[2024-01-24 14:20:14,479] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:20:14,481] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:20:14,481] [INFO] DQC Reference Directory: /var/lib/cwl/stg254fbbd3-bdbc-47e1-8e05-dffd41ba4b97/dqc_reference
[2024-01-24 14:20:15,797] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:20:15,798] [INFO] Task started: Prodigal
[2024-01-24 14:20:15,798] [INFO] Running command: gunzip -c /var/lib/cwl/stg70e5f537-4745-45b4-85bf-77faeac42587/GCF_003254475.1_ASM325447v1_genomic.fna.gz | prodigal -d GCF_003254475.1_ASM325447v1_genomic.fna/cds.fna -a GCF_003254475.1_ASM325447v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:20:26,985] [INFO] Task succeeded: Prodigal
[2024-01-24 14:20:26,986] [INFO] Task started: HMMsearch
[2024-01-24 14:20:26,986] [INFO] Running command: hmmsearch --tblout GCF_003254475.1_ASM325447v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg254fbbd3-bdbc-47e1-8e05-dffd41ba4b97/dqc_reference/reference_markers.hmm GCF_003254475.1_ASM325447v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:20:27,304] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:20:27,305] [INFO] Found 6/6 markers.
[2024-01-24 14:20:27,346] [INFO] Query marker FASTA was written to GCF_003254475.1_ASM325447v1_genomic.fna/markers.fasta
[2024-01-24 14:20:27,347] [INFO] Task started: Blastn
[2024-01-24 14:20:27,347] [INFO] Running command: blastn -query GCF_003254475.1_ASM325447v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg254fbbd3-bdbc-47e1-8e05-dffd41ba4b97/dqc_reference/reference_markers.fasta -out GCF_003254475.1_ASM325447v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:28,438] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:28,442] [INFO] Selected 12 target genomes.
[2024-01-24 14:20:28,442] [INFO] Target genome list was writen to GCF_003254475.1_ASM325447v1_genomic.fna/target_genomes.txt
[2024-01-24 14:20:28,478] [INFO] Task started: fastANI
[2024-01-24 14:20:28,478] [INFO] Running command: fastANI --query /var/lib/cwl/stg70e5f537-4745-45b4-85bf-77faeac42587/GCF_003254475.1_ASM325447v1_genomic.fna.gz --refList GCF_003254475.1_ASM325447v1_genomic.fna/target_genomes.txt --output GCF_003254475.1_ASM325447v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:20:39,979] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:39,980] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg254fbbd3-bdbc-47e1-8e05-dffd41ba4b97/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:20:39,981] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg254fbbd3-bdbc-47e1-8e05-dffd41ba4b97/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:20:39,996] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:20:39,996] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:20:39,996] [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 soli	strain=LX32	GCA_003254475.1	2170551	2170551	type	True	100.0	1336	1336	95	conclusive
Phenylobacterium hankyongense	strain=HKS-05	GCA_003254505.1	1813876	1813876	type	True	83.1006	807	1336	95	below_threshold
Phenylobacterium zucineum	strain=HLK1	GCA_000017265.1	284016	284016	type	True	82.6011	819	1336	95	below_threshold
Phenylobacterium kunshanense	strain=BUT-10	GCA_003254525.1	1445034	1445034	type	True	81.5455	715	1336	95	below_threshold
Phenylobacterium deserti	strain=YIM 73061	GCA_003254705.1	1914756	1914756	type	True	81.0002	637	1336	95	below_threshold
Phenylobacterium aquaticum	strain=KACC 18306	GCA_022695515.1	1763816	1763816	type	True	80.8654	751	1336	95	below_threshold
Phenylobacterium glaciei	strain=20VBR1	GCA_016772415.2	2803784	2803784	type	True	80.4419	699	1336	95	below_threshold
Caulobacter flavus	strain=RHGG3	GCA_003722335.1	1679497	1679497	type	True	79.5623	656	1336	95	below_threshold
Caulobacter flavus	strain=CGMCC1 15093	GCA_002858845.1	1679497	1679497	type	True	79.5288	647	1336	95	below_threshold
Caulobacter rhizosphaerae	strain=CGMCC 1.15915	GCA_014645055.1	2010972	2010972	type	True	79.3759	618	1336	95	below_threshold
Brevundimonas albigilva	strain=KEME 9005-016	GCA_023503965.1	1312364	1312364	type	True	78.4225	400	1336	95	below_threshold
Starkeya koreensis	strain=Jip08	GCA_023016525.1	266121	266121	type	True	76.4994	266	1336	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:20:39,998] [INFO] DFAST Taxonomy check result was written to GCF_003254475.1_ASM325447v1_genomic.fna/tc_result.tsv
[2024-01-24 14:20:39,998] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:20:39,999] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:20:39,999] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg254fbbd3-bdbc-47e1-8e05-dffd41ba4b97/dqc_reference/checkm_data
[2024-01-24 14:20:40,000] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:20:40,039] [INFO] Task started: CheckM
[2024-01-24 14:20:40,040] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003254475.1_ASM325447v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003254475.1_ASM325447v1_genomic.fna/checkm_input GCF_003254475.1_ASM325447v1_genomic.fna/checkm_result
[2024-01-24 14:21:14,416] [INFO] Task succeeded: CheckM
[2024-01-24 14:21:14,417] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:21:14,440] [INFO] ===== Completeness check finished =====
[2024-01-24 14:21:14,440] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:21:14,440] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003254475.1_ASM325447v1_genomic.fna/markers.fasta)
[2024-01-24 14:21:14,441] [INFO] Task started: Blastn
[2024-01-24 14:21:14,441] [INFO] Running command: blastn -query GCF_003254475.1_ASM325447v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg254fbbd3-bdbc-47e1-8e05-dffd41ba4b97/dqc_reference/reference_markers_gtdb.fasta -out GCF_003254475.1_ASM325447v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:21:16,546] [INFO] Task succeeded: Blastn
[2024-01-24 14:21:16,550] [INFO] Selected 12 target genomes.
[2024-01-24 14:21:16,551] [INFO] Target genome list was writen to GCF_003254475.1_ASM325447v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:21:16,584] [INFO] Task started: fastANI
[2024-01-24 14:21:16,585] [INFO] Running command: fastANI --query /var/lib/cwl/stg70e5f537-4745-45b4-85bf-77faeac42587/GCF_003254475.1_ASM325447v1_genomic.fna.gz --refList GCF_003254475.1_ASM325447v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003254475.1_ASM325447v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:21:28,353] [INFO] Task succeeded: fastANI
[2024-01-24 14:21:28,368] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:21:28,369] [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_003254475.1	s__Phenylobacterium soli	100.0	1336	1336	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_004799545.1	s__Phenylobacterium sp004799545	84.0147	848	1336	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003254505.1	s__Phenylobacterium hankyongense	83.1456	802	1336	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000017265.1	s__Phenylobacterium zucineum	82.5763	822	1336	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	99.11	99.11	0.98	0.98	2	-
GCA_004799515.1	s__Phenylobacterium sp004799515	82.0497	757	1336	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018241625.1	s__Phenylobacterium sp018241625	81.8753	655	1336	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003254525.1	s__Phenylobacterium kunshanense	81.5179	718	1336	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	81.5142	774	1336	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	81.378	771	1336	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003136395.1	s__Phenylobacterium sp003136395	81.054	687	1336	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	80.9899	638	1336	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013911965.1	s__Phenylobacterium sp013911965	80.9443	652	1336	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	98.20	98.20	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:21:28,370] [INFO] GTDB search result was written to GCF_003254475.1_ASM325447v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:21:28,371] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:21:28,376] [INFO] DFAST_QC result json was written to GCF_003254475.1_ASM325447v1_genomic.fna/dqc_result.json
[2024-01-24 14:21:28,376] [INFO] DFAST_QC completed!
[2024-01-24 14:21:28,376] [INFO] Total running time: 0h1m14s