[2024-01-25 18:44:20,368] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:44:20,370] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:44:20,370] [INFO] DQC Reference Directory: /var/lib/cwl/stg2b05cecb-4be7-4274-9731-051c8fd18925/dqc_reference
[2024-01-25 18:44:21,497] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:44:21,498] [INFO] Task started: Prodigal
[2024-01-25 18:44:21,498] [INFO] Running command: gunzip -c /var/lib/cwl/stg152aacc4-18f6-442a-9cc7-fe8a01259276/GCF_014196335.1_ASM1419633v1_genomic.fna.gz | prodigal -d GCF_014196335.1_ASM1419633v1_genomic.fna/cds.fna -a GCF_014196335.1_ASM1419633v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:44:29,175] [INFO] Task succeeded: Prodigal
[2024-01-25 18:44:29,175] [INFO] Task started: HMMsearch
[2024-01-25 18:44:29,175] [INFO] Running command: hmmsearch --tblout GCF_014196335.1_ASM1419633v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2b05cecb-4be7-4274-9731-051c8fd18925/dqc_reference/reference_markers.hmm GCF_014196335.1_ASM1419633v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:44:29,378] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:44:29,380] [INFO] Found 6/6 markers.
[2024-01-25 18:44:29,408] [INFO] Query marker FASTA was written to GCF_014196335.1_ASM1419633v1_genomic.fna/markers.fasta
[2024-01-25 18:44:29,408] [INFO] Task started: Blastn
[2024-01-25 18:44:29,409] [INFO] Running command: blastn -query GCF_014196335.1_ASM1419633v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2b05cecb-4be7-4274-9731-051c8fd18925/dqc_reference/reference_markers.fasta -out GCF_014196335.1_ASM1419633v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:44:30,335] [INFO] Task succeeded: Blastn
[2024-01-25 18:44:30,338] [INFO] Selected 15 target genomes.
[2024-01-25 18:44:30,338] [INFO] Target genome list was writen to GCF_014196335.1_ASM1419633v1_genomic.fna/target_genomes.txt
[2024-01-25 18:44:30,343] [INFO] Task started: fastANI
[2024-01-25 18:44:30,343] [INFO] Running command: fastANI --query /var/lib/cwl/stg152aacc4-18f6-442a-9cc7-fe8a01259276/GCF_014196335.1_ASM1419633v1_genomic.fna.gz --refList GCF_014196335.1_ASM1419633v1_genomic.fna/target_genomes.txt --output GCF_014196335.1_ASM1419633v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:44:41,583] [INFO] Task succeeded: fastANI
[2024-01-25 18:44:41,584] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2b05cecb-4be7-4274-9731-051c8fd18925/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:44:41,584] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2b05cecb-4be7-4274-9731-051c8fd18925/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:44:41,594] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:44:41,594] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:44:41,594] [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 lenta	strain=DSM 23960	GCA_014196335.1	424796	424796	type	True	100.0	1116	1117	95	conclusive
Brevundimonas alba	strain=DSM 4736	GCA_011927945.1	74314	74314	type	True	84.6654	785	1117	95	below_threshold
Brevundimonas viscosa	strain=CGMCC 1.10683	GCA_900116065.1	871741	871741	type	True	84.1228	748	1117	95	below_threshold
Brevundimonas basaltis	strain=DSM 25335	GCA_014202075.1	472166	472166	type	True	83.8742	696	1117	95	below_threshold
Brevundimonas pondensis	strain=LVF1	GCA_017487345.1	2774189	2774189	type	True	82.2358	642	1117	95	below_threshold
Brevundimonas albigilva	strain=KEME 9005-016	GCA_023503965.1	1312364	1312364	type	True	82.2166	641	1117	95	below_threshold
Brevundimonas bullata	strain=HAMBI_262	GCA_003350205.1	13160	13160	type	True	82.1588	634	1117	95	below_threshold
Brevundimonas guildfordensis	strain=Sa3CVA3	GCA_014836405.1	2762241	2762241	type	True	81.8739	596	1117	95	below_threshold
Brevundimonas fluminis	strain=LA-55	GCA_003934285.1	2487274	2487274	type	True	81.7507	621	1117	95	below_threshold
Brevundimonas huaxiensis	strain=090558	GCA_014218725.1	2725493	2725493	type	True	81.6979	619	1117	95	below_threshold
Brevundimonas vesicularis	strain=NBRC 12165	GCA_001592205.1	41276	41276	suspected-type	True	81.5278	611	1117	95	below_threshold
Brevundimonas nasdae	strain=JCM 11415	GCA_016654005.1	172043	172043	type	True	81.3869	625	1117	95	below_threshold
Brevundimonas vitisensis	strain=GR-TSA-9	GCA_016656965.1	2800818	2800818	type	True	80.4468	552	1117	95	below_threshold
Brevundimonas pishanensis	strain=CHPC 1.3453	GCA_022750635.1	2896315	2896315	type	True	79.0687	395	1117	95	below_threshold
Phenylobacterium aquaticum	strain=KACC 18306	GCA_022695515.1	1763816	1763816	type	True	78.3959	412	1117	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:44:41,596] [INFO] DFAST Taxonomy check result was written to GCF_014196335.1_ASM1419633v1_genomic.fna/tc_result.tsv
[2024-01-25 18:44:41,597] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:44:41,598] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:44:41,598] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2b05cecb-4be7-4274-9731-051c8fd18925/dqc_reference/checkm_data
[2024-01-25 18:44:41,599] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:44:41,636] [INFO] Task started: CheckM
[2024-01-25 18:44:41,636] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014196335.1_ASM1419633v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014196335.1_ASM1419633v1_genomic.fna/checkm_input GCF_014196335.1_ASM1419633v1_genomic.fna/checkm_result
[2024-01-25 18:45:09,124] [INFO] Task succeeded: CheckM
[2024-01-25 18:45:09,125] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:45:09,146] [INFO] ===== Completeness check finished =====
[2024-01-25 18:45:09,147] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:45:09,147] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014196335.1_ASM1419633v1_genomic.fna/markers.fasta)
[2024-01-25 18:45:09,147] [INFO] Task started: Blastn
[2024-01-25 18:45:09,147] [INFO] Running command: blastn -query GCF_014196335.1_ASM1419633v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2b05cecb-4be7-4274-9731-051c8fd18925/dqc_reference/reference_markers_gtdb.fasta -out GCF_014196335.1_ASM1419633v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:45:11,026] [INFO] Task succeeded: Blastn
[2024-01-25 18:45:11,028] [INFO] Selected 17 target genomes.
[2024-01-25 18:45:11,028] [INFO] Target genome list was writen to GCF_014196335.1_ASM1419633v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:45:11,048] [INFO] Task started: fastANI
[2024-01-25 18:45:11,048] [INFO] Running command: fastANI --query /var/lib/cwl/stg152aacc4-18f6-442a-9cc7-fe8a01259276/GCF_014196335.1_ASM1419633v1_genomic.fna.gz --refList GCF_014196335.1_ASM1419633v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014196335.1_ASM1419633v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:45:24,584] [INFO] Task succeeded: fastANI
[2024-01-25 18:45:24,594] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:45:24,595] [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_014196335.1	s__Brevundimonas lenta	100.0	1116	1117	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_001425945.1	s__Brevundimonas sp001425945	85.8233	866	1117	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011927945.1	s__Brevundimonas alba	84.6671	786	1117	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016742215.1	s__Brevundimonas sp016742215	84.5739	526	1117	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	84.5476	728	1117	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	84.4972	682	1117	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	84.3998	725	1117	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006547065.1	s__Brevundimonas sp006547065	84.2626	772	1117	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	84.2544	721	1117	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	84.1357	747	1117	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018826515.1	s__Brevundimonas sp018826515	83.9442	714	1117	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	99.85	99.80	0.97	0.95	6	-
GCF_014202075.1	s__Brevundimonas basaltis	83.8732	697	1117	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006515835.1	s__Brevundimonas sp006515835	83.2652	566	1117	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	82.246	642	1117	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003350205.1	s__Brevundimonas bullata	82.1945	631	1117	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	96.07	95.78	0.81	0.78	3	-
GCA_018820275.1	s__Brevundimonas sp018820275	81.9768	629	1117	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	99.93	99.85	0.97	0.95	5	-
GCA_013912065.1	s__Brevundimonas sp013912065	81.6525	603	1117	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 18:45:24,596] [INFO] GTDB search result was written to GCF_014196335.1_ASM1419633v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:45:24,597] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:45:24,600] [INFO] DFAST_QC result json was written to GCF_014196335.1_ASM1419633v1_genomic.fna/dqc_result.json
[2024-01-25 18:45:24,601] [INFO] DFAST_QC completed!
[2024-01-25 18:45:24,601] [INFO] Total running time: 0h1m4s