	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	96.28	96.28	0.79	0.79	2	-
GCA_002430835.1	s__Brevundimonas sp002430835	86.7543	679	1183	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	99.55	99.55	0.86	0.86	2	-
GCF_003938605.1	s__Brevundimonas sp003938605	86.5409	757	1183	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	96.78	96.68	0.85	0.83	3	-
GCF_900163625.1	s__Brevundimonas diminuta_A	86.514	756	1183	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 11:49:26,961] [INFO] GTDB search result was written to GCF_017487345.1_ASM1748734v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:49:26,961] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:49:26,965] [INFO] DFAST_QC result json was written to GCF_017487345.1_ASM1748734v1_genomic.fna/dqc_result.json
[2024-01-24 11:49:26,965] [INFO] DFAST_QC completed!
[2024-01-24 11:49:26,965] [INFO] Total running time: 0h1m6s