[2023-06-28 21:58:10,241] [INFO] DFAST_QC pipeline started.
[2023-06-28 21:58:10,245] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 21:58:10,245] [INFO] DQC Reference Directory: /var/lib/cwl/stg1f81d36a-a131-48e8-a8d4-9d668d272051/dqc_reference
[2023-06-28 21:58:12,102] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 21:58:12,103] [INFO] Task started: Prodigal
[2023-06-28 21:58:12,104] [INFO] Running command: gunzip -c /var/lib/cwl/stg83dc56b3-d0d1-4455-bcd6-be40fd7d1262/GCA_913778635.1_SP60_2_metabat2_genome_mining.39_genomic.fna.gz | prodigal -d GCA_913778635.1_SP60_2_metabat2_genome_mining.39_genomic.fna/cds.fna -a GCA_913778635.1_SP60_2_metabat2_genome_mining.39_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 21:58:17,630] [INFO] Task succeeded: Prodigal
[2023-06-28 21:58:17,631] [INFO] Task started: HMMsearch
[2023-06-28 21:58:17,631] [INFO] Running command: hmmsearch --tblout GCA_913778635.1_SP60_2_metabat2_genome_mining.39_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1f81d36a-a131-48e8-a8d4-9d668d272051/dqc_reference/reference_markers.hmm GCA_913778635.1_SP60_2_metabat2_genome_mining.39_genomic.fna/protein.faa > /dev/null
[2023-06-28 21:58:17,851] [INFO] Task succeeded: HMMsearch
[2023-06-28 21:58:17,853] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg83dc56b3-d0d1-4455-bcd6-be40fd7d1262/GCA_913778635.1_SP60_2_metabat2_genome_mining.39_genomic.fna.gz]
[2023-06-28 21:58:17,880] [INFO] Query marker FASTA was written to GCA_913778635.1_SP60_2_metabat2_genome_mining.39_genomic.fna/markers.fasta
[2023-06-28 21:58:17,880] [INFO] Task started: Blastn
[2023-06-28 21:58:17,880] [INFO] Running command: blastn -query GCA_913778635.1_SP60_2_metabat2_genome_mining.39_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f81d36a-a131-48e8-a8d4-9d668d272051/dqc_reference/reference_markers.fasta -out GCA_913778635.1_SP60_2_metabat2_genome_mining.39_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 21:58:18,681] [INFO] Task succeeded: Blastn
[2023-06-28 21:58:18,686] [INFO] Selected 12 target genomes.
[2023-06-28 21:58:18,687] [INFO] Target genome list was writen to GCA_913778635.1_SP60_2_metabat2_genome_mining.39_genomic.fna/target_genomes.txt
[2023-06-28 21:58:18,688] [INFO] Task started: fastANI
[2023-06-28 21:58:18,688] [INFO] Running command: fastANI --query /var/lib/cwl/stg83dc56b3-d0d1-4455-bcd6-be40fd7d1262/GCA_913778635.1_SP60_2_metabat2_genome_mining.39_genomic.fna.gz --refList GCA_913778635.1_SP60_2_metabat2_genome_mining.39_genomic.fna/target_genomes.txt --output GCA_913778635.1_SP60_2_metabat2_genome_mining.39_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 21:58:26,941] [INFO] Task succeeded: fastANI
[2023-06-28 21:58:26,942] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1f81d36a-a131-48e8-a8d4-9d668d272051/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 21:58:26,942] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1f81d36a-a131-48e8-a8d4-9d668d272051/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 21:58:26,954] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2023-06-28 21:58:26,954] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-28 21:58:26,954] [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 huaxiensis	strain=090558	GCA_014218725.1	2725493	2725493	type	True	95.1748	544	640	95	conclusive
Brevundimonas vesicularis	strain=NBRC 12165	GCA_001592205.1	41276	41276	suspected-type	True	94.06	537	640	95	below_threshold
Brevundimonas mediterranea	strain=DSM 14878	GCA_014196125.1	74329	74329	type	True	86.4828	495	640	95	below_threshold
Brevundimonas aurantiaca	strain=DSM 4731	GCA_014199955.1	74316	74316	type	True	85.5231	497	640	95	below_threshold
Brevundimonas nasdae	strain=JCM 11415	GCA_016654005.1	172043	172043	type	True	85.0407	484	640	95	below_threshold
Brevundimonas albigilva	strain=KEME 9005-016	GCA_023503965.1	1312364	1312364	type	True	84.6037	475	640	95	below_threshold
Brevundimonas guildfordensis	strain=Sa3CVA3	GCA_014836405.1	2762241	2762241	type	True	81.8686	403	640	95	below_threshold
Brevundimonas vitisensis	strain=GR-TSA-9	GCA_016656965.1	2800818	2800818	type	True	80.1802	364	640	95	below_threshold
Brevundimonas pishanensis	strain=CHPC 1.3453	GCA_022750635.1	2896315	2896315	type	True	79.2634	249	640	95	below_threshold
Caulobacter rhizosphaerae	strain=CGMCC 1.15915	GCA_014645055.1	2010972	2010972	type	True	78.524	278	640	95	below_threshold
Phenylobacterium aquaticum	strain=KACC 18306	GCA_022695515.1	1763816	1763816	type	True	77.9858	234	640	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	75.5721	85	640	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 21:58:26,956] [INFO] DFAST Taxonomy check result was written to GCA_913778635.1_SP60_2_metabat2_genome_mining.39_genomic.fna/tc_result.tsv
[2023-06-28 21:58:26,957] [INFO] ===== Taxonomy check completed =====
[2023-06-28 21:58:26,957] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 21:58:26,957] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1f81d36a-a131-48e8-a8d4-9d668d272051/dqc_reference/checkm_data
[2023-06-28 21:58:26,958] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 21:58:26,987] [INFO] Task started: CheckM
[2023-06-28 21:58:26,988] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_913778635.1_SP60_2_metabat2_genome_mining.39_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_913778635.1_SP60_2_metabat2_genome_mining.39_genomic.fna/checkm_input GCA_913778635.1_SP60_2_metabat2_genome_mining.39_genomic.fna/checkm_result
[2023-06-28 21:58:50,094] [INFO] Task succeeded: CheckM
[2023-06-28 21:58:50,095] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 4.07%
Strain heterogeneity: 11.11%
--------------------------------------------------------------------------------
[2023-06-28 21:58:50,120] [INFO] ===== Completeness check finished =====
[2023-06-28 21:58:50,120] [INFO] ===== Start GTDB Search =====
[2023-06-28 21:58:50,120] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_913778635.1_SP60_2_metabat2_genome_mining.39_genomic.fna/markers.fasta)
[2023-06-28 21:58:50,121] [INFO] Task started: Blastn
[2023-06-28 21:58:50,121] [INFO] Running command: blastn -query GCA_913778635.1_SP60_2_metabat2_genome_mining.39_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f81d36a-a131-48e8-a8d4-9d668d272051/dqc_reference/reference_markers_gtdb.fasta -out GCA_913778635.1_SP60_2_metabat2_genome_mining.39_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 21:58:51,415] [INFO] Task succeeded: Blastn
[2023-06-28 21:58:51,422] [INFO] Selected 8 target genomes.
[2023-06-28 21:58:51,422] [INFO] Target genome list was writen to GCA_913778635.1_SP60_2_metabat2_genome_mining.39_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 21:58:51,425] [INFO] Task started: fastANI
[2023-06-28 21:58:51,425] [INFO] Running command: fastANI --query /var/lib/cwl/stg83dc56b3-d0d1-4455-bcd6-be40fd7d1262/GCA_913778635.1_SP60_2_metabat2_genome_mining.39_genomic.fna.gz --refList GCA_913778635.1_SP60_2_metabat2_genome_mining.39_genomic.fna/target_genomes_gtdb.txt --output GCA_913778635.1_SP60_2_metabat2_genome_mining.39_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 21:58:56,645] [INFO] Task succeeded: fastANI
[2023-06-28 21:58:56,657] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 21:58:56,657] [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_005484585.1	s__Brevundimonas sp005484585	95.346	556	640	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	95.32	95.32	0.86	0.86	2	conclusive
GCF_000813765.1	s__Brevundimonas nasdae_A	94.5396	541	640	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	95.42	95.42	0.82	0.82	2	-
GCF_001592205.1	s__Brevundimonas vesicularis	94.06	537	640	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	95.70	95.00	0.85	0.82	10	-
GCF_014204545.1	s__Brevundimonas vesicularis_B	93.9294	542	640	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000335735.1	s__Brevundimonas sp000335735	93.7622	526	640	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017086445.1	s__Brevundimonas vesicularis_A	93.5545	546	640	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	95.13	95.13	0.83	0.83	2	-
GCF_002157625.1	s__Brevundimonas sp002157625	87.8517	518	640	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016656965.1	s__Brevundimonas sp016656965	80.1653	365	640	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 21:58:56,659] [INFO] GTDB search result was written to GCA_913778635.1_SP60_2_metabat2_genome_mining.39_genomic.fna/result_gtdb.tsv
[2023-06-28 21:58:56,659] [INFO] ===== GTDB Search completed =====
[2023-06-28 21:58:56,663] [INFO] DFAST_QC result json was written to GCA_913778635.1_SP60_2_metabat2_genome_mining.39_genomic.fna/dqc_result.json
[2023-06-28 21:58:56,663] [INFO] DFAST_QC completed!
[2023-06-28 21:58:56,663] [INFO] Total running time: 0h0m46s