[2023-06-19 01:24:42,013] [INFO] DFAST_QC pipeline started.
[2023-06-19 01:24:42,017] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 01:24:42,017] [INFO] DQC Reference Directory: /var/lib/cwl/stgf41ebbcb-f0ee-46e8-8b53-bb852b8436b0/dqc_reference
[2023-06-19 01:24:44,115] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 01:24:44,115] [INFO] Task started: Prodigal
[2023-06-19 01:24:44,116] [INFO] Running command: gunzip -c /var/lib/cwl/stgf3594d98-4e8c-408d-81c5-d2bdf71da914/GCA_018058385.1_ASM1805838v1_genomic.fna.gz | prodigal -d GCA_018058385.1_ASM1805838v1_genomic.fna/cds.fna -a GCA_018058385.1_ASM1805838v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 01:24:50,711] [INFO] Task succeeded: Prodigal
[2023-06-19 01:24:50,712] [INFO] Task started: HMMsearch
[2023-06-19 01:24:50,712] [INFO] Running command: hmmsearch --tblout GCA_018058385.1_ASM1805838v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf41ebbcb-f0ee-46e8-8b53-bb852b8436b0/dqc_reference/reference_markers.hmm GCA_018058385.1_ASM1805838v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 01:24:50,959] [INFO] Task succeeded: HMMsearch
[2023-06-19 01:24:50,960] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgf3594d98-4e8c-408d-81c5-d2bdf71da914/GCA_018058385.1_ASM1805838v1_genomic.fna.gz]
[2023-06-19 01:24:50,995] [INFO] Query marker FASTA was written to GCA_018058385.1_ASM1805838v1_genomic.fna/markers.fasta
[2023-06-19 01:24:50,996] [INFO] Task started: Blastn
[2023-06-19 01:24:50,996] [INFO] Running command: blastn -query GCA_018058385.1_ASM1805838v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf41ebbcb-f0ee-46e8-8b53-bb852b8436b0/dqc_reference/reference_markers.fasta -out GCA_018058385.1_ASM1805838v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 01:24:51,751] [INFO] Task succeeded: Blastn
[2023-06-19 01:24:51,759] [INFO] Selected 11 target genomes.
[2023-06-19 01:24:51,760] [INFO] Target genome list was writen to GCA_018058385.1_ASM1805838v1_genomic.fna/target_genomes.txt
[2023-06-19 01:24:51,766] [INFO] Task started: fastANI
[2023-06-19 01:24:51,766] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3594d98-4e8c-408d-81c5-d2bdf71da914/GCA_018058385.1_ASM1805838v1_genomic.fna.gz --refList GCA_018058385.1_ASM1805838v1_genomic.fna/target_genomes.txt --output GCA_018058385.1_ASM1805838v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 01:25:02,878] [INFO] Task succeeded: fastANI
[2023-06-19 01:25:02,879] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf41ebbcb-f0ee-46e8-8b53-bb852b8436b0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 01:25:02,879] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf41ebbcb-f0ee-46e8-8b53-bb852b8436b0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 01:25:02,893] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 01:25:02,893] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 01:25:02,893] [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 glaciei	strain=20VBR1	GCA_016772415.2	2803784	2803784	type	True	89.1107	668	761	95	below_threshold
Phenylobacterium aquaticum	strain=KACC 18306	GCA_022695515.1	1763816	1763816	type	True	82.0495	574	761	95	below_threshold
Phenylobacterium hankyongense	strain=HKS-05	GCA_003254505.1	1813876	1813876	type	True	81.0744	457	761	95	below_threshold
Phenylobacterium haematophilum	strain=DSM 21793	GCA_014196295.1	98513	98513	type	True	80.4818	496	761	95	below_threshold
Phenylobacterium soli	strain=LX32	GCA_003254475.1	2170551	2170551	type	True	80.099	444	761	95	below_threshold
Phenylobacterium zucineum	strain=HLK1	GCA_000017265.1	284016	284016	type	True	79.586	453	761	95	below_threshold
Phenylobacterium kunshanense	strain=BUT-10	GCA_003254525.1	1445034	1445034	type	True	79.3083	405	761	95	below_threshold
Phenylobacterium parvum	strain=HYN0004	GCA_003150835.1	2201350	2201350	type	True	79.2466	317	761	95	below_threshold
Caulobacter flavus	strain=CGMCC1 15093	GCA_002858845.1	1679497	1679497	type	True	79.1024	397	761	95	below_threshold
Caulobacter mirabilis	strain=FWC 38	GCA_002749615.1	69666	69666	type	True	78.805	381	761	95	below_threshold
Brevundimonas subvibrioides	strain=ATCC 15264	GCA_000144605.1	74313	74313	type	True	77.9087	199	761	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 01:25:02,898] [INFO] DFAST Taxonomy check result was written to GCA_018058385.1_ASM1805838v1_genomic.fna/tc_result.tsv
[2023-06-19 01:25:02,899] [INFO] ===== Taxonomy check completed =====
[2023-06-19 01:25:02,899] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 01:25:02,900] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf41ebbcb-f0ee-46e8-8b53-bb852b8436b0/dqc_reference/checkm_data
[2023-06-19 01:25:02,902] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 01:25:02,959] [INFO] Task started: CheckM
[2023-06-19 01:25:02,959] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018058385.1_ASM1805838v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018058385.1_ASM1805838v1_genomic.fna/checkm_input GCA_018058385.1_ASM1805838v1_genomic.fna/checkm_result
[2023-06-19 01:25:27,440] [INFO] Task succeeded: CheckM
[2023-06-19 01:25:27,443] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 63.26%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-19 01:25:27,477] [INFO] ===== Completeness check finished =====
[2023-06-19 01:25:27,477] [INFO] ===== Start GTDB Search =====
[2023-06-19 01:25:27,477] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018058385.1_ASM1805838v1_genomic.fna/markers.fasta)
[2023-06-19 01:25:27,478] [INFO] Task started: Blastn
[2023-06-19 01:25:27,478] [INFO] Running command: blastn -query GCA_018058385.1_ASM1805838v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf41ebbcb-f0ee-46e8-8b53-bb852b8436b0/dqc_reference/reference_markers_gtdb.fasta -out GCA_018058385.1_ASM1805838v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 01:25:28,733] [INFO] Task succeeded: Blastn
[2023-06-19 01:25:28,739] [INFO] Selected 12 target genomes.
[2023-06-19 01:25:28,739] [INFO] Target genome list was writen to GCA_018058385.1_ASM1805838v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 01:25:28,748] [INFO] Task started: fastANI
[2023-06-19 01:25:28,748] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3594d98-4e8c-408d-81c5-d2bdf71da914/GCA_018058385.1_ASM1805838v1_genomic.fna.gz --refList GCA_018058385.1_ASM1805838v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018058385.1_ASM1805838v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 01:25:38,244] [INFO] Task succeeded: fastANI
[2023-06-19 01:25:38,267] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 01:25:38,268] [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
GCA_018001015.1	s__Phenylobacterium sp018001015	99.7832	731	761	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	99.74	99.70	0.93	0.91	3	conclusive
GCF_016772415.1	s__Phenylobacterium sp016772415	89.1052	669	761	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	81.0743	457	761	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017991675.1	s__Phenylobacterium sp017991675	80.9544	346	761	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013822795.1	s__Phenylobacterium sp013822795	80.8863	493	761	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425305.1	s__Phenylobacterium sp001425305	80.7945	499	761	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	99.99	99.99	1.00	1.00	3	-
GCF_014196295.1	s__Phenylobacterium haematophilum	80.4476	500	761	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	80.4129	458	761	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	98.20	98.20	0.93	0.93	2	-
GCA_004799515.1	s__Phenylobacterium sp004799515	80.1243	453	761	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	80.0866	378	761	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	79.9448	449	761	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	99.99	99.99	0.99	0.99	6	-
GCA_903909375.1	s__Phenylobacterium sp903909375	78.7475	307	761	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 01:25:38,270] [INFO] GTDB search result was written to GCA_018058385.1_ASM1805838v1_genomic.fna/result_gtdb.tsv
[2023-06-19 01:25:38,270] [INFO] ===== GTDB Search completed =====
[2023-06-19 01:25:38,274] [INFO] DFAST_QC result json was written to GCA_018058385.1_ASM1805838v1_genomic.fna/dqc_result.json
[2023-06-19 01:25:38,274] [INFO] DFAST_QC completed!
[2023-06-19 01:25:38,274] [INFO] Total running time: 0h0m56s