[2024-01-24 11:35:34,565] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:35:34,567] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:35:34,567] [INFO] DQC Reference Directory: /var/lib/cwl/stg26ec36c7-6df7-4389-bec0-a98bdd163e9b/dqc_reference
[2024-01-24 11:35:35,796] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:35:35,797] [INFO] Task started: Prodigal
[2024-01-24 11:35:35,797] [INFO] Running command: gunzip -c /var/lib/cwl/stga870114f-1ab1-46c6-b678-b72663e37121/GCF_900100255.1_IMG-taxon_2596583650_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900100255.1_IMG-taxon_2596583650_annotated_assembly_genomic.fna/cds.fna -a GCF_900100255.1_IMG-taxon_2596583650_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:47,073] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:47,074] [INFO] Task started: HMMsearch
[2024-01-24 11:35:47,074] [INFO] Running command: hmmsearch --tblout GCF_900100255.1_IMG-taxon_2596583650_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg26ec36c7-6df7-4389-bec0-a98bdd163e9b/dqc_reference/reference_markers.hmm GCF_900100255.1_IMG-taxon_2596583650_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:47,340] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:47,341] [INFO] Found 6/6 markers.
[2024-01-24 11:35:47,383] [INFO] Query marker FASTA was written to GCF_900100255.1_IMG-taxon_2596583650_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 11:35:47,384] [INFO] Task started: Blastn
[2024-01-24 11:35:47,384] [INFO] Running command: blastn -query GCF_900100255.1_IMG-taxon_2596583650_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg26ec36c7-6df7-4389-bec0-a98bdd163e9b/dqc_reference/reference_markers.fasta -out GCF_900100255.1_IMG-taxon_2596583650_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:48,214] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:48,217] [INFO] Selected 14 target genomes.
[2024-01-24 11:35:48,218] [INFO] Target genome list was writen to GCF_900100255.1_IMG-taxon_2596583650_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 11:35:48,225] [INFO] Task started: fastANI
[2024-01-24 11:35:48,225] [INFO] Running command: fastANI --query /var/lib/cwl/stga870114f-1ab1-46c6-b678-b72663e37121/GCF_900100255.1_IMG-taxon_2596583650_annotated_assembly_genomic.fna.gz --refList GCF_900100255.1_IMG-taxon_2596583650_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900100255.1_IMG-taxon_2596583650_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:57,749] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:57,750] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg26ec36c7-6df7-4389-bec0-a98bdd163e9b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:57,751] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg26ec36c7-6df7-4389-bec0-a98bdd163e9b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:57,774] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:35:57,774] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:57,774] [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
Asticcacaulis taihuensis	strain=CGMCC 1.3431	GCA_900100255.1	260084	260084	type	True	100.0	1312	1313	95	conclusive
Asticcacaulis benevestitus	strain=DSM 16100	GCA_000376105.1	347481	347481	type	True	82.1623	850	1313	95	below_threshold
Asticcacaulis benevestitus	strain=DSM 16100	GCA_000495775.1	347481	347481	type	True	82.1166	827	1313	95	below_threshold
Asticcacaulis biprosthecium	strain=C19	GCA_000204015.1	76891	76891	type	True	78.8283	578	1313	95	below_threshold
Asticcacaulis excentricus	strain=CB 48	GCA_000175215.2	78587	78587	type	True	78.2055	355	1313	95	below_threshold
Asticcacaulis endophyticus	strain=KCTC 32296	GCA_014652575.1	1395890	1395890	type	True	77.7279	312	1313	95	below_threshold
Brevundimonas halotolerans	strain=DSM 24448	GCA_014199165.1	69670	69670	type	True	77.6792	171	1313	95	below_threshold
Brevundimonas halotolerans	strain=MCS24	GCA_003730275.1	69670	69670	type	True	77.6658	171	1313	95	below_threshold
Brevundimonas guildfordensis	strain=Sa3CVA3	GCA_014836405.1	2762241	2762241	type	True	77.4958	187	1313	95	below_threshold
Asticcacaulis tiandongensis	strain=3.1105	GCA_006475605.1	2565365	2565365	type	True	77.4821	248	1313	95	below_threshold
Brevundimonas albigilva	strain=KEME 9005-016	GCA_023503965.1	1312364	1312364	type	True	77.4212	214	1313	95	below_threshold
Brevundimonas vitisensis	strain=GR-TSA-9	GCA_016656965.1	2800818	2800818	type	True	77.1306	162	1313	95	below_threshold
Microvirga lenta	strain=SM9	GCA_020532555.1	2881337	2881337	type	True	76.3977	94	1313	95	below_threshold
Hoeflea alexandrii	strain=DSM 16655	GCA_024105735.1	288436	288436	type	True	76.0067	91	1313	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:57,776] [INFO] DFAST Taxonomy check result was written to GCF_900100255.1_IMG-taxon_2596583650_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 11:35:57,777] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:57,777] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:57,777] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg26ec36c7-6df7-4389-bec0-a98bdd163e9b/dqc_reference/checkm_data
[2024-01-24 11:35:57,778] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:57,816] [INFO] Task started: CheckM
[2024-01-24 11:35:57,816] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900100255.1_IMG-taxon_2596583650_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900100255.1_IMG-taxon_2596583650_annotated_assembly_genomic.fna/checkm_input GCF_900100255.1_IMG-taxon_2596583650_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 11:36:33,726] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:33,727] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:33,747] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:33,747] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:33,748] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900100255.1_IMG-taxon_2596583650_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 11:36:33,748] [INFO] Task started: Blastn
[2024-01-24 11:36:33,748] [INFO] Running command: blastn -query GCF_900100255.1_IMG-taxon_2596583650_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg26ec36c7-6df7-4389-bec0-a98bdd163e9b/dqc_reference/reference_markers_gtdb.fasta -out GCF_900100255.1_IMG-taxon_2596583650_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:35,344] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:35,349] [INFO] Selected 11 target genomes.
[2024-01-24 11:36:35,349] [INFO] Target genome list was writen to GCF_900100255.1_IMG-taxon_2596583650_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:35,359] [INFO] Task started: fastANI
[2024-01-24 11:36:35,359] [INFO] Running command: fastANI --query /var/lib/cwl/stga870114f-1ab1-46c6-b678-b72663e37121/GCF_900100255.1_IMG-taxon_2596583650_annotated_assembly_genomic.fna.gz --refList GCF_900100255.1_IMG-taxon_2596583650_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900100255.1_IMG-taxon_2596583650_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:45,143] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:45,159] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:36:45,159] [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_900100255.1	s__Asticcacaulis taihuensis	100.0	1312	1313	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Asticcacaulis	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000376105.1	s__Asticcacaulis benevestitus	82.1316	854	1313	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Asticcacaulis	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000495815.1	s__Asticcacaulis sp000495815	79.9922	728	1313	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Asticcacaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017875235.1	s__Asticcacaulis solisilvae	79.4592	621	1313	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Asticcacaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000495795.1	s__Asticcacaulis sp000495795	79.2546	647	1313	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Asticcacaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873225.1	s__Asticcacaulis sp014873225	79.2428	602	1313	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Asticcacaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000495855.1	s__Asticcacaulis sp000495855	78.7983	452	1313	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Asticcacaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003053985.1	s__Asticcacaulis sp003053985	78.7624	501	1313	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Asticcacaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000495835.1	s__Asticcacaulis sp000495835	78.5286	483	1313	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Asticcacaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003730275.1	s__Brevundimonas halotolerans	77.6451	172	1313	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	97.75	97.09	0.92	0.85	7	-
GCF_000466985.1	s__Brevundimonas abyssalis	77.2758	155	1313	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	99.78	99.71	0.94	0.89	3	-
--------------------------------------------------------------------------------
[2024-01-24 11:36:45,161] [INFO] GTDB search result was written to GCF_900100255.1_IMG-taxon_2596583650_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:45,161] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:45,164] [INFO] DFAST_QC result json was written to GCF_900100255.1_IMG-taxon_2596583650_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 11:36:45,165] [INFO] DFAST_QC completed!
[2024-01-24 11:36:45,165] [INFO] Total running time: 0h1m11s