[2024-01-24 13:10:19,225] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:10:19,226] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:10:19,227] [INFO] DQC Reference Directory: /var/lib/cwl/stga851cc83-79f6-4965-b77f-b393954e7735/dqc_reference
[2024-01-24 13:10:20,524] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:10:20,525] [INFO] Task started: Prodigal
[2024-01-24 13:10:20,525] [INFO] Running command: gunzip -c /var/lib/cwl/stg878a6d29-72f5-498b-aa21-1183e620b921/GCF_003704105.1_ASM370410v1_genomic.fna.gz | prodigal -d GCF_003704105.1_ASM370410v1_genomic.fna/cds.fna -a GCF_003704105.1_ASM370410v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:10:28,550] [INFO] Task succeeded: Prodigal
[2024-01-24 13:10:28,551] [INFO] Task started: HMMsearch
[2024-01-24 13:10:28,551] [INFO] Running command: hmmsearch --tblout GCF_003704105.1_ASM370410v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga851cc83-79f6-4965-b77f-b393954e7735/dqc_reference/reference_markers.hmm GCF_003704105.1_ASM370410v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:10:28,847] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:10:28,848] [INFO] Found 6/6 markers.
[2024-01-24 13:10:28,875] [INFO] Query marker FASTA was written to GCF_003704105.1_ASM370410v1_genomic.fna/markers.fasta
[2024-01-24 13:10:28,876] [INFO] Task started: Blastn
[2024-01-24 13:10:28,876] [INFO] Running command: blastn -query GCF_003704105.1_ASM370410v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga851cc83-79f6-4965-b77f-b393954e7735/dqc_reference/reference_markers.fasta -out GCF_003704105.1_ASM370410v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:29,848] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:29,852] [INFO] Selected 16 target genomes.
[2024-01-24 13:10:29,852] [INFO] Target genome list was writen to GCF_003704105.1_ASM370410v1_genomic.fna/target_genomes.txt
[2024-01-24 13:10:29,868] [INFO] Task started: fastANI
[2024-01-24 13:10:29,869] [INFO] Running command: fastANI --query /var/lib/cwl/stg878a6d29-72f5-498b-aa21-1183e620b921/GCF_003704105.1_ASM370410v1_genomic.fna.gz --refList GCF_003704105.1_ASM370410v1_genomic.fna/target_genomes.txt --output GCF_003704105.1_ASM370410v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:10:41,161] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:41,162] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga851cc83-79f6-4965-b77f-b393954e7735/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:10:41,162] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga851cc83-79f6-4965-b77f-b393954e7735/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:10:41,181] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:10:41,181] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:10:41,181] [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 lutea	strain=NS26	GCA_003704105.1	2293980	2293980	type	True	100.0	988	989	95	conclusive
Brevundimonas albigilva	strain=KEME 9005-016	GCA_023503965.1	1312364	1312364	type	True	81.2866	553	989	95	below_threshold
Brevundimonas viscosa	strain=CGMCC 1.10683	GCA_900116065.1	871741	871741	type	True	81.0496	522	989	95	below_threshold
Brevundimonas basaltis	strain=DSM 25335	GCA_014202075.1	472166	472166	type	True	80.6462	500	989	95	below_threshold
Brevundimonas aurantiaca	strain=DSM 4731	GCA_014199955.1	74316	74316	type	True	80.6439	523	989	95	below_threshold
Brevundimonas lenta	strain=DSM 23960	GCA_014196335.1	424796	424796	type	True	80.4251	549	989	95	below_threshold
Brevundimonas guildfordensis	strain=Sa3CVA3	GCA_014836405.1	2762241	2762241	type	True	80.3818	501	989	95	below_threshold
Brevundimonas diminuta	strain=NCTC8545	GCA_900445995.1	293	293	type	True	80.3764	528	989	95	below_threshold
Brevundimonas diminuta	strain=ATCC 11568	GCA_000204035.1	293	293	type	True	80.3605	520	989	95	below_threshold
Brevundimonas mediterranea	strain=DSM 14878	GCA_014196125.1	74329	74329	type	True	80.3345	540	989	95	below_threshold
Brevundimonas subvibrioides	strain=ATCC 15264	GCA_000144605.1	74313	74313	type	True	80.2702	526	989	95	below_threshold
Brevundimonas nasdae	strain=JCM 11415	GCA_016654005.1	172043	172043	type	True	80.2308	493	989	95	below_threshold
Brevundimonas vesicularis	strain=NBRC 12165	GCA_001592205.1	41276	41276	suspected-type	True	80.1671	509	989	95	below_threshold
Brevundimonas vitisensis	strain=GR-TSA-9	GCA_016656965.1	2800818	2800818	type	True	79.9034	468	989	95	below_threshold
Phenylobacterium glaciei	strain=20VBR1	GCA_016772415.2	2803784	2803784	type	True	78.1015	336	989	95	below_threshold
Phenylobacterium aquaticum	strain=KACC 18306	GCA_022695515.1	1763816	1763816	type	True	78.0629	350	989	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:10:41,183] [INFO] DFAST Taxonomy check result was written to GCF_003704105.1_ASM370410v1_genomic.fna/tc_result.tsv
[2024-01-24 13:10:41,184] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:10:41,184] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:10:41,184] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga851cc83-79f6-4965-b77f-b393954e7735/dqc_reference/checkm_data
[2024-01-24 13:10:41,185] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:10:41,225] [INFO] Task started: CheckM
[2024-01-24 13:10:41,225] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003704105.1_ASM370410v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003704105.1_ASM370410v1_genomic.fna/checkm_input GCF_003704105.1_ASM370410v1_genomic.fna/checkm_result
[2024-01-24 13:11:09,677] [INFO] Task succeeded: CheckM
[2024-01-24 13:11:09,678] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:11:09,697] [INFO] ===== Completeness check finished =====
[2024-01-24 13:11:09,697] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:11:09,698] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003704105.1_ASM370410v1_genomic.fna/markers.fasta)
[2024-01-24 13:11:09,698] [INFO] Task started: Blastn
[2024-01-24 13:11:09,699] [INFO] Running command: blastn -query GCF_003704105.1_ASM370410v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga851cc83-79f6-4965-b77f-b393954e7735/dqc_reference/reference_markers_gtdb.fasta -out GCF_003704105.1_ASM370410v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:11:11,546] [INFO] Task succeeded: Blastn
[2024-01-24 13:11:11,550] [INFO] Selected 21 target genomes.
[2024-01-24 13:11:11,551] [INFO] Target genome list was writen to GCF_003704105.1_ASM370410v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:11:11,616] [INFO] Task started: fastANI
[2024-01-24 13:11:11,617] [INFO] Running command: fastANI --query /var/lib/cwl/stg878a6d29-72f5-498b-aa21-1183e620b921/GCF_003704105.1_ASM370410v1_genomic.fna.gz --refList GCF_003704105.1_ASM370410v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003704105.1_ASM370410v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:11:25,623] [INFO] Task succeeded: fastANI
[2024-01-24 13:11:25,645] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:11:25,646] [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_003704105.1	s__Brevundimonas lutea	100.0	988	989	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_013912005.1	s__Brevundimonas sp013912005	81.0159	526	989	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116065.1	s__Brevundimonas viscosa	81.0053	526	989	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001427825.1	s__Brevundimonas sp001427825	80.9674	521	989	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	80.8455	536	989	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	80.7622	541	989	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016183935.1	s__Brevundimonas sp016183935	80.7266	492	989	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002479325.1	s__Brevundimonas sp002479325	80.6999	472	989	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004210735.1	s__Brevundimonas sp004210735	80.6775	482	989	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	80.649	508	989	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	99.93	99.85	0.97	0.95	5	-
GCF_002002865.1	s__Brevundimonas sp002002865	80.6379	536	989	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	80.597	546	989	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0657	98.11	97.23	0.89	0.83	17	-
GCA_003248925.1	s__Brevundimonas sp003248925	80.5572	468	989	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	80.5079	540	989	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	80.5066	496	989	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	99.78	99.71	0.94	0.89	3	-
GCA_013823285.1	s__Brevundimonas sp013823285	80.4596	474	989	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013912065.1	s__Brevundimonas sp013912065	80.4528	521	989	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196335.1	s__Brevundimonas lenta	80.4387	549	989	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017418605.1	s__CAISGS01 sp017418605	78.6348	398	989	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__CAISGS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016125585.1	s__Caulobacter sp016125585	78.2794	366	989	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016234625.1	s__Caulobacter sp016234625	78.2252	305	989	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:11:25,647] [INFO] GTDB search result was written to GCF_003704105.1_ASM370410v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:11:25,648] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:11:25,652] [INFO] DFAST_QC result json was written to GCF_003704105.1_ASM370410v1_genomic.fna/dqc_result.json
[2024-01-24 13:11:25,652] [INFO] DFAST_QC completed!
[2024-01-24 13:11:25,652] [INFO] Total running time: 0h1m6s