[2024-01-25 18:09:20,348] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:09:20,350] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:09:20,350] [INFO] DQC Reference Directory: /var/lib/cwl/stgf3738856-ff05-445e-9809-3b5555067dc3/dqc_reference
[2024-01-25 18:09:21,480] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:09:21,482] [INFO] Task started: Prodigal
[2024-01-25 18:09:21,482] [INFO] Running command: gunzip -c /var/lib/cwl/stg77739648-8515-478e-807f-3a81bbc44d32/GCF_014652575.1_ASM1465257v1_genomic.fna.gz | prodigal -d GCF_014652575.1_ASM1465257v1_genomic.fna/cds.fna -a GCF_014652575.1_ASM1465257v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:09:31,277] [INFO] Task succeeded: Prodigal
[2024-01-25 18:09:31,278] [INFO] Task started: HMMsearch
[2024-01-25 18:09:31,278] [INFO] Running command: hmmsearch --tblout GCF_014652575.1_ASM1465257v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf3738856-ff05-445e-9809-3b5555067dc3/dqc_reference/reference_markers.hmm GCF_014652575.1_ASM1465257v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:09:31,507] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:09:31,509] [INFO] Found 6/6 markers.
[2024-01-25 18:09:31,540] [INFO] Query marker FASTA was written to GCF_014652575.1_ASM1465257v1_genomic.fna/markers.fasta
[2024-01-25 18:09:31,540] [INFO] Task started: Blastn
[2024-01-25 18:09:31,540] [INFO] Running command: blastn -query GCF_014652575.1_ASM1465257v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf3738856-ff05-445e-9809-3b5555067dc3/dqc_reference/reference_markers.fasta -out GCF_014652575.1_ASM1465257v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:09:32,147] [INFO] Task succeeded: Blastn
[2024-01-25 18:09:32,151] [INFO] Selected 21 target genomes.
[2024-01-25 18:09:32,151] [INFO] Target genome list was writen to GCF_014652575.1_ASM1465257v1_genomic.fna/target_genomes.txt
[2024-01-25 18:09:32,162] [INFO] Task started: fastANI
[2024-01-25 18:09:32,163] [INFO] Running command: fastANI --query /var/lib/cwl/stg77739648-8515-478e-807f-3a81bbc44d32/GCF_014652575.1_ASM1465257v1_genomic.fna.gz --refList GCF_014652575.1_ASM1465257v1_genomic.fna/target_genomes.txt --output GCF_014652575.1_ASM1465257v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:09:46,969] [INFO] Task succeeded: fastANI
[2024-01-25 18:09:46,969] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf3738856-ff05-445e-9809-3b5555067dc3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:09:46,969] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf3738856-ff05-445e-9809-3b5555067dc3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:09:46,980] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:09:46,980] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:09:46,980] [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 endophyticus	strain=KCTC 32296	GCA_014652575.1	1395890	1395890	type	True	100.0	1310	1310	95	conclusive
Asticcacaulis tiandongensis	strain=3.1105	GCA_006475605.1	2565365	2565365	type	True	78.115	344	1310	95	below_threshold
Asticcacaulis benevestitus	strain=DSM 16100	GCA_000495775.1	347481	347481	type	True	77.9467	327	1310	95	below_threshold
Asticcacaulis benevestitus	strain=DSM 16100	GCA_000376105.1	347481	347481	type	True	77.918	333	1310	95	below_threshold
Asticcacaulis excentricus	strain=CB 48	GCA_000175215.2	78587	78587	type	True	77.8363	408	1310	95	below_threshold
Asticcacaulis taihuensis	strain=CGMCC 1.3431	GCA_900100255.1	260084	260084	type	True	77.8155	307	1310	95	below_threshold
Asticcacaulis biprosthecium	strain=C19	GCA_000204015.1	76891	76891	type	True	77.1903	307	1310	95	below_threshold
Caulobacter zeae	strain=410	GCA_002858925.1	2055137	2055137	type	True	76.8466	130	1310	95	below_threshold
Brevundimonas diminuta	strain=ATCC 11568	GCA_000204035.1	293	293	type	True	76.7458	117	1310	95	below_threshold
Brevundimonas naejangsanensis	strain=DSM 23858	GCA_000421705.1	588932	588932	type	True	76.6459	116	1310	95	below_threshold
Caulobacter flavus	strain=RHGG3	GCA_003722335.1	1679497	1679497	type	True	76.608	154	1310	95	below_threshold
Brevundimonas vesicularis	strain=NBRC 12165	GCA_001592205.1	41276	41276	suspected-type	True	76.5711	108	1310	95	below_threshold
Brevundimonas vitisensis	strain=GR-TSA-9	GCA_016656965.1	2800818	2800818	type	True	76.5419	100	1310	95	below_threshold
Caulobacter hibisci	strain=KACC 18849	GCA_016135805.1	2035993	2035993	type	True	76.5327	139	1310	95	below_threshold
Brevundimonas variabilis	strain=DSM 4737	GCA_014199945.1	74312	74312	type	True	76.2268	93	1310	95	below_threshold
Sphingomonas suaedae	strain=XS-10	GCA_007833215.1	2599297	2599297	type	True	75.6254	52	1310	95	below_threshold
Sphingomonas panni	strain=DSM 15761	GCA_022664435.1	237612	237612	type	True	75.4832	74	1310	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:09:46,981] [INFO] DFAST Taxonomy check result was written to GCF_014652575.1_ASM1465257v1_genomic.fna/tc_result.tsv
[2024-01-25 18:09:46,982] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:09:46,982] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:09:46,982] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf3738856-ff05-445e-9809-3b5555067dc3/dqc_reference/checkm_data
[2024-01-25 18:09:46,983] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:09:47,021] [INFO] Task started: CheckM
[2024-01-25 18:09:47,021] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014652575.1_ASM1465257v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014652575.1_ASM1465257v1_genomic.fna/checkm_input GCF_014652575.1_ASM1465257v1_genomic.fna/checkm_result
[2024-01-25 18:10:19,708] [INFO] Task succeeded: CheckM
[2024-01-25 18:10:19,709] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:10:19,743] [INFO] ===== Completeness check finished =====
[2024-01-25 18:10:19,744] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:10:19,745] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014652575.1_ASM1465257v1_genomic.fna/markers.fasta)
[2024-01-25 18:10:19,745] [INFO] Task started: Blastn
[2024-01-25 18:10:19,745] [INFO] Running command: blastn -query GCF_014652575.1_ASM1465257v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf3738856-ff05-445e-9809-3b5555067dc3/dqc_reference/reference_markers_gtdb.fasta -out GCF_014652575.1_ASM1465257v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:10:20,745] [INFO] Task succeeded: Blastn
[2024-01-25 18:10:20,748] [INFO] Selected 10 target genomes.
[2024-01-25 18:10:20,748] [INFO] Target genome list was writen to GCF_014652575.1_ASM1465257v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:10:20,773] [INFO] Task started: fastANI
[2024-01-25 18:10:20,774] [INFO] Running command: fastANI --query /var/lib/cwl/stg77739648-8515-478e-807f-3a81bbc44d32/GCF_014652575.1_ASM1465257v1_genomic.fna.gz --refList GCF_014652575.1_ASM1465257v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014652575.1_ASM1465257v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:10:29,498] [INFO] Task succeeded: fastANI
[2024-01-25 18:10:29,505] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:10:29,505] [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_014652575.1	s__Asticcacaulis endophyticus	100.0	1310	1310	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Asticcacaulis	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002342035.1	s__Asticcacaulis sp002342035	93.8331	1056	1310	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	78.3839	466	1310	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	78.3588	474	1310	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Asticcacaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003966695.1	s__Asticcacaulis excentricus_A	78.3424	446	1310	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Asticcacaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006475605.1	s__Asticcacaulis tiandongensis	78.1043	345	1310	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Asticcacaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000376105.1	s__Asticcacaulis benevestitus	77.9015	334	1310	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Asticcacaulis	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000175215.2	s__Asticcacaulis excentricus	77.8537	406	1310	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Asticcacaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100255.1	s__Asticcacaulis taihuensis	77.8284	305	1310	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	77.7638	332	1310	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Asticcacaulis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:10:29,508] [INFO] GTDB search result was written to GCF_014652575.1_ASM1465257v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:10:29,509] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:10:29,512] [INFO] DFAST_QC result json was written to GCF_014652575.1_ASM1465257v1_genomic.fna/dqc_result.json
[2024-01-25 18:10:29,512] [INFO] DFAST_QC completed!
[2024-01-25 18:10:29,512] [INFO] Total running time: 0h1m9s