[2024-01-24 13:40:43,016] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:43,018] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:43,019] [INFO] DQC Reference Directory: /var/lib/cwl/stgc188cd07-4754-41a9-a8da-75a375145e27/dqc_reference
[2024-01-24 13:40:44,397] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:44,398] [INFO] Task started: Prodigal
[2024-01-24 13:40:44,398] [INFO] Running command: gunzip -c /var/lib/cwl/stg71a63b44-8ffb-46cb-b155-078e720d52c5/GCF_000017265.1_ASM1726v1_genomic.fna.gz | prodigal -d GCF_000017265.1_ASM1726v1_genomic.fna/cds.fna -a GCF_000017265.1_ASM1726v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:56,513] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:56,513] [INFO] Task started: HMMsearch
[2024-01-24 13:40:56,513] [INFO] Running command: hmmsearch --tblout GCF_000017265.1_ASM1726v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc188cd07-4754-41a9-a8da-75a375145e27/dqc_reference/reference_markers.hmm GCF_000017265.1_ASM1726v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:56,811] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:56,813] [INFO] Found 6/6 markers.
[2024-01-24 13:40:56,861] [INFO] Query marker FASTA was written to GCF_000017265.1_ASM1726v1_genomic.fna/markers.fasta
[2024-01-24 13:40:56,861] [INFO] Task started: Blastn
[2024-01-24 13:40:56,861] [INFO] Running command: blastn -query GCF_000017265.1_ASM1726v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc188cd07-4754-41a9-a8da-75a375145e27/dqc_reference/reference_markers.fasta -out GCF_000017265.1_ASM1726v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:57,983] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:57,986] [INFO] Selected 12 target genomes.
[2024-01-24 13:40:57,986] [INFO] Target genome list was writen to GCF_000017265.1_ASM1726v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:57,997] [INFO] Task started: fastANI
[2024-01-24 13:40:57,997] [INFO] Running command: fastANI --query /var/lib/cwl/stg71a63b44-8ffb-46cb-b155-078e720d52c5/GCF_000017265.1_ASM1726v1_genomic.fna.gz --refList GCF_000017265.1_ASM1726v1_genomic.fna/target_genomes.txt --output GCF_000017265.1_ASM1726v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:11,005] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:11,006] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc188cd07-4754-41a9-a8da-75a375145e27/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:11,006] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc188cd07-4754-41a9-a8da-75a375145e27/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:11,017] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:11,017] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:11,018] [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
Phenylobacterium zucineum	strain=HLK1	GCA_000017265.1	284016	284016	type	True	100.0	1459	1459	95	conclusive
Phenylobacterium hankyongense	strain=HKS-05	GCA_003254505.1	1813876	1813876	type	True	82.8286	797	1459	95	below_threshold
Phenylobacterium kunshanense	strain=BUT-10	GCA_003254525.1	1445034	1445034	type	True	82.6637	808	1459	95	below_threshold
Phenylobacterium soli	strain=LX32	GCA_003254475.1	2170551	2170551	type	True	82.5547	823	1459	95	below_threshold
Phenylobacterium deserti	strain=YIM 73061	GCA_003254705.1	1914756	1914756	type	True	81.2167	702	1459	95	below_threshold
Phenylobacterium glaciei	strain=20VBR1	GCA_016772415.2	2803784	2803784	type	True	80.4233	689	1459	95	below_threshold
Phenylobacterium aquaticum	strain=KACC 18306	GCA_022695515.1	1763816	1763816	type	True	80.4105	762	1459	95	below_threshold
Caulobacter rhizosphaerae	strain=CGMCC 1.15915	GCA_014645055.1	2010972	2010972	type	True	79.5779	652	1459	95	below_threshold
Caulobacter flavus	strain=CGMCC1 15093	GCA_002858845.1	1679497	1679497	type	True	79.4986	713	1459	95	below_threshold
Caulobacter hibisci	strain=KACC 18849	GCA_016135805.1	2035993	2035993	type	True	79.4487	671	1459	95	below_threshold
Brevundimonas albigilva	strain=KEME 9005-016	GCA_023503965.1	1312364	1312364	type	True	78.6586	456	1459	95	below_threshold
Brevundimonas guildfordensis	strain=Sa3CVA3	GCA_014836405.1	2762241	2762241	type	True	78.1855	384	1459	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:11,020] [INFO] DFAST Taxonomy check result was written to GCF_000017265.1_ASM1726v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:11,020] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:11,021] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:11,021] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc188cd07-4754-41a9-a8da-75a375145e27/dqc_reference/checkm_data
[2024-01-24 13:41:11,022] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:11,070] [INFO] Task started: CheckM
[2024-01-24 13:41:11,071] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000017265.1_ASM1726v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000017265.1_ASM1726v1_genomic.fna/checkm_input GCF_000017265.1_ASM1726v1_genomic.fna/checkm_result
[2024-01-24 13:41:51,133] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:51,135] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:51,162] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:51,162] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:51,163] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000017265.1_ASM1726v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:51,163] [INFO] Task started: Blastn
[2024-01-24 13:41:51,164] [INFO] Running command: blastn -query GCF_000017265.1_ASM1726v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc188cd07-4754-41a9-a8da-75a375145e27/dqc_reference/reference_markers_gtdb.fasta -out GCF_000017265.1_ASM1726v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:53,301] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:53,304] [INFO] Selected 14 target genomes.
[2024-01-24 13:41:53,304] [INFO] Target genome list was writen to GCF_000017265.1_ASM1726v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:53,338] [INFO] Task started: fastANI
[2024-01-24 13:41:53,338] [INFO] Running command: fastANI --query /var/lib/cwl/stg71a63b44-8ffb-46cb-b155-078e720d52c5/GCF_000017265.1_ASM1726v1_genomic.fna.gz --refList GCF_000017265.1_ASM1726v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000017265.1_ASM1726v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:08,977] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:08,995] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:08,996] [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_000017265.1	s__Phenylobacterium zucineum	100.0	1459	1459	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	99.11	99.11	0.98	0.98	2	conclusive
GCF_003254505.1	s__Phenylobacterium hankyongense	82.9135	787	1459	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001824475.1	s__Phenylobacterium sp001824475	82.7272	928	1459	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	96.46	96.46	0.87	0.87	2	-
GCF_001557235.1	s__Phenylobacterium sp001557235	82.6745	868	1459	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	99.95	99.95	0.94	0.94	2	-
GCF_003254525.1	s__Phenylobacterium kunshanense	82.6609	809	1459	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003254475.1	s__Phenylobacterium soli	82.5812	820	1459	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004297125.1	s__Phenylobacterium sp004297125	82.499	903	1459	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016124325.1	s__Phenylobacterium sp016124325	82.3093	827	1459	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793285.1	s__Phenylobacterium sp016793285	82.2191	756	1459	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018821435.1	s__Phenylobacterium sp018821435	82.0542	852	1459	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	99.99	99.99	0.99	0.99	6	-
GCA_001724605.1	s__Phenylobacterium sp001724605	81.9687	788	1459	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004299445.1	s__Phenylobacterium sp004299445	81.9067	797	1459	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793225.1	s__Phenylobacterium sp016793225	81.8791	811	1459	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003254705.1	s__Phenylobacterium deserti	81.2203	702	1459	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:08,997] [INFO] GTDB search result was written to GCF_000017265.1_ASM1726v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:08,998] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:09,001] [INFO] DFAST_QC result json was written to GCF_000017265.1_ASM1726v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:09,001] [INFO] DFAST_QC completed!
[2024-01-24 13:42:09,001] [INFO] Total running time: 0h1m26s