[2024-01-24 12:06:14,255] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:14,258] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:14,258] [INFO] DQC Reference Directory: /var/lib/cwl/stg1f57ed2e-27c0-4b65-87ad-c1bb3f983dfe/dqc_reference
[2024-01-24 12:06:15,704] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:15,705] [INFO] Task started: Prodigal
[2024-01-24 12:06:15,705] [INFO] Running command: gunzip -c /var/lib/cwl/stg7b9853f7-dd1f-4e38-a741-24da93036e3a/GCF_014196125.1_ASM1419612v1_genomic.fna.gz | prodigal -d GCF_014196125.1_ASM1419612v1_genomic.fna/cds.fna -a GCF_014196125.1_ASM1419612v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:24,833] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:24,833] [INFO] Task started: HMMsearch
[2024-01-24 12:06:24,833] [INFO] Running command: hmmsearch --tblout GCF_014196125.1_ASM1419612v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1f57ed2e-27c0-4b65-87ad-c1bb3f983dfe/dqc_reference/reference_markers.hmm GCF_014196125.1_ASM1419612v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:25,079] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:25,080] [INFO] Found 6/6 markers.
[2024-01-24 12:06:25,118] [INFO] Query marker FASTA was written to GCF_014196125.1_ASM1419612v1_genomic.fna/markers.fasta
[2024-01-24 12:06:25,118] [INFO] Task started: Blastn
[2024-01-24 12:06:25,118] [INFO] Running command: blastn -query GCF_014196125.1_ASM1419612v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f57ed2e-27c0-4b65-87ad-c1bb3f983dfe/dqc_reference/reference_markers.fasta -out GCF_014196125.1_ASM1419612v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:26,080] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:26,083] [INFO] Selected 11 target genomes.
[2024-01-24 12:06:26,083] [INFO] Target genome list was writen to GCF_014196125.1_ASM1419612v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:26,088] [INFO] Task started: fastANI
[2024-01-24 12:06:26,088] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b9853f7-dd1f-4e38-a741-24da93036e3a/GCF_014196125.1_ASM1419612v1_genomic.fna.gz --refList GCF_014196125.1_ASM1419612v1_genomic.fna/target_genomes.txt --output GCF_014196125.1_ASM1419612v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:35,139] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:35,139] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1f57ed2e-27c0-4b65-87ad-c1bb3f983dfe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:35,140] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1f57ed2e-27c0-4b65-87ad-c1bb3f983dfe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:35,149] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:06:35,150] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:35,150] [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 mediterranea	strain=DSM 14878	GCA_014196125.1	74329	74329	type	True	100.0	1131	1131	95	conclusive
Brevundimonas aurantiaca	strain=DSM 4731	GCA_014199955.1	74316	74316	type	True	87.7172	848	1131	95	below_threshold
Brevundimonas vesicularis	strain=NBRC 12165	GCA_001592205.1	41276	41276	suspected-type	True	86.1112	780	1131	95	below_threshold
Brevundimonas huaxiensis	strain=090558	GCA_014218725.1	2725493	2725493	type	True	86.0524	771	1131	95	below_threshold
Brevundimonas nasdae	strain=JCM 11415	GCA_016654005.1	172043	172043	type	True	85.1169	777	1131	95	below_threshold
Brevundimonas albigilva	strain=KEME 9005-016	GCA_023503965.1	1312364	1312364	type	True	85.0923	772	1131	95	below_threshold
Brevundimonas bullata	strain=HAMBI_262	GCA_003350205.1	13160	13160	type	True	82.8408	679	1131	95	below_threshold
Brevundimonas guildfordensis	strain=Sa3CVA3	GCA_014836405.1	2762241	2762241	type	True	82.0405	610	1131	95	below_threshold
Brevundimonas vitisensis	strain=GR-TSA-9	GCA_016656965.1	2800818	2800818	type	True	80.4995	565	1131	95	below_threshold
Brevundimonas pishanensis	strain=CHPC 1.3453	GCA_022750635.1	2896315	2896315	type	True	79.2202	373	1131	95	below_threshold
Caulobacter rhizosphaerae	strain=CGMCC 1.15915	GCA_014645055.1	2010972	2010972	type	True	78.5787	466	1131	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:35,153] [INFO] DFAST Taxonomy check result was written to GCF_014196125.1_ASM1419612v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:35,154] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:35,154] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:35,154] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1f57ed2e-27c0-4b65-87ad-c1bb3f983dfe/dqc_reference/checkm_data
[2024-01-24 12:06:35,155] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:35,200] [INFO] Task started: CheckM
[2024-01-24 12:06:35,201] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014196125.1_ASM1419612v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014196125.1_ASM1419612v1_genomic.fna/checkm_input GCF_014196125.1_ASM1419612v1_genomic.fna/checkm_result
[2024-01-24 12:07:07,146] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:07,147] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:07,174] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:07,175] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:07,176] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014196125.1_ASM1419612v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:07,176] [INFO] Task started: Blastn
[2024-01-24 12:07:07,176] [INFO] Running command: blastn -query GCF_014196125.1_ASM1419612v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f57ed2e-27c0-4b65-87ad-c1bb3f983dfe/dqc_reference/reference_markers_gtdb.fasta -out GCF_014196125.1_ASM1419612v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:09,099] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:09,107] [INFO] Selected 11 target genomes.
[2024-01-24 12:07:09,107] [INFO] Target genome list was writen to GCF_014196125.1_ASM1419612v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:09,135] [INFO] Task started: fastANI
[2024-01-24 12:07:09,136] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b9853f7-dd1f-4e38-a741-24da93036e3a/GCF_014196125.1_ASM1419612v1_genomic.fna.gz --refList GCF_014196125.1_ASM1419612v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014196125.1_ASM1419612v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:18,321] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:18,333] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:18,333] [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_014196125.1	s__Brevundimonas mediterranea	100.0	1131	1131	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0657	N/A	N/A	N/A	N/A	1	conclusive
GCF_011064825.1	s__Brevundimonas mediterranea_A	95.0657	942	1131	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0657	98.11	97.23	0.89	0.83	17	conclusive
GCA_013912065.1	s__Brevundimonas sp013912065	88.4675	842	1131	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004614235.1	s__Brevundimonas intermedia	87.9379	814	1131	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001796045.1	s__Brevundimonas sp001796045	87.8303	656	1131	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199955.1	s__Brevundimonas aurantiaca	87.702	849	1131	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	97.57	96.95	0.92	0.85	12	-
GCF_902506205.1	s__Brevundimonas sp902506205	87.0512	794	1131	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	86.7086	761	1131	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	86.4534	803	1131	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	99.71	99.71	0.98	0.98	2	-
GCF_017086445.1	s__Brevundimonas vesicularis_A	86.3849	781	1131	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	95.13	95.13	0.83	0.83	2	-
GCF_001592205.1	s__Brevundimonas vesicularis	86.1275	778	1131	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	95.70	95.00	0.85	0.82	10	-
--------------------------------------------------------------------------------
[2024-01-24 12:07:18,337] [INFO] GTDB search result was written to GCF_014196125.1_ASM1419612v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:18,337] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:18,342] [INFO] DFAST_QC result json was written to GCF_014196125.1_ASM1419612v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:18,342] [INFO] DFAST_QC completed!
[2024-01-24 12:07:18,342] [INFO] Total running time: 0h1m4s