[2024-01-24 15:10:19,846] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:19,848] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:19,848] [INFO] DQC Reference Directory: /var/lib/cwl/stga75bf7fb-16cc-4075-aca1-01246db4baa7/dqc_reference
[2024-01-24 15:10:22,720] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:22,721] [INFO] Task started: Prodigal
[2024-01-24 15:10:22,721] [INFO] Running command: gunzip -c /var/lib/cwl/stg5188e6ad-7f2b-4972-8e52-938c37e8982e/GCF_003382365.1_ASM338236v1_genomic.fna.gz | prodigal -d GCF_003382365.1_ASM338236v1_genomic.fna/cds.fna -a GCF_003382365.1_ASM338236v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:10:36,320] [INFO] Task succeeded: Prodigal
[2024-01-24 15:10:36,321] [INFO] Task started: HMMsearch
[2024-01-24 15:10:36,321] [INFO] Running command: hmmsearch --tblout GCF_003382365.1_ASM338236v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga75bf7fb-16cc-4075-aca1-01246db4baa7/dqc_reference/reference_markers.hmm GCF_003382365.1_ASM338236v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:10:36,585] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:10:36,586] [INFO] Found 6/6 markers.
[2024-01-24 15:10:36,627] [INFO] Query marker FASTA was written to GCF_003382365.1_ASM338236v1_genomic.fna/markers.fasta
[2024-01-24 15:10:36,627] [INFO] Task started: Blastn
[2024-01-24 15:10:36,627] [INFO] Running command: blastn -query GCF_003382365.1_ASM338236v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga75bf7fb-16cc-4075-aca1-01246db4baa7/dqc_reference/reference_markers.fasta -out GCF_003382365.1_ASM338236v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:10:37,693] [INFO] Task succeeded: Blastn
[2024-01-24 15:10:37,697] [INFO] Selected 13 target genomes.
[2024-01-24 15:10:37,697] [INFO] Target genome list was writen to GCF_003382365.1_ASM338236v1_genomic.fna/target_genomes.txt
[2024-01-24 15:10:37,724] [INFO] Task started: fastANI
[2024-01-24 15:10:37,725] [INFO] Running command: fastANI --query /var/lib/cwl/stg5188e6ad-7f2b-4972-8e52-938c37e8982e/GCF_003382365.1_ASM338236v1_genomic.fna.gz --refList GCF_003382365.1_ASM338236v1_genomic.fna/target_genomes.txt --output GCF_003382365.1_ASM338236v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:10:55,517] [INFO] Task succeeded: fastANI
[2024-01-24 15:10:55,518] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga75bf7fb-16cc-4075-aca1-01246db4baa7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:10:55,518] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga75bf7fb-16cc-4075-aca1-01246db4baa7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:10:55,530] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:10:55,530] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:10:55,530] [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 silvisoli	strain=zong2l5	GCA_003382365.1	2293254	2293254	type	True	100.0	1506	1507	95	conclusive
Lysobacter enzymogenes	strain=ATCC 29487	GCA_900106525.1	69	69	suspected-type	True	84.6381	1085	1507	95	below_threshold
Vulcaniibacterium tengchongense	strain=YIM 77520	GCA_008033455.1	1273429	1273429	type	True	84.3089	778	1507	95	below_threshold
Vulcaniibacterium tengchongense	strain=DSM 25623	GCA_003814555.1	1273429	1273429	type	True	84.2146	834	1507	95	below_threshold
Lysobacter antibioticus	strain=ATCC 29479	GCA_001442535.1	84531	84531	type	True	83.882	1008	1507	95	below_threshold
Lysobacter capsici	strain=VKM B-2533	GCA_014779555.2	435897	435897	type	True	83.7714	1075	1507	95	below_threshold
Lysobacter panacisoli	strain=JCM 19212	GCA_009765165.1	1255263	1255263	type	True	83.0504	810	1507	95	below_threshold
Lysobacter terrestris	strain=II4	GCA_014489475.1	2865112	2865112	type	True	82.9286	741	1507	95	below_threshold
Lysobacter arseniciresistens	strain=ZS79	GCA_000768335.1	1385522	1385522	type	True	82.8144	637	1507	95	below_threshold
Lysobacter niastensis	strain=DSM 18481	GCA_015453285.1	380629	380629	type	True	82.632	801	1507	95	below_threshold
Lysobacter chinensis	strain=TLK-CK17	GCA_021725675.1	2912247	2912247	type	True	81.7189	793	1507	95	below_threshold
Lysobacter luteus	strain=CECT 30171	GCA_907164845.1	2822368	2822368	type	True	81.5481	616	1507	95	below_threshold
Lysobacter penaei	strain=SG-8	GCA_014145395.1	2759900	2759900	type	True	81.1132	627	1507	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:10:55,532] [INFO] DFAST Taxonomy check result was written to GCF_003382365.1_ASM338236v1_genomic.fna/tc_result.tsv
[2024-01-24 15:10:55,533] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:10:55,533] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:10:55,533] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga75bf7fb-16cc-4075-aca1-01246db4baa7/dqc_reference/checkm_data
[2024-01-24 15:10:55,534] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:10:55,582] [INFO] Task started: CheckM
[2024-01-24 15:10:55,583] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003382365.1_ASM338236v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003382365.1_ASM338236v1_genomic.fna/checkm_input GCF_003382365.1_ASM338236v1_genomic.fna/checkm_result
[2024-01-24 15:11:39,770] [INFO] Task succeeded: CheckM
[2024-01-24 15:11:39,772] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:11:39,794] [INFO] ===== Completeness check finished =====
[2024-01-24 15:11:39,795] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:11:39,795] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003382365.1_ASM338236v1_genomic.fna/markers.fasta)
[2024-01-24 15:11:39,796] [INFO] Task started: Blastn
[2024-01-24 15:11:39,796] [INFO] Running command: blastn -query GCF_003382365.1_ASM338236v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga75bf7fb-16cc-4075-aca1-01246db4baa7/dqc_reference/reference_markers_gtdb.fasta -out GCF_003382365.1_ASM338236v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:42,047] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:42,050] [INFO] Selected 13 target genomes.
[2024-01-24 15:11:42,050] [INFO] Target genome list was writen to GCF_003382365.1_ASM338236v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:11:42,060] [INFO] Task started: fastANI
[2024-01-24 15:11:42,061] [INFO] Running command: fastANI --query /var/lib/cwl/stg5188e6ad-7f2b-4972-8e52-938c37e8982e/GCF_003382365.1_ASM338236v1_genomic.fna.gz --refList GCF_003382365.1_ASM338236v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003382365.1_ASM338236v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:12:06,308] [INFO] Task succeeded: fastANI
[2024-01-24 15:12:06,320] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:12:06,320] [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_003382365.1	s__Lysobacter silvisoli	100.0	1506	1507	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_013361435.1	s__Lysobacter sp013361435	88.3817	1061	1507	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114355.1	s__Lysobacter sp900114355	88.0845	1240	1507	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	87.9896	1224	1507	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	98.47	98.45	0.97	0.97	3	-
GCF_001428685.1	s__Lysobacter sp001428685	87.9262	1170	1507	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	99.42	98.61	0.98	0.96	4	-
GCF_900107375.1	s__Lysobacter sp900107375	84.8566	1070	1507	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	84.7872	982	1507	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	84.6829	1097	1507	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	97.93	95.70	0.94	0.91	4	-
GCF_900106525.1	s__Lysobacter enzymogenes	84.6545	1083	1507	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	96.14	95.07	0.91	0.91	3	-
GCF_018847975.1	s__Lysobacter sp018847975	84.5817	1071	1507	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017355525.1	s__Lysobacter enzymogenes_C	84.4714	1076	1507	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001442805.1	s__Lysobacter gummosus	84.0517	1042	1507	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014489475.1	s__Lysobacter solisilvae	82.9057	743	1507	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 15:12:06,322] [INFO] GTDB search result was written to GCF_003382365.1_ASM338236v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:12:06,323] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:12:06,327] [INFO] DFAST_QC result json was written to GCF_003382365.1_ASM338236v1_genomic.fna/dqc_result.json
[2024-01-24 15:12:06,327] [INFO] DFAST_QC completed!
[2024-01-24 15:12:06,327] [INFO] Total running time: 0h1m46s