[2024-01-24 14:19:17,422] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:17,424] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:17,424] [INFO] DQC Reference Directory: /var/lib/cwl/stg6e771d75-3b7a-42c4-a5d8-8339aeef4f79/dqc_reference
[2024-01-24 14:19:18,718] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:18,718] [INFO] Task started: Prodigal
[2024-01-24 14:19:18,719] [INFO] Running command: gunzip -c /var/lib/cwl/stg85245cdb-b824-43f3-933c-9dc1ad820ebc/GCF_907164845.1_Lysobacter_CECT30171_genomic.fna.gz | prodigal -d GCF_907164845.1_Lysobacter_CECT30171_genomic.fna/cds.fna -a GCF_907164845.1_Lysobacter_CECT30171_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:28,146] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:28,147] [INFO] Task started: HMMsearch
[2024-01-24 14:19:28,147] [INFO] Running command: hmmsearch --tblout GCF_907164845.1_Lysobacter_CECT30171_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6e771d75-3b7a-42c4-a5d8-8339aeef4f79/dqc_reference/reference_markers.hmm GCF_907164845.1_Lysobacter_CECT30171_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:28,439] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:28,440] [INFO] Found 6/6 markers.
[2024-01-24 14:19:28,465] [INFO] Query marker FASTA was written to GCF_907164845.1_Lysobacter_CECT30171_genomic.fna/markers.fasta
[2024-01-24 14:19:28,466] [INFO] Task started: Blastn
[2024-01-24 14:19:28,466] [INFO] Running command: blastn -query GCF_907164845.1_Lysobacter_CECT30171_genomic.fna/markers.fasta -db /var/lib/cwl/stg6e771d75-3b7a-42c4-a5d8-8339aeef4f79/dqc_reference/reference_markers.fasta -out GCF_907164845.1_Lysobacter_CECT30171_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:29,596] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:29,601] [INFO] Selected 17 target genomes.
[2024-01-24 14:19:29,601] [INFO] Target genome list was writen to GCF_907164845.1_Lysobacter_CECT30171_genomic.fna/target_genomes.txt
[2024-01-24 14:19:29,612] [INFO] Task started: fastANI
[2024-01-24 14:19:29,613] [INFO] Running command: fastANI --query /var/lib/cwl/stg85245cdb-b824-43f3-933c-9dc1ad820ebc/GCF_907164845.1_Lysobacter_CECT30171_genomic.fna.gz --refList GCF_907164845.1_Lysobacter_CECT30171_genomic.fna/target_genomes.txt --output GCF_907164845.1_Lysobacter_CECT30171_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:19:42,999] [INFO] Task succeeded: fastANI
[2024-01-24 14:19:42,999] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6e771d75-3b7a-42c4-a5d8-8339aeef4f79/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:19:42,999] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6e771d75-3b7a-42c4-a5d8-8339aeef4f79/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:19:43,013] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:19:43,014] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:19:43,014] [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 luteus	strain=CECT 30171	GCA_907164845.1	2822368	2822368	type	True	100.0	921	922	95	conclusive
Lysobacter arseniciresistens	strain=ZS79	GCA_000768335.1	1385522	1385522	type	True	88.0195	747	922	95	below_threshold
Lysobacter concretionis	strain=Ko07	GCA_000768345.1	262325	262325	type	True	82.8464	634	922	95	below_threshold
Lysobacter spongiicola	strain=DSM 21749	GCA_900167055.1	435289	435289	type	True	82.7228	644	922	95	below_threshold
Lysobacter defluvii	strain=IMMIB APB-9	GCA_000769985.1	391738	391738	type	True	82.5214	483	922	95	below_threshold
Lysobacter defluvii	strain=DSM 18482	GCA_000423325.1	391738	391738	type	True	82.4625	602	922	95	below_threshold
Lysobacter silvisoli	strain=zong2l5	GCA_003382365.1	2293254	2293254	type	True	81.7534	600	922	95	below_threshold
Lysobacter chinensis	strain=TLK-CK17	GCA_021725675.1	2912247	2912247	type	True	81.7522	605	922	95	below_threshold
Lysobacter panacisoli	strain=JCM 19212	GCA_009765165.1	1255263	1255263	type	True	81.6937	609	922	95	below_threshold
Lysobacter psychrotolerans	strain=ZS60	GCA_003719825.1	1327343	1327343	type	True	81.5706	582	922	95	below_threshold
Lysobacter avium	strain=H23M41	GCA_015209745.1	2781023	2781023	type	True	81.5463	558	922	95	below_threshold
Vulcaniibacterium thermophilum	strain=KCTC 32020	GCA_007923255.1	1169913	1169913	type	True	81.4288	575	922	95	below_threshold
Vulcaniibacterium thermophilum	strain=KCTC 32020	GCA_014656335.1	1169913	1169913	type	True	81.416	585	922	95	below_threshold
Luteimonas marina	strain=FR1330	GCA_007859325.1	488485	488485	type	True	81.4126	578	922	95	below_threshold
Luteimonas mephitis	strain=DSM 12574	GCA_000422305.1	83615	83615	type	True	81.3382	598	922	95	below_threshold
Lysobacter capsici	strain=VKM B-2533	GCA_014779555.2	435897	435897	type	True	81.3366	587	922	95	below_threshold
Luteimonas yindakuii	strain=S-1072	GCA_004803715.2	2565782	2565782	type	True	80.7473	545	922	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:19:43,015] [INFO] DFAST Taxonomy check result was written to GCF_907164845.1_Lysobacter_CECT30171_genomic.fna/tc_result.tsv
[2024-01-24 14:19:43,016] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:19:43,016] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:19:43,016] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6e771d75-3b7a-42c4-a5d8-8339aeef4f79/dqc_reference/checkm_data
[2024-01-24 14:19:43,018] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:19:43,050] [INFO] Task started: CheckM
[2024-01-24 14:19:43,051] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_907164845.1_Lysobacter_CECT30171_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_907164845.1_Lysobacter_CECT30171_genomic.fna/checkm_input GCF_907164845.1_Lysobacter_CECT30171_genomic.fna/checkm_result
[2024-01-24 14:20:22,872] [INFO] Task succeeded: CheckM
[2024-01-24 14:20:22,873] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:20:22,892] [INFO] ===== Completeness check finished =====
[2024-01-24 14:20:22,892] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:20:22,893] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_907164845.1_Lysobacter_CECT30171_genomic.fna/markers.fasta)
[2024-01-24 14:20:22,893] [INFO] Task started: Blastn
[2024-01-24 14:20:22,893] [INFO] Running command: blastn -query GCF_907164845.1_Lysobacter_CECT30171_genomic.fna/markers.fasta -db /var/lib/cwl/stg6e771d75-3b7a-42c4-a5d8-8339aeef4f79/dqc_reference/reference_markers_gtdb.fasta -out GCF_907164845.1_Lysobacter_CECT30171_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:25,022] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:25,028] [INFO] Selected 15 target genomes.
[2024-01-24 14:20:25,028] [INFO] Target genome list was writen to GCF_907164845.1_Lysobacter_CECT30171_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:20:25,042] [INFO] Task started: fastANI
[2024-01-24 14:20:25,043] [INFO] Running command: fastANI --query /var/lib/cwl/stg85245cdb-b824-43f3-933c-9dc1ad820ebc/GCF_907164845.1_Lysobacter_CECT30171_genomic.fna.gz --refList GCF_907164845.1_Lysobacter_CECT30171_genomic.fna/target_genomes_gtdb.txt --output GCF_907164845.1_Lysobacter_CECT30171_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:20:36,707] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:36,719] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:20:36,720] [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_907164845.1	s__Lysobacter sp907164845	100.0	921	922	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_000768335.1	s__Lysobacter arseniciresistens	88.0274	747	922	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000768345.1	s__Lysobacter concretionis	82.8726	632	922	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003586305.1	s__Lysobacter tabacisoli	82.7547	622	922	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900167055.1	s__Lysobacter spongiicola	82.7132	645	922	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001830245.1	s__Lysobacter sp001830245	82.6665	614	922	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	99.71	99.71	0.92	0.92	2	-
GCF_000423325.1	s__Lysobacter defluvii	82.4189	605	922	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900114355.1	s__Lysobacter sp900114355	81.8459	611	922	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	81.7889	638	922	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	97.93	95.70	0.94	0.91	4	-
GCF_015209725.1	s__Lysobacter sp015209725	81.741	571	922	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	96.91	96.91	0.94	0.94	2	-
GCF_009765165.1	s__Lysobacter panacisoli	81.7218	609	922	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003719825.1	s__Lysobacter psychrotolerans	81.59	581	922	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	81.5046	606	922	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422305.1	s__Luteimonas mephitis	81.3426	598	922	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016735495.2	s__Lysobacter sp016735495	81.3072	603	922	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 14:20:36,721] [INFO] GTDB search result was written to GCF_907164845.1_Lysobacter_CECT30171_genomic.fna/result_gtdb.tsv
[2024-01-24 14:20:36,722] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:20:36,726] [INFO] DFAST_QC result json was written to GCF_907164845.1_Lysobacter_CECT30171_genomic.fna/dqc_result.json
[2024-01-24 14:20:36,726] [INFO] DFAST_QC completed!
[2024-01-24 14:20:36,726] [INFO] Total running time: 0h1m19s