[2023-06-08 09:05:13,075] [INFO] DFAST_QC pipeline started.
[2023-06-08 09:05:13,076] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 09:05:13,077] [INFO] DQC Reference Directory: /var/lib/cwl/stg00506efb-3ca6-41f5-bc80-084edfee5783/dqc_reference
[2023-06-08 09:05:14,535] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 09:05:14,536] [INFO] Task started: Prodigal
[2023-06-08 09:05:14,536] [INFO] Running command: gunzip -c /var/lib/cwl/stg7023de0f-c9ce-4429-9e60-20240d9ea4db/GCA_945874855.1_MiE-14oct19-195_genomic.fna.gz | prodigal -d GCA_945874855.1_MiE-14oct19-195_genomic.fna/cds.fna -a GCA_945874855.1_MiE-14oct19-195_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 09:05:19,608] [INFO] Task succeeded: Prodigal
[2023-06-08 09:05:19,609] [INFO] Task started: HMMsearch
[2023-06-08 09:05:19,609] [INFO] Running command: hmmsearch --tblout GCA_945874855.1_MiE-14oct19-195_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg00506efb-3ca6-41f5-bc80-084edfee5783/dqc_reference/reference_markers.hmm GCA_945874855.1_MiE-14oct19-195_genomic.fna/protein.faa > /dev/null
[2023-06-08 09:05:19,846] [INFO] Task succeeded: HMMsearch
[2023-06-08 09:05:19,848] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg7023de0f-c9ce-4429-9e60-20240d9ea4db/GCA_945874855.1_MiE-14oct19-195_genomic.fna.gz]
[2023-06-08 09:05:19,875] [INFO] Query marker FASTA was written to GCA_945874855.1_MiE-14oct19-195_genomic.fna/markers.fasta
[2023-06-08 09:05:19,875] [INFO] Task started: Blastn
[2023-06-08 09:05:19,876] [INFO] Running command: blastn -query GCA_945874855.1_MiE-14oct19-195_genomic.fna/markers.fasta -db /var/lib/cwl/stg00506efb-3ca6-41f5-bc80-084edfee5783/dqc_reference/reference_markers.fasta -out GCA_945874855.1_MiE-14oct19-195_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 09:05:20,814] [INFO] Task succeeded: Blastn
[2023-06-08 09:05:20,818] [INFO] Selected 16 target genomes.
[2023-06-08 09:05:20,819] [INFO] Target genome list was writen to GCA_945874855.1_MiE-14oct19-195_genomic.fna/target_genomes.txt
[2023-06-08 09:05:20,821] [INFO] Task started: fastANI
[2023-06-08 09:05:20,821] [INFO] Running command: fastANI --query /var/lib/cwl/stg7023de0f-c9ce-4429-9e60-20240d9ea4db/GCA_945874855.1_MiE-14oct19-195_genomic.fna.gz --refList GCA_945874855.1_MiE-14oct19-195_genomic.fna/target_genomes.txt --output GCA_945874855.1_MiE-14oct19-195_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 09:05:32,300] [INFO] Task succeeded: fastANI
[2023-06-08 09:05:32,301] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg00506efb-3ca6-41f5-bc80-084edfee5783/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 09:05:32,301] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg00506efb-3ca6-41f5-bc80-084edfee5783/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 09:05:32,315] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 09:05:32,316] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 09:05:32,316] [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 fluminis	strain=LA-55	GCA_003934285.1	2487274	2487274	type	True	83.3304	507	625	95	below_threshold
Brevundimonas basaltis	strain=DSM 25335	GCA_014202075.1	472166	472166	type	True	81.6593	416	625	95	below_threshold
Brevundimonas alba	strain=DSM 4736	GCA_011927945.1	74314	74314	type	True	81.3315	436	625	95	below_threshold
Brevundimonas lenta	strain=DSM 23960	GCA_014196335.1	424796	424796	type	True	81.2583	445	625	95	below_threshold
Brevundimonas viscosa	strain=CGMCC 1.10683	GCA_900116065.1	871741	871741	type	True	81.1546	441	625	95	below_threshold
Brevundimonas subvibrioides	strain=ATCC 15264	GCA_000144605.1	74313	74313	type	True	81.0328	446	625	95	below_threshold
Brevundimonas albigilva	strain=KEME 9005-016	GCA_023503965.1	1312364	1312364	type	True	81.0123	415	625	95	below_threshold
Brevundimonas bacteroides	strain=DSM 4726	GCA_000701445.1	74311	74311	type	True	80.9901	429	625	95	below_threshold
Brevundimonas halotolerans	strain=DSM 24448	GCA_014199165.1	69670	69670	type	True	80.841	402	625	95	below_threshold
Brevundimonas halotolerans	strain=MCS24	GCA_003730275.1	69670	69670	type	True	80.8363	403	625	95	below_threshold
Brevundimonas goettingensis	strain=LVF2	GCA_017487405.1	2774190	2774190	type	True	80.7741	429	625	95	below_threshold
Brevundimonas guildfordensis	strain=Sa3CVA3	GCA_014836405.1	2762241	2762241	type	True	80.6333	385	625	95	below_threshold
Brevundimonas lutea	strain=NS26	GCA_003704105.1	2293980	2293980	type	True	80.5629	363	625	95	below_threshold
Brevundimonas vitisensis	strain=GR-TSA-9	GCA_016656965.1	2800818	2800818	type	True	80.4301	408	625	95	below_threshold
Phenylobacterium glaciei	strain=20VBR1	GCA_016772415.2	2803784	2803784	type	True	78.1314	225	625	95	below_threshold
Brevundimonas pishanensis	strain=CHPC 1.3453	GCA_022750635.1	2896315	2896315	type	True	77.939	222	625	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 09:05:32,318] [INFO] DFAST Taxonomy check result was written to GCA_945874855.1_MiE-14oct19-195_genomic.fna/tc_result.tsv
[2023-06-08 09:05:32,319] [INFO] ===== Taxonomy check completed =====
[2023-06-08 09:05:32,319] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 09:05:32,319] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg00506efb-3ca6-41f5-bc80-084edfee5783/dqc_reference/checkm_data
[2023-06-08 09:05:32,321] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 09:05:32,355] [INFO] Task started: CheckM
[2023-06-08 09:05:32,356] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945874855.1_MiE-14oct19-195_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945874855.1_MiE-14oct19-195_genomic.fna/checkm_input GCA_945874855.1_MiE-14oct19-195_genomic.fna/checkm_result
[2023-06-08 09:05:54,163] [INFO] Task succeeded: CheckM
[2023-06-08 09:05:54,164] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 09:05:54,193] [INFO] ===== Completeness check finished =====
[2023-06-08 09:05:54,193] [INFO] ===== Start GTDB Search =====
[2023-06-08 09:05:54,194] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945874855.1_MiE-14oct19-195_genomic.fna/markers.fasta)
[2023-06-08 09:05:54,194] [INFO] Task started: Blastn
[2023-06-08 09:05:54,194] [INFO] Running command: blastn -query GCA_945874855.1_MiE-14oct19-195_genomic.fna/markers.fasta -db /var/lib/cwl/stg00506efb-3ca6-41f5-bc80-084edfee5783/dqc_reference/reference_markers_gtdb.fasta -out GCA_945874855.1_MiE-14oct19-195_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 09:05:55,886] [INFO] Task succeeded: Blastn
[2023-06-08 09:05:55,891] [INFO] Selected 19 target genomes.
[2023-06-08 09:05:55,891] [INFO] Target genome list was writen to GCA_945874855.1_MiE-14oct19-195_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 09:05:55,907] [INFO] Task started: fastANI
[2023-06-08 09:05:55,907] [INFO] Running command: fastANI --query /var/lib/cwl/stg7023de0f-c9ce-4429-9e60-20240d9ea4db/GCA_945874855.1_MiE-14oct19-195_genomic.fna.gz --refList GCA_945874855.1_MiE-14oct19-195_genomic.fna/target_genomes_gtdb.txt --output GCA_945874855.1_MiE-14oct19-195_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 09:06:06,757] [INFO] Task succeeded: fastANI
[2023-06-08 09:06:06,777] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 09:06:06,777] [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
GCA_018820275.1	s__Brevundimonas sp018820275	84.3105	500	625	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	99.93	99.85	0.97	0.95	5	-
GCF_003934285.1	s__Brevundimonas fluminis	83.324	508	625	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002483305.1	s__Brevundimonas sp002483305	81.9799	427	625	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	81.9716	443	625	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	81.8942	440	625	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	81.6535	416	625	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	81.4013	444	625	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	81.3366	435	625	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	81.3214	427	625	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	81.3164	433	625	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	81.2831	443	625	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	81.1829	437	625	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	81.147	443	625	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	81.1462	353	625	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015234495.1	s__Brevundimonas sp015234495	81.1197	303	625	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018820665.1	s__Brevundimonas sp018820665	81.1141	377	625	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	99.88	99.88	0.93	0.93	2	-
GCF_001425945.1	s__Brevundimonas sp001425945	81.1107	460	625	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004683885.1	s__Brevundimonas sp004683885	80.7533	376	625	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000466985.1	s__Brevundimonas abyssalis	80.2753	353	625	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	99.78	99.71	0.94	0.89	3	-
--------------------------------------------------------------------------------
[2023-06-08 09:06:06,779] [INFO] GTDB search result was written to GCA_945874855.1_MiE-14oct19-195_genomic.fna/result_gtdb.tsv
[2023-06-08 09:06:06,780] [INFO] ===== GTDB Search completed =====
[2023-06-08 09:06:06,784] [INFO] DFAST_QC result json was written to GCA_945874855.1_MiE-14oct19-195_genomic.fna/dqc_result.json
[2023-06-08 09:06:06,784] [INFO] DFAST_QC completed!
[2023-06-08 09:06:06,784] [INFO] Total running time: 0h0m54s