[2024-01-24 13:17:59,217] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:59,218] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:59,218] [INFO] DQC Reference Directory: /var/lib/cwl/stg02180dc8-2944-47dd-837b-8e21c6d04bf4/dqc_reference
[2024-01-24 13:18:00,556] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:00,557] [INFO] Task started: Prodigal
[2024-01-24 13:18:00,557] [INFO] Running command: gunzip -c /var/lib/cwl/stg6fb6d6bf-6218-480e-968b-f9d5c09bfe5e/GCF_008033455.1_ASM803345v1_genomic.fna.gz | prodigal -d GCF_008033455.1_ASM803345v1_genomic.fna/cds.fna -a GCF_008033455.1_ASM803345v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:10,041] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:10,041] [INFO] Task started: HMMsearch
[2024-01-24 13:18:10,042] [INFO] Running command: hmmsearch --tblout GCF_008033455.1_ASM803345v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg02180dc8-2944-47dd-837b-8e21c6d04bf4/dqc_reference/reference_markers.hmm GCF_008033455.1_ASM803345v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:10,297] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:10,298] [INFO] Found 6/6 markers.
[2024-01-24 13:18:10,327] [INFO] Query marker FASTA was written to GCF_008033455.1_ASM803345v1_genomic.fna/markers.fasta
[2024-01-24 13:18:10,328] [INFO] Task started: Blastn
[2024-01-24 13:18:10,328] [INFO] Running command: blastn -query GCF_008033455.1_ASM803345v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg02180dc8-2944-47dd-837b-8e21c6d04bf4/dqc_reference/reference_markers.fasta -out GCF_008033455.1_ASM803345v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:11,426] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:11,429] [INFO] Selected 17 target genomes.
[2024-01-24 13:18:11,429] [INFO] Target genome list was writen to GCF_008033455.1_ASM803345v1_genomic.fna/target_genomes.txt
[2024-01-24 13:18:11,450] [INFO] Task started: fastANI
[2024-01-24 13:18:11,450] [INFO] Running command: fastANI --query /var/lib/cwl/stg6fb6d6bf-6218-480e-968b-f9d5c09bfe5e/GCF_008033455.1_ASM803345v1_genomic.fna.gz --refList GCF_008033455.1_ASM803345v1_genomic.fna/target_genomes.txt --output GCF_008033455.1_ASM803345v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:27,728] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:27,729] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg02180dc8-2944-47dd-837b-8e21c6d04bf4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:27,729] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg02180dc8-2944-47dd-837b-8e21c6d04bf4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:27,743] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:18:27,743] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:18:27,743] [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
Vulcaniibacterium tengchongense	strain=YIM 77520	GCA_008033455.1	1273429	1273429	type	True	100.0	1123	1128	95	conclusive
Vulcaniibacterium tengchongense	strain=DSM 25623	GCA_003814555.1	1273429	1273429	type	True	99.9924	1117	1128	95	conclusive
Lysobacter silvisoli	strain=zong2l5	GCA_003382365.1	2293254	2293254	type	True	84.3752	782	1128	95	below_threshold
Vulcaniibacterium gelatinicum	strain=R-5-52-3	GCA_008033445.1	2598725	2598725	type	True	84.3281	611	1128	95	below_threshold
Lysobacter panacisoli	strain=JCM 19212	GCA_009765165.1	1255263	1255263	type	True	84.1581	785	1128	95	below_threshold
Lysobacter arenosi	strain=R7	GCA_016613475.2	2795387	2795387	type	True	83.9782	754	1128	95	below_threshold
Lysobacter enzymogenes	strain=ATCC 29487	GCA_900106525.1	69	69	suspected-type	True	83.7473	809	1128	95	below_threshold
Lysobacter maris	strain=KCTC 42381	GCA_006546735.2	1605891	1605891	type	True	83.6922	653	1128	95	below_threshold
Lysobacter niastensis	strain=DSM 18481	GCA_015453285.1	380629	380629	type	True	83.6758	733	1128	95	below_threshold
Lysobacter prati	strain=SYSU H10001	GCA_009765215.1	2596704	2596704	type	True	83.6296	750	1128	95	below_threshold
Vulcaniibacterium thermophilum	strain=KCTC 32020	GCA_007923255.1	1169913	1169913	type	True	83.5912	672	1128	95	below_threshold
Lysobacter soli	strain=KCTC 22011	GCA_003382285.1	453783	453783	type	True	83.3677	766	1128	95	below_threshold
Lysobacter chinensis	strain=TLK-CK17	GCA_021725675.1	2912247	2912247	type	True	83.1134	708	1128	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	83.0107	557	1128	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	82.8461	726	1128	95	below_threshold
Lysobacter capsici	strain=VKM B-2533	GCA_014779555.2	435897	435897	type	True	82.6543	800	1128	95	below_threshold
Xanthomonas translucens	strain=ATCC 19319	GCA_020880735.1	343	343	type	True	81.6094	594	1128	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:18:27,745] [INFO] DFAST Taxonomy check result was written to GCF_008033455.1_ASM803345v1_genomic.fna/tc_result.tsv
[2024-01-24 13:18:27,745] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:27,745] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:27,745] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg02180dc8-2944-47dd-837b-8e21c6d04bf4/dqc_reference/checkm_data
[2024-01-24 13:18:27,746] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:27,791] [INFO] Task started: CheckM
[2024-01-24 13:18:27,791] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008033455.1_ASM803345v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008033455.1_ASM803345v1_genomic.fna/checkm_input GCF_008033455.1_ASM803345v1_genomic.fna/checkm_result
[2024-01-24 13:19:00,237] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:00,238] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:00,255] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:00,255] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:00,256] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008033455.1_ASM803345v1_genomic.fna/markers.fasta)
[2024-01-24 13:19:00,256] [INFO] Task started: Blastn
[2024-01-24 13:19:00,256] [INFO] Running command: blastn -query GCF_008033455.1_ASM803345v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg02180dc8-2944-47dd-837b-8e21c6d04bf4/dqc_reference/reference_markers_gtdb.fasta -out GCF_008033455.1_ASM803345v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:02,609] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:02,613] [INFO] Selected 19 target genomes.
[2024-01-24 13:19:02,613] [INFO] Target genome list was writen to GCF_008033455.1_ASM803345v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:02,643] [INFO] Task started: fastANI
[2024-01-24 13:19:02,643] [INFO] Running command: fastANI --query /var/lib/cwl/stg6fb6d6bf-6218-480e-968b-f9d5c09bfe5e/GCF_008033455.1_ASM803345v1_genomic.fna.gz --refList GCF_008033455.1_ASM803345v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008033455.1_ASM803345v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:21,232] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:21,248] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:19:21,248] [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_003814555.1	s__Lysobacter tengchongensis	99.9924	1117	1128	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCF_008033445.1	s__Vulcaniibacterium_B gelatinicum	84.324	611	1128	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Vulcaniibacterium_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009765165.1	s__Lysobacter panacisoli	84.1809	783	1128	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003586305.1	s__Lysobacter tabacisoli	84.0519	706	1128	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001442515.1	s__Lysobacter enzymogenes_B	83.9989	845	1128	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	97.93	95.70	0.94	0.91	4	-
GCF_001428685.1	s__Lysobacter sp001428685	83.9864	772	1128	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	99.42	98.61	0.98	0.96	4	-
GCF_016613475.2	s__Lysobacter arenosi	83.9655	755	1128	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	83.9192	793	1128	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013361435.1	s__Lysobacter sp013361435	83.8462	698	1128	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000336385.2	s__Lysobacter antibioticus_A	83.8221	770	1128	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001429785.1	s__Lysobacter sp001429785	83.7725	786	1128	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	98.47	98.45	0.97	0.97	3	-
GCF_015453285.1	s__Lysobacter niastensis	83.6759	733	1128	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007923255.1	s__Lysobacter thermophilus	83.6584	667	1128	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	99.99	99.99	0.98	0.98	2	-
GCF_016735495.2	s__Lysobacter sp016735495	83.6554	792	1128	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009765215.1	s__Lysobacter prati	83.6162	752	1128	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	83.3734	766	1128	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	96.84	96.81	0.94	0.93	3	-
GCF_010093135.1	s__Pseudoxanthomonas taiwanensis	82.7812	620	1128	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	99.04	99.04	0.90	0.90	2	-
GCF_000510725.1	s__Pseudoxanthomonas sp000510725	82.5595	667	1128	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	99.33	99.13	0.95	0.92	5	-
GCF_000185965.1	s__Pseudoxanthomonas suwonensis_A	82.2031	650	1128	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:19:21,250] [INFO] GTDB search result was written to GCF_008033455.1_ASM803345v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:21,250] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:21,254] [INFO] DFAST_QC result json was written to GCF_008033455.1_ASM803345v1_genomic.fna/dqc_result.json
[2024-01-24 13:19:21,255] [INFO] DFAST_QC completed!
[2024-01-24 13:19:21,255] [INFO] Total running time: 0h1m22s