[2024-01-24 13:19:12,749] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:19:12,751] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:19:12,751] [INFO] DQC Reference Directory: /var/lib/cwl/stgc96f9102-4423-4779-9e18-e4bbd1191844/dqc_reference
[2024-01-24 13:19:13,941] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:19:13,941] [INFO] Task started: Prodigal
[2024-01-24 13:19:13,942] [INFO] Running command: gunzip -c /var/lib/cwl/stg07676ab9-9422-4869-8456-c50e6540d3ab/GCF_020866925.1_ASM2086692v1_genomic.fna.gz | prodigal -d GCF_020866925.1_ASM2086692v1_genomic.fna/cds.fna -a GCF_020866925.1_ASM2086692v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:19:24,926] [INFO] Task succeeded: Prodigal
[2024-01-24 13:19:24,926] [INFO] Task started: HMMsearch
[2024-01-24 13:19:24,927] [INFO] Running command: hmmsearch --tblout GCF_020866925.1_ASM2086692v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc96f9102-4423-4779-9e18-e4bbd1191844/dqc_reference/reference_markers.hmm GCF_020866925.1_ASM2086692v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:25,220] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:25,222] [INFO] Found 6/6 markers.
[2024-01-24 13:19:25,272] [INFO] Query marker FASTA was written to GCF_020866925.1_ASM2086692v1_genomic.fna/markers.fasta
[2024-01-24 13:19:25,274] [INFO] Task started: Blastn
[2024-01-24 13:19:25,274] [INFO] Running command: blastn -query GCF_020866925.1_ASM2086692v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc96f9102-4423-4779-9e18-e4bbd1191844/dqc_reference/reference_markers.fasta -out GCF_020866925.1_ASM2086692v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:26,261] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:26,264] [INFO] Selected 19 target genomes.
[2024-01-24 13:19:26,264] [INFO] Target genome list was writen to GCF_020866925.1_ASM2086692v1_genomic.fna/target_genomes.txt
[2024-01-24 13:19:26,273] [INFO] Task started: fastANI
[2024-01-24 13:19:26,273] [INFO] Running command: fastANI --query /var/lib/cwl/stg07676ab9-9422-4869-8456-c50e6540d3ab/GCF_020866925.1_ASM2086692v1_genomic.fna.gz --refList GCF_020866925.1_ASM2086692v1_genomic.fna/target_genomes.txt --output GCF_020866925.1_ASM2086692v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:40,695] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:40,696] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc96f9102-4423-4779-9e18-e4bbd1191844/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:40,696] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc96f9102-4423-4779-9e18-e4bbd1191844/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:40,710] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:19:40,710] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:19:40,710] [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 gilvus	strain=HX-5-24	GCA_009740395.1	2682097	2682097	type	True	86.1038	843	1135	95	below_threshold
Lysobacter dokdonensis	strain=DS-58	GCA_000770795.1	414050	414050	type	True	85.9616	827	1135	95	below_threshold
Lysobacter panacisoli	strain=JCM 19212	GCA_009765165.1	1255263	1255263	type	True	81.4812	638	1135	95	below_threshold
Lysobacter soli	strain=KCTC 22011	GCA_003382285.1	453783	453783	type	True	81.3495	643	1135	95	below_threshold
Vulcaniibacterium gelatinicum	strain=R-5-52-3	GCA_008033445.1	2598725	2598725	type	True	81.3469	522	1135	95	below_threshold
Lysobacter arenosi	strain=R7	GCA_016613475.2	2795387	2795387	type	True	80.9607	584	1135	95	below_threshold
Thermomonas aquatica	strain=SY21	GCA_006337105.1	2202149	2202149	type	True	80.8907	542	1135	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	80.87	492	1135	95	below_threshold
Lysobacter segetis	strain=17J68-2	GCA_004359965.1	2492394	2492394	type	True	80.8687	508	1135	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	80.6212	563	1135	95	below_threshold
Luteimonas gilva	strain=H23	GCA_005239095.1	2572684	2572684	type	True	80.6016	568	1135	95	below_threshold
Luteimonas cucumeris	strain=CGMCC 1.10821	GCA_007830035.1	985012	985012	type	True	80.5341	553	1135	95	below_threshold
Pseudoxanthomonas sangjuensis	strain=DSM 28345	GCA_010211755.1	1503750	1503750	type	True	80.4657	536	1135	95	below_threshold
Lysobacter silvisoli	strain=zong2l5	GCA_003382365.1	2293254	2293254	type	True	80.4555	589	1135	95	below_threshold
Luteimonas panaciterrae	strain=Gsoil 068	GCA_020511115.1	363885	363885	type	True	80.3949	527	1135	95	below_threshold
Pseudoxanthomonas helianthi	strain=110414	GCA_017939625.1	1453541	1453541	type	True	80.2468	509	1135	95	below_threshold
Pseudoxanthomonas japonensis	strain=DSM 17109	GCA_010093445.1	69284	69284	type	True	80.0215	519	1135	95	below_threshold
Lysobacter chinensis	strain=TLK-CK17	GCA_021725675.1	2912247	2912247	type	True	79.9497	522	1135	95	below_threshold
Lysobacter aestuarii	strain=JCM 31130	GCA_006546775.1	1706195	1706195	type	True	79.8441	482	1135	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:40,712] [INFO] DFAST Taxonomy check result was written to GCF_020866925.1_ASM2086692v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:40,713] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:40,713] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:40,713] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc96f9102-4423-4779-9e18-e4bbd1191844/dqc_reference/checkm_data
[2024-01-24 13:19:40,714] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:40,752] [INFO] Task started: CheckM
[2024-01-24 13:19:40,752] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020866925.1_ASM2086692v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020866925.1_ASM2086692v1_genomic.fna/checkm_input GCF_020866925.1_ASM2086692v1_genomic.fna/checkm_result
[2024-01-24 13:20:28,759] [INFO] Task succeeded: CheckM
[2024-01-24 13:20:28,760] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:20:28,778] [INFO] ===== Completeness check finished =====
[2024-01-24 13:20:28,778] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:20:28,779] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020866925.1_ASM2086692v1_genomic.fna/markers.fasta)
[2024-01-24 13:20:28,779] [INFO] Task started: Blastn
[2024-01-24 13:20:28,780] [INFO] Running command: blastn -query GCF_020866925.1_ASM2086692v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc96f9102-4423-4779-9e18-e4bbd1191844/dqc_reference/reference_markers_gtdb.fasta -out GCF_020866925.1_ASM2086692v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:20:30,697] [INFO] Task succeeded: Blastn
[2024-01-24 13:20:30,702] [INFO] Selected 18 target genomes.
[2024-01-24 13:20:30,702] [INFO] Target genome list was writen to GCF_020866925.1_ASM2086692v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:20:30,762] [INFO] Task started: fastANI
[2024-01-24 13:20:30,763] [INFO] Running command: fastANI --query /var/lib/cwl/stg07676ab9-9422-4869-8456-c50e6540d3ab/GCF_020866925.1_ASM2086692v1_genomic.fna.gz --refList GCF_020866925.1_ASM2086692v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020866925.1_ASM2086692v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:20:43,602] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:43,622] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:20:43,622] [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_009740395.1	s__Lysobacter_A gilvus	86.12	842	1135	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000770795.1	s__Lysobacter_A dokdonensis	85.9801	826	1135	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018406645.1	s__Lysobacter_A helvus	84.8052	787	1135	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_017308985.1	s__Lysobacter sp017308985	81.5152	651	1135	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013362405.1	s__JABFWF01 sp013362405	81.5141	462	1135	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__JABFWF01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014489475.1	s__Lysobacter solisilvae	81.484	612	1135	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	81.3637	642	1135	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	96.84	96.81	0.94	0.93	3	-
GCF_008033445.1	s__Vulcaniibacterium_B gelatinicum	81.3606	521	1135	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_016735495.2	s__Lysobacter sp016735495	81.2366	624	1135	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006337105.1	s__Thermomonas sp006337105	80.8911	542	1135	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011320095.1	s__Luteimonas_B telluris	80.8483	486	1135	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422305.1	s__Luteimonas mephitis	80.8355	558	1135	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005502915.1	s__SCMT01 sp005502915	80.6746	550	1135	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__SCMT01	95.0	99.99	99.99	0.99	0.99	2	-
GCF_001428685.1	s__Lysobacter sp001428685	80.6168	584	1135	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	99.42	98.61	0.98	0.96	4	-
GCF_014395425.1	s__Thermomonas brevis	80.5193	519	1135	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010211755.1	s__Pseudoxanthomonas_A sangjuensis	80.485	534	1135	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013361435.1	s__Lysobacter sp013361435	80.3363	520	1135	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016789405.1	s__SCMT01 sp016789405	80.2961	481	1135	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__SCMT01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:20:43,624] [INFO] GTDB search result was written to GCF_020866925.1_ASM2086692v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:20:43,625] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:20:43,629] [INFO] DFAST_QC result json was written to GCF_020866925.1_ASM2086692v1_genomic.fna/dqc_result.json
[2024-01-24 13:20:43,630] [INFO] DFAST_QC completed!
[2024-01-24 13:20:43,630] [INFO] Total running time: 0h1m31s