[2024-01-24 13:47:11,709] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:47:11,712] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:47:11,712] [INFO] DQC Reference Directory: /var/lib/cwl/stg3b32325b-3eaa-435b-b889-cf20d5f6b7fd/dqc_reference
[2024-01-24 13:47:13,021] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:47:13,024] [INFO] Task started: Prodigal
[2024-01-24 13:47:13,026] [INFO] Running command: gunzip -c /var/lib/cwl/stg19700b42-9b45-441b-8615-51f9be0d85cc/GCF_009765165.1_ASM976516v1_genomic.fna.gz | prodigal -d GCF_009765165.1_ASM976516v1_genomic.fna/cds.fna -a GCF_009765165.1_ASM976516v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:47:25,927] [INFO] Task succeeded: Prodigal
[2024-01-24 13:47:25,927] [INFO] Task started: HMMsearch
[2024-01-24 13:47:25,927] [INFO] Running command: hmmsearch --tblout GCF_009765165.1_ASM976516v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3b32325b-3eaa-435b-b889-cf20d5f6b7fd/dqc_reference/reference_markers.hmm GCF_009765165.1_ASM976516v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:47:26,188] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:47:26,189] [INFO] Found 6/6 markers.
[2024-01-24 13:47:26,231] [INFO] Query marker FASTA was written to GCF_009765165.1_ASM976516v1_genomic.fna/markers.fasta
[2024-01-24 13:47:26,232] [INFO] Task started: Blastn
[2024-01-24 13:47:26,232] [INFO] Running command: blastn -query GCF_009765165.1_ASM976516v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3b32325b-3eaa-435b-b889-cf20d5f6b7fd/dqc_reference/reference_markers.fasta -out GCF_009765165.1_ASM976516v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:27,301] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:27,306] [INFO] Selected 12 target genomes.
[2024-01-24 13:47:27,306] [INFO] Target genome list was writen to GCF_009765165.1_ASM976516v1_genomic.fna/target_genomes.txt
[2024-01-24 13:47:27,313] [INFO] Task started: fastANI
[2024-01-24 13:47:27,314] [INFO] Running command: fastANI --query /var/lib/cwl/stg19700b42-9b45-441b-8615-51f9be0d85cc/GCF_009765165.1_ASM976516v1_genomic.fna.gz --refList GCF_009765165.1_ASM976516v1_genomic.fna/target_genomes.txt --output GCF_009765165.1_ASM976516v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:47:38,677] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:38,678] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3b32325b-3eaa-435b-b889-cf20d5f6b7fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:47:38,678] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3b32325b-3eaa-435b-b889-cf20d5f6b7fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:47:38,688] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:47:38,688] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:47:38,688] [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
Lysobacter panacisoli	strain=JCM 19212	GCA_009765165.1	1255263	1255263	type	True	100.0	1291	1292	95	conclusive
Lysobacter soli	strain=KCTC 22011	GCA_003382285.1	453783	453783	type	True	86.0361	995	1292	95	below_threshold
Lysobacter arenosi	strain=R7	GCA_016613475.2	2795387	2795387	type	True	84.9639	929	1292	95	below_threshold
Lysobacter prati	strain=SYSU H10001	GCA_009765215.1	2596704	2596704	type	True	84.5797	927	1292	95	below_threshold
Vulcaniibacterium tengchongense	strain=YIM 77520	GCA_008033455.1	1273429	1273429	type	True	84.2951	772	1292	95	below_threshold
Vulcaniibacterium tengchongense	strain=DSM 25623	GCA_003814555.1	1273429	1273429	type	True	84.1737	822	1292	95	below_threshold
Lysobacter niastensis	strain=DSM 18481	GCA_015453285.1	380629	380629	type	True	84.0562	857	1292	95	below_threshold
Lysobacter silvisoli	strain=zong2l5	GCA_003382365.1	2293254	2293254	type	True	83.0403	802	1292	95	below_threshold
Lysobacter arseniciresistens	strain=ZS79	GCA_000768335.1	1385522	1385522	type	True	82.3384	641	1292	95	below_threshold
Lysobacter capsici	strain=VKM B-2533	GCA_014779555.2	435897	435897	type	True	82.1453	832	1292	95	below_threshold
Lysobacter luteus	strain=CECT 30171	GCA_907164845.1	2822368	2822368	type	True	81.6086	605	1292	95	below_threshold
Lysobacter chinensis	strain=TLK-CK17	GCA_021725675.1	2912247	2912247	type	True	81.521	725	1292	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:47:38,690] [INFO] DFAST Taxonomy check result was written to GCF_009765165.1_ASM976516v1_genomic.fna/tc_result.tsv
[2024-01-24 13:47:38,691] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:47:38,691] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:47:38,691] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3b32325b-3eaa-435b-b889-cf20d5f6b7fd/dqc_reference/checkm_data
[2024-01-24 13:47:38,693] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:47:38,733] [INFO] Task started: CheckM
[2024-01-24 13:47:38,733] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009765165.1_ASM976516v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009765165.1_ASM976516v1_genomic.fna/checkm_input GCF_009765165.1_ASM976516v1_genomic.fna/checkm_result
[2024-01-24 13:48:26,853] [INFO] Task succeeded: CheckM
[2024-01-24 13:48:26,854] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:48:26,874] [INFO] ===== Completeness check finished =====
[2024-01-24 13:48:26,874] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:48:26,874] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009765165.1_ASM976516v1_genomic.fna/markers.fasta)
[2024-01-24 13:48:26,875] [INFO] Task started: Blastn
[2024-01-24 13:48:26,875] [INFO] Running command: blastn -query GCF_009765165.1_ASM976516v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3b32325b-3eaa-435b-b889-cf20d5f6b7fd/dqc_reference/reference_markers_gtdb.fasta -out GCF_009765165.1_ASM976516v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:48:28,900] [INFO] Task succeeded: Blastn
[2024-01-24 13:48:28,903] [INFO] Selected 6 target genomes.
[2024-01-24 13:48:28,904] [INFO] Target genome list was writen to GCF_009765165.1_ASM976516v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:48:28,923] [INFO] Task started: fastANI
[2024-01-24 13:48:28,923] [INFO] Running command: fastANI --query /var/lib/cwl/stg19700b42-9b45-441b-8615-51f9be0d85cc/GCF_009765165.1_ASM976516v1_genomic.fna.gz --refList GCF_009765165.1_ASM976516v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009765165.1_ASM976516v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:48:35,875] [INFO] Task succeeded: fastANI
[2024-01-24 13:48:35,885] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:48:35,885] [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_009765165.1	s__Lysobacter panacisoli	100.0	1291	1292	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016735495.2	s__Lysobacter sp016735495	86.4088	1047	1292	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017308985.1	s__Lysobacter sp017308985	86.2909	1028	1292	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003382285.1	s__Lysobacter soli	86.0494	994	1292	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	96.84	96.81	0.94	0.93	3	-
GCA_005503055.1	s__Lysobacter sp005503055	85.8624	1002	1292	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016613475.2	s__Lysobacter arenosi	84.9482	930	1292	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:48:35,886] [INFO] GTDB search result was written to GCF_009765165.1_ASM976516v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:48:35,887] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:48:35,890] [INFO] DFAST_QC result json was written to GCF_009765165.1_ASM976516v1_genomic.fna/dqc_result.json
[2024-01-24 13:48:35,890] [INFO] DFAST_QC completed!
[2024-01-24 13:48:35,890] [INFO] Total running time: 0h1m24s