[2023-06-18 18:17:42,679] [INFO] DFAST_QC pipeline started.
[2023-06-18 18:17:42,688] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 18:17:42,689] [INFO] DQC Reference Directory: /var/lib/cwl/stg482ff2ef-93eb-48e1-845e-09ef98cecb1c/dqc_reference
[2023-06-18 18:17:45,077] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 18:17:45,078] [INFO] Task started: Prodigal
[2023-06-18 18:17:45,079] [INFO] Running command: gunzip -c /var/lib/cwl/stgf18f4a37-e780-41ae-82a2-248b23a02d70/GCA_018895795.1_ASM1889579v1_genomic.fna.gz | prodigal -d GCA_018895795.1_ASM1889579v1_genomic.fna/cds.fna -a GCA_018895795.1_ASM1889579v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 18:17:53,552] [INFO] Task succeeded: Prodigal
[2023-06-18 18:17:53,553] [INFO] Task started: HMMsearch
[2023-06-18 18:17:53,553] [INFO] Running command: hmmsearch --tblout GCA_018895795.1_ASM1889579v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg482ff2ef-93eb-48e1-845e-09ef98cecb1c/dqc_reference/reference_markers.hmm GCA_018895795.1_ASM1889579v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 18:17:53,811] [INFO] Task succeeded: HMMsearch
[2023-06-18 18:17:53,814] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgf18f4a37-e780-41ae-82a2-248b23a02d70/GCA_018895795.1_ASM1889579v1_genomic.fna.gz]
[2023-06-18 18:17:53,859] [INFO] Query marker FASTA was written to GCA_018895795.1_ASM1889579v1_genomic.fna/markers.fasta
[2023-06-18 18:17:53,860] [INFO] Task started: Blastn
[2023-06-18 18:17:53,860] [INFO] Running command: blastn -query GCA_018895795.1_ASM1889579v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg482ff2ef-93eb-48e1-845e-09ef98cecb1c/dqc_reference/reference_markers.fasta -out GCA_018895795.1_ASM1889579v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 18:17:54,702] [INFO] Task succeeded: Blastn
[2023-06-18 18:17:54,706] [INFO] Selected 15 target genomes.
[2023-06-18 18:17:54,707] [INFO] Target genome list was writen to GCA_018895795.1_ASM1889579v1_genomic.fna/target_genomes.txt
[2023-06-18 18:17:54,716] [INFO] Task started: fastANI
[2023-06-18 18:17:54,716] [INFO] Running command: fastANI --query /var/lib/cwl/stgf18f4a37-e780-41ae-82a2-248b23a02d70/GCA_018895795.1_ASM1889579v1_genomic.fna.gz --refList GCA_018895795.1_ASM1889579v1_genomic.fna/target_genomes.txt --output GCA_018895795.1_ASM1889579v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 18:18:09,369] [INFO] Task succeeded: fastANI
[2023-06-18 18:18:09,369] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg482ff2ef-93eb-48e1-845e-09ef98cecb1c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 18:18:09,369] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg482ff2ef-93eb-48e1-845e-09ef98cecb1c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 18:18:09,382] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 18:18:09,383] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 18:18:09,383] [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
Caulobacter henricii	strain=CB4	GCA_001414055.1	69395	69395	type	True	84.649	762	1025	95	below_threshold
Caulobacter soli	strain=Ji-3-8	GCA_011045195.1	2708539	2708539	type	True	83.4869	738	1025	95	below_threshold
Caulobacter rhizosphaerae	strain=CGMCC 1.15915	GCA_014645055.1	2010972	2010972	type	True	83.271	739	1025	95	below_threshold
Caulobacter rhizosphaerae	strain=KCTC 52515	GCA_010977555.1	2010972	2010972	type	True	83.1985	740	1025	95	below_threshold
Caulobacter hibisci	strain=KACC 18849	GCA_016135805.1	2035993	2035993	type	True	82.7914	721	1025	95	below_threshold
Caulobacter radicis	strain=695	GCA_003094615.1	2172650	2172650	type	True	82.7007	724	1025	95	below_threshold
Caulobacter vibrioides	strain=DSM 9893	GCA_002858865.1	155892	155892	type	True	82.695	712	1025	95	below_threshold
Caulobacter segnis	strain=ATCC 21756	GCA_000092285.1	88688	88688	type	True	82.6796	733	1025	95	below_threshold
Caulobacter segnis	strain=TK0059	GCA_003015125.1	88688	88688	type	True	82.6762	734	1025	95	below_threshold
Caulobacter flavus	strain=RHGG3	GCA_003722335.1	1679497	1679497	type	True	82.5993	722	1025	95	below_threshold
Caulobacter flavus	strain=CGMCC1 15093	GCA_002858845.1	1679497	1679497	type	True	82.5166	734	1025	95	below_threshold
Phenylobacterium aquaticum	strain=KACC 18306	GCA_022695515.1	1763816	1763816	type	True	79.0721	506	1025	95	below_threshold
Phenylobacterium glaciei	strain=20VBR1	GCA_016772415.2	2803784	2803784	type	True	78.678	454	1025	95	below_threshold
Brevundimonas pishanensis	strain=CHPC 1.3453	GCA_022750635.1	2896315	2896315	type	True	76.4573	144	1025	95	below_threshold
Starkeya koreensis	strain=Jip08	GCA_023016525.1	266121	266121	type	True	76.1027	131	1025	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 18:18:09,385] [INFO] DFAST Taxonomy check result was written to GCA_018895795.1_ASM1889579v1_genomic.fna/tc_result.tsv
[2023-06-18 18:18:09,386] [INFO] ===== Taxonomy check completed =====
[2023-06-18 18:18:09,386] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 18:18:09,386] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg482ff2ef-93eb-48e1-845e-09ef98cecb1c/dqc_reference/checkm_data
[2023-06-18 18:18:09,387] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 18:18:09,425] [INFO] Task started: CheckM
[2023-06-18 18:18:09,426] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018895795.1_ASM1889579v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018895795.1_ASM1889579v1_genomic.fna/checkm_input GCA_018895795.1_ASM1889579v1_genomic.fna/checkm_result
[2023-06-18 18:18:38,691] [INFO] Task succeeded: CheckM
[2023-06-18 18:18:38,693] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 68.06%
Contamintation: 1.04%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-18 18:18:38,716] [INFO] ===== Completeness check finished =====
[2023-06-18 18:18:38,716] [INFO] ===== Start GTDB Search =====
[2023-06-18 18:18:38,717] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018895795.1_ASM1889579v1_genomic.fna/markers.fasta)
[2023-06-18 18:18:38,717] [INFO] Task started: Blastn
[2023-06-18 18:18:38,717] [INFO] Running command: blastn -query GCA_018895795.1_ASM1889579v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg482ff2ef-93eb-48e1-845e-09ef98cecb1c/dqc_reference/reference_markers_gtdb.fasta -out GCA_018895795.1_ASM1889579v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 18:18:40,245] [INFO] Task succeeded: Blastn
[2023-06-18 18:18:40,249] [INFO] Selected 14 target genomes.
[2023-06-18 18:18:40,249] [INFO] Target genome list was writen to GCA_018895795.1_ASM1889579v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 18:18:40,363] [INFO] Task started: fastANI
[2023-06-18 18:18:40,364] [INFO] Running command: fastANI --query /var/lib/cwl/stgf18f4a37-e780-41ae-82a2-248b23a02d70/GCA_018895795.1_ASM1889579v1_genomic.fna.gz --refList GCA_018895795.1_ASM1889579v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018895795.1_ASM1889579v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 18:18:55,098] [INFO] Task succeeded: fastANI
[2023-06-18 18:18:55,115] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 18:18:55,116] [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_018895795.1	s__Caulobacter sp018895795	100.0	1012	1025	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000744465.1	s__Caulobacter henricii_A	86.5301	832	1025	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002280875.1	s__Caulobacter sp002280875	85.9308	769	1025	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	99.61	99.61	0.91	0.91	2	-
GCF_001414055.1	s__Caulobacter henricii	84.6261	763	1025	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003060965.1	s__Caulobacter sp003060965	84.0122	729	1025	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	99.90	99.90	0.96	0.96	2	-
GCF_002737765.1	s__Caulobacter sp002737765	83.9579	415	1025	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000281955.1	s__Caulobacter sp000281955	83.8457	738	1025	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001426905.1	s__Caulobacter sp001426905	83.8182	767	1025	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	99.12	99.12	0.97	0.97	2	-
GCF_001427665.1	s__Caulobacter sp001427665	83.7561	757	1025	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011045195.1	s__Caulobacter soli	83.4979	738	1025	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903900155.1	s__Caulobacter sp903900155	83.425	739	1025	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	99.93	99.90	0.95	0.93	3	-
GCF_010977555.1	s__Caulobacter rhizosphaerae	83.1897	741	1025	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	98.18	95.88	0.94	0.91	4	-
GCF_002742625.1	s__Caulobacter sp002742625	83.1799	777	1025	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014207215.1	s__Caulobacter sp014207215	83.0599	742	1025	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 18:18:55,117] [INFO] GTDB search result was written to GCA_018895795.1_ASM1889579v1_genomic.fna/result_gtdb.tsv
[2023-06-18 18:18:55,118] [INFO] ===== GTDB Search completed =====
[2023-06-18 18:18:55,121] [INFO] DFAST_QC result json was written to GCA_018895795.1_ASM1889579v1_genomic.fna/dqc_result.json
[2023-06-18 18:18:55,121] [INFO] DFAST_QC completed!
[2023-06-18 18:18:55,122] [INFO] Total running time: 0h1m12s