[2024-01-25 18:33:35,618] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:33:35,620] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:33:35,620] [INFO] DQC Reference Directory: /var/lib/cwl/stgac7d029e-91f5-4c3f-9588-16b3014c5fba/dqc_reference
[2024-01-25 18:33:36,778] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:33:36,779] [INFO] Task started: Prodigal
[2024-01-25 18:33:36,779] [INFO] Running command: gunzip -c /var/lib/cwl/stg1e715fcd-9bb4-4f53-81e6-4118982331ef/GCF_017487405.1_ASM1748740v1_genomic.fna.gz | prodigal -d GCF_017487405.1_ASM1748740v1_genomic.fna/cds.fna -a GCF_017487405.1_ASM1748740v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:33:45,982] [INFO] Task succeeded: Prodigal
[2024-01-25 18:33:45,982] [INFO] Task started: HMMsearch
[2024-01-25 18:33:45,982] [INFO] Running command: hmmsearch --tblout GCF_017487405.1_ASM1748740v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgac7d029e-91f5-4c3f-9588-16b3014c5fba/dqc_reference/reference_markers.hmm GCF_017487405.1_ASM1748740v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:33:46,223] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:33:46,224] [INFO] Found 6/6 markers.
[2024-01-25 18:33:46,257] [INFO] Query marker FASTA was written to GCF_017487405.1_ASM1748740v1_genomic.fna/markers.fasta
[2024-01-25 18:33:46,257] [INFO] Task started: Blastn
[2024-01-25 18:33:46,258] [INFO] Running command: blastn -query GCF_017487405.1_ASM1748740v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgac7d029e-91f5-4c3f-9588-16b3014c5fba/dqc_reference/reference_markers.fasta -out GCF_017487405.1_ASM1748740v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:33:47,107] [INFO] Task succeeded: Blastn
[2024-01-25 18:33:47,111] [INFO] Selected 20 target genomes.
[2024-01-25 18:33:47,111] [INFO] Target genome list was writen to GCF_017487405.1_ASM1748740v1_genomic.fna/target_genomes.txt
[2024-01-25 18:33:47,123] [INFO] Task started: fastANI
[2024-01-25 18:33:47,123] [INFO] Running command: fastANI --query /var/lib/cwl/stg1e715fcd-9bb4-4f53-81e6-4118982331ef/GCF_017487405.1_ASM1748740v1_genomic.fna.gz --refList GCF_017487405.1_ASM1748740v1_genomic.fna/target_genomes.txt --output GCF_017487405.1_ASM1748740v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:34:03,166] [INFO] Task succeeded: fastANI
[2024-01-25 18:34:03,167] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgac7d029e-91f5-4c3f-9588-16b3014c5fba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:34:03,167] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgac7d029e-91f5-4c3f-9588-16b3014c5fba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:34:03,179] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:34:03,179] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:34:03,180] [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 goettingensis	strain=LVF2	GCA_017487405.1	2774190	2774190	type	True	100.0	1327	1328	95	conclusive
Brevundimonas lenta	strain=DSM 23960	GCA_014196335.1	424796	424796	type	True	82.4093	722	1328	95	below_threshold
Brevundimonas albigilva	strain=KEME 9005-016	GCA_023503965.1	1312364	1312364	type	True	82.2383	700	1328	95	below_threshold
Brevundimonas subvibrioides	strain=ATCC 15264	GCA_000144605.1	74313	74313	type	True	82.2051	749	1328	95	below_threshold
Brevundimonas mediterranea	strain=DSM 14878	GCA_014196125.1	74329	74329	type	True	82.1306	690	1328	95	below_threshold
Brevundimonas huaxiensis	strain=090558	GCA_014218725.1	2725493	2725493	type	True	81.9551	685	1328	95	below_threshold
Brevundimonas bullata	strain=HAMBI_262	GCA_003350205.1	13160	13160	type	True	81.9494	679	1328	95	below_threshold
Brevundimonas alba	strain=DSM 4736	GCA_011927945.1	74314	74314	type	True	81.922	676	1328	95	below_threshold
Brevundimonas pondensis	strain=LVF1	GCA_017487345.1	2774189	2774189	type	True	81.9122	698	1328	95	below_threshold
Brevundimonas vesicularis	strain=NBRC 12165	GCA_001592205.1	41276	41276	suspected-type	True	81.8313	676	1328	95	below_threshold
Brevundimonas aurantiaca	strain=DSM 4731	GCA_014199955.1	74316	74316	type	True	81.7305	702	1328	95	below_threshold
Brevundimonas diminuta	strain=ATCC 11568	GCA_000204035.1	293	293	type	True	81.6378	651	1328	95	below_threshold
Brevundimonas basaltis	strain=DSM 25335	GCA_014202075.1	472166	472166	type	True	81.5659	593	1328	95	below_threshold
Brevundimonas guildfordensis	strain=Sa3CVA3	GCA_014836405.1	2762241	2762241	type	True	81.5246	601	1328	95	below_threshold
Brevundimonas nasdae	strain=JCM 11415	GCA_016654005.1	172043	172043	type	True	81.5233	688	1328	95	below_threshold
Brevundimonas bacteroides	strain=DSM 4726	GCA_000701445.1	74311	74311	type	True	81.2722	658	1328	95	below_threshold
Brevundimonas viscosa	strain=CGMCC 1.10683	GCA_900116065.1	871741	871741	type	True	81.1071	646	1328	95	below_threshold
Brevundimonas vitisensis	strain=GR-TSA-9	GCA_016656965.1	2800818	2800818	type	True	80.5235	590	1328	95	below_threshold
Brevundimonas pishanensis	strain=CHPC 1.3453	GCA_022750635.1	2896315	2896315	type	True	78.5696	381	1328	95	below_threshold
Phenylobacterium aquaticum	strain=KACC 18306	GCA_022695515.1	1763816	1763816	type	True	78.0853	457	1328	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:34:03,181] [INFO] DFAST Taxonomy check result was written to GCF_017487405.1_ASM1748740v1_genomic.fna/tc_result.tsv
[2024-01-25 18:34:03,181] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:34:03,182] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:34:03,182] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgac7d029e-91f5-4c3f-9588-16b3014c5fba/dqc_reference/checkm_data
[2024-01-25 18:34:03,183] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:34:03,223] [INFO] Task started: CheckM
[2024-01-25 18:34:03,223] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017487405.1_ASM1748740v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017487405.1_ASM1748740v1_genomic.fna/checkm_input GCF_017487405.1_ASM1748740v1_genomic.fna/checkm_result
[2024-01-25 18:34:33,850] [INFO] Task succeeded: CheckM
[2024-01-25 18:34:33,851] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:34:33,890] [INFO] ===== Completeness check finished =====
[2024-01-25 18:34:33,890] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:34:33,890] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017487405.1_ASM1748740v1_genomic.fna/markers.fasta)
[2024-01-25 18:34:33,891] [INFO] Task started: Blastn
[2024-01-25 18:34:33,891] [INFO] Running command: blastn -query GCF_017487405.1_ASM1748740v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgac7d029e-91f5-4c3f-9588-16b3014c5fba/dqc_reference/reference_markers_gtdb.fasta -out GCF_017487405.1_ASM1748740v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:34:35,620] [INFO] Task succeeded: Blastn
[2024-01-25 18:34:35,625] [INFO] Selected 18 target genomes.
[2024-01-25 18:34:35,625] [INFO] Target genome list was writen to GCF_017487405.1_ASM1748740v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:34:35,653] [INFO] Task started: fastANI
[2024-01-25 18:34:35,653] [INFO] Running command: fastANI --query /var/lib/cwl/stg1e715fcd-9bb4-4f53-81e6-4118982331ef/GCF_017487405.1_ASM1748740v1_genomic.fna.gz --refList GCF_017487405.1_ASM1748740v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017487405.1_ASM1748740v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:34:50,193] [INFO] Task succeeded: fastANI
[2024-01-25 18:34:50,205] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:34:50,205] [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_017487405.1	s__Brevundimonas sp017487405	100.0	1328	1328	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002292165.1	s__Brevundimonas sp002292165	90.6855	875	1328	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016463485.1	s__Brevundimonas sp016463485	82.798	698	1328	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002002865.1	s__Brevundimonas sp002002865	82.596	713	1328	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002280785.1	s__Brevundimonas subvibrioides_B	82.4433	716	1328	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011064825.1	s__Brevundimonas mediterranea_A	82.3614	708	1328	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0657	98.11	97.23	0.89	0.83	17	-
GCF_000144605.1	s__Brevundimonas subvibrioides	82.2166	747	1328	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196125.1	s__Brevundimonas mediterranea	82.121	692	1328	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0657	N/A	N/A	N/A	N/A	1	-
GCF_017795885.1	s__Brevundimonas sp017795885	82.0169	657	1328	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002434505.1	s__Brevundimonas sp002434505	81.9678	710	1328	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	99.71	99.71	0.98	0.98	2	-
GCF_011927945.1	s__Brevundimonas alba	81.9407	674	1328	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	81.9262	664	1328	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001592205.1	s__Brevundimonas vesicularis	81.8402	675	1328	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	95.70	95.00	0.85	0.82	10	-
GCA_018826515.1	s__Brevundimonas sp018826515	81.8242	669	1328	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	99.85	99.80	0.97	0.95	6	-
GCA_003248925.1	s__Brevundimonas sp003248925	81.8139	541	1328	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001424025.1	s__Brevundimonas sp001424025	81.7957	680	1328	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002484265.1	s__Brevundimonas sp002484265	81.6113	688	1328	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	99.51	99.05	0.94	0.88	3	-
GCA_016183935.1	s__Brevundimonas sp016183935	81.5883	627	1328	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:34:50,207] [INFO] GTDB search result was written to GCF_017487405.1_ASM1748740v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:34:50,208] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:34:50,212] [INFO] DFAST_QC result json was written to GCF_017487405.1_ASM1748740v1_genomic.fna/dqc_result.json
[2024-01-25 18:34:50,212] [INFO] DFAST_QC completed!
[2024-01-25 18:34:50,212] [INFO] Total running time: 0h1m15s