[2023-06-18 19:52:00,408] [INFO] DFAST_QC pipeline started.
[2023-06-18 19:52:00,413] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 19:52:00,413] [INFO] DQC Reference Directory: /var/lib/cwl/stg6800f373-9c6b-4c66-acd3-70724259f7be/dqc_reference
[2023-06-18 19:52:01,963] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 19:52:01,964] [INFO] Task started: Prodigal
[2023-06-18 19:52:01,964] [INFO] Running command: gunzip -c /var/lib/cwl/stge85164a6-ab46-4d4d-b091-7455c8e7ee5b/GCA_018897895.1_ASM1889789v1_genomic.fna.gz | prodigal -d GCA_018897895.1_ASM1889789v1_genomic.fna/cds.fna -a GCA_018897895.1_ASM1889789v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 19:52:06,037] [INFO] Task succeeded: Prodigal
[2023-06-18 19:52:06,038] [INFO] Task started: HMMsearch
[2023-06-18 19:52:06,038] [INFO] Running command: hmmsearch --tblout GCA_018897895.1_ASM1889789v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6800f373-9c6b-4c66-acd3-70724259f7be/dqc_reference/reference_markers.hmm GCA_018897895.1_ASM1889789v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 19:52:06,217] [INFO] Task succeeded: HMMsearch
[2023-06-18 19:52:06,219] [WARNING] Found 3/6 markers. [/var/lib/cwl/stge85164a6-ab46-4d4d-b091-7455c8e7ee5b/GCA_018897895.1_ASM1889789v1_genomic.fna.gz]
[2023-06-18 19:52:06,244] [INFO] Query marker FASTA was written to GCA_018897895.1_ASM1889789v1_genomic.fna/markers.fasta
[2023-06-18 19:52:06,244] [INFO] Task started: Blastn
[2023-06-18 19:52:06,245] [INFO] Running command: blastn -query GCA_018897895.1_ASM1889789v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6800f373-9c6b-4c66-acd3-70724259f7be/dqc_reference/reference_markers.fasta -out GCA_018897895.1_ASM1889789v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 19:52:06,935] [INFO] Task succeeded: Blastn
[2023-06-18 19:52:06,942] [INFO] Selected 12 target genomes.
[2023-06-18 19:52:06,943] [INFO] Target genome list was writen to GCA_018897895.1_ASM1889789v1_genomic.fna/target_genomes.txt
[2023-06-18 19:52:06,944] [INFO] Task started: fastANI
[2023-06-18 19:52:06,944] [INFO] Running command: fastANI --query /var/lib/cwl/stge85164a6-ab46-4d4d-b091-7455c8e7ee5b/GCA_018897895.1_ASM1889789v1_genomic.fna.gz --refList GCA_018897895.1_ASM1889789v1_genomic.fna/target_genomes.txt --output GCA_018897895.1_ASM1889789v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 19:52:14,553] [INFO] Task succeeded: fastANI
[2023-06-18 19:52:14,553] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6800f373-9c6b-4c66-acd3-70724259f7be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 19:52:14,554] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6800f373-9c6b-4c66-acd3-70724259f7be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 19:52:14,570] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2023-06-18 19:52:14,570] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-18 19:52:14,570] [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	95.035	373	396	95	conclusive
Brevundimonas aurantiaca	strain=DSM 4731	GCA_014199955.1	74316	74316	type	True	87.6217	365	396	95	below_threshold
Brevundimonas vesicularis	strain=NBRC 12165	GCA_001592205.1	41276	41276	suspected-type	True	85.633	341	396	95	below_threshold
Brevundimonas huaxiensis	strain=090558	GCA_014218725.1	2725493	2725493	type	True	85.3648	340	396	95	below_threshold
Brevundimonas albigilva	strain=KEME 9005-016	GCA_023503965.1	1312364	1312364	type	True	84.4667	331	396	95	below_threshold
Brevundimonas nasdae	strain=JCM 11415	GCA_016654005.1	172043	172043	type	True	84.3422	336	396	95	below_threshold
Brevundimonas pondensis	strain=LVF1	GCA_017487345.1	2774189	2774189	type	True	81.5841	293	396	95	below_threshold
Brevundimonas guildfordensis	strain=Sa3CVA3	GCA_014836405.1	2762241	2762241	type	True	80.9065	270	396	95	below_threshold
Brevundimonas viscosa	strain=CGMCC 1.10683	GCA_900116065.1	871741	871741	type	True	80.2567	255	396	95	below_threshold
Brevundimonas vitisensis	strain=GR-TSA-9	GCA_016656965.1	2800818	2800818	type	True	79.7036	230	396	95	below_threshold
Caulobacter rhizosphaerae	strain=CGMCC 1.15915	GCA_014645055.1	2010972	2010972	type	True	77.2911	190	396	95	below_threshold
Phenylobacterium aquaticum	strain=KACC 18306	GCA_022695515.1	1763816	1763816	type	True	77.2792	174	396	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 19:52:14,573] [INFO] DFAST Taxonomy check result was written to GCA_018897895.1_ASM1889789v1_genomic.fna/tc_result.tsv
[2023-06-18 19:52:14,573] [INFO] ===== Taxonomy check completed =====
[2023-06-18 19:52:14,573] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 19:52:14,574] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6800f373-9c6b-4c66-acd3-70724259f7be/dqc_reference/checkm_data
[2023-06-18 19:52:14,575] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 19:52:14,599] [INFO] Task started: CheckM
[2023-06-18 19:52:14,599] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018897895.1_ASM1889789v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018897895.1_ASM1889789v1_genomic.fna/checkm_input GCA_018897895.1_ASM1889789v1_genomic.fna/checkm_result
[2023-06-18 19:52:33,493] [INFO] Task succeeded: CheckM
[2023-06-18 19:52:33,494] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 35.88%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 19:52:33,519] [INFO] ===== Completeness check finished =====
[2023-06-18 19:52:33,519] [INFO] ===== Start GTDB Search =====
[2023-06-18 19:52:33,519] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018897895.1_ASM1889789v1_genomic.fna/markers.fasta)
[2023-06-18 19:52:33,520] [INFO] Task started: Blastn
[2023-06-18 19:52:33,520] [INFO] Running command: blastn -query GCA_018897895.1_ASM1889789v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6800f373-9c6b-4c66-acd3-70724259f7be/dqc_reference/reference_markers_gtdb.fasta -out GCA_018897895.1_ASM1889789v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 19:52:34,574] [INFO] Task succeeded: Blastn
[2023-06-18 19:52:34,578] [INFO] Selected 12 target genomes.
[2023-06-18 19:52:34,579] [INFO] Target genome list was writen to GCA_018897895.1_ASM1889789v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 19:52:34,583] [INFO] Task started: fastANI
[2023-06-18 19:52:34,583] [INFO] Running command: fastANI --query /var/lib/cwl/stge85164a6-ab46-4d4d-b091-7455c8e7ee5b/GCA_018897895.1_ASM1889789v1_genomic.fna.gz --refList GCA_018897895.1_ASM1889789v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018897895.1_ASM1889789v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 19:52:41,432] [INFO] Task succeeded: fastANI
[2023-06-18 19:52:41,449] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 19:52:41,449] [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_011064825.1	s__Brevundimonas mediterranea_A	98.277	389	396	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0657	98.11	97.23	0.89	0.83	17	conclusive
GCF_014196125.1	s__Brevundimonas mediterranea	95.035	373	396	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0657	N/A	N/A	N/A	N/A	1	-
GCA_013912065.1	s__Brevundimonas sp013912065	88.0281	353	396	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	87.7001	310	396	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	87.6217	365	396	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	97.57	96.95	0.92	0.85	12	-
GCF_004614235.1	s__Brevundimonas intermedia	86.7458	348	396	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	85.9264	350	396	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	99.71	99.71	0.98	0.98	2	-
GCF_000813765.1	s__Brevundimonas nasdae_A	85.537	337	396	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	95.42	95.42	0.82	0.82	2	-
GCF_005484585.1	s__Brevundimonas sp005484585	85.4546	341	396	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	95.32	95.32	0.86	0.86	2	-
GCA_003248455.1	s__Brevundimonas sp003248455	85.2344	327	396	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	83.9988	311	396	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	80.6859	266	396	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 19:52:41,452] [INFO] GTDB search result was written to GCA_018897895.1_ASM1889789v1_genomic.fna/result_gtdb.tsv
[2023-06-18 19:52:41,452] [INFO] ===== GTDB Search completed =====
[2023-06-18 19:52:41,456] [INFO] DFAST_QC result json was written to GCA_018897895.1_ASM1889789v1_genomic.fna/dqc_result.json
[2023-06-18 19:52:41,456] [INFO] DFAST_QC completed!
[2023-06-18 19:52:41,456] [INFO] Total running time: 0h0m41s