[2024-01-25 19:37:05,631] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:37:05,632] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:37:05,633] [INFO] DQC Reference Directory: /var/lib/cwl/stgf28a703a-e98d-4de7-a38d-752713c2177b/dqc_reference
[2024-01-25 19:37:06,828] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:37:06,829] [INFO] Task started: Prodigal
[2024-01-25 19:37:06,829] [INFO] Running command: gunzip -c /var/lib/cwl/stga3ff4d51-34d3-459b-99cd-31fa289e013b/GCF_020511115.1_ASM2051111v1_genomic.fna.gz | prodigal -d GCF_020511115.1_ASM2051111v1_genomic.fna/cds.fna -a GCF_020511115.1_ASM2051111v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:37:18,682] [INFO] Task succeeded: Prodigal
[2024-01-25 19:37:18,682] [INFO] Task started: HMMsearch
[2024-01-25 19:37:18,682] [INFO] Running command: hmmsearch --tblout GCF_020511115.1_ASM2051111v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf28a703a-e98d-4de7-a38d-752713c2177b/dqc_reference/reference_markers.hmm GCF_020511115.1_ASM2051111v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:37:18,920] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:37:18,921] [INFO] Found 6/6 markers.
[2024-01-25 19:37:18,954] [INFO] Query marker FASTA was written to GCF_020511115.1_ASM2051111v1_genomic.fna/markers.fasta
[2024-01-25 19:37:18,955] [INFO] Task started: Blastn
[2024-01-25 19:37:18,955] [INFO] Running command: blastn -query GCF_020511115.1_ASM2051111v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf28a703a-e98d-4de7-a38d-752713c2177b/dqc_reference/reference_markers.fasta -out GCF_020511115.1_ASM2051111v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:37:19,886] [INFO] Task succeeded: Blastn
[2024-01-25 19:37:19,890] [INFO] Selected 18 target genomes.
[2024-01-25 19:37:19,891] [INFO] Target genome list was writen to GCF_020511115.1_ASM2051111v1_genomic.fna/target_genomes.txt
[2024-01-25 19:37:19,907] [INFO] Task started: fastANI
[2024-01-25 19:37:19,907] [INFO] Running command: fastANI --query /var/lib/cwl/stga3ff4d51-34d3-459b-99cd-31fa289e013b/GCF_020511115.1_ASM2051111v1_genomic.fna.gz --refList GCF_020511115.1_ASM2051111v1_genomic.fna/target_genomes.txt --output GCF_020511115.1_ASM2051111v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:37:33,245] [INFO] Task succeeded: fastANI
[2024-01-25 19:37:33,245] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf28a703a-e98d-4de7-a38d-752713c2177b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:37:33,246] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf28a703a-e98d-4de7-a38d-752713c2177b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:37:33,259] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:37:33,259] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:37:33,259] [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
Luteimonas panaciterrae	strain=Gsoil 068	GCA_020511115.1	363885	363885	type	True	100.0	1327	1328	95	conclusive
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	85.5329	1002	1328	95	below_threshold
Luteimonas mephitis	strain=DSM 12574	GCA_000422305.1	83615	83615	type	True	81.7269	649	1328	95	below_threshold
Luteimonas marina	strain=FR1330	GCA_007859325.1	488485	488485	type	True	81.3859	665	1328	95	below_threshold
Luteimonas arsenica	strain=26-35	GCA_004352825.1	1586242	1586242	type	True	81.0911	556	1328	95	below_threshold
Luteimonas gilva	strain=H23	GCA_005239095.1	2572684	2572684	type	True	81.0625	689	1328	95	below_threshold
Thermomonas aquatica	strain=SY21	GCA_006337105.1	2202149	2202149	type	True	80.8142	552	1328	95	below_threshold
Vulcaniibacterium tengchongense	strain=DSM 25623	GCA_003814555.1	1273429	1273429	type	True	80.8065	666	1328	95	below_threshold
Vulcaniibacterium tengchongense	strain=YIM 77520	GCA_008033455.1	1273429	1273429	type	True	80.8046	642	1328	95	below_threshold
Luteimonas viscosa	strain=XBU10	GCA_008244685.1	1132694	1132694	type	True	80.7195	615	1328	95	below_threshold
Luteimonas colneyensis	strain=Sa2BVA3	GCA_014836665.1	2762230	2762230	type	True	80.7007	544	1328	95	below_threshold
Pseudoxanthomonas helianthi	strain=110414	GCA_017939625.1	1453541	1453541	type	True	80.6648	574	1328	95	below_threshold
Luteimonas saliphila	strain=SJ-9	GCA_016774335.1	2804919	2804919	type	True	80.6552	619	1328	95	below_threshold
Luteimonas aestuarii	strain=B9	GCA_004357985.1	453837	453837	type	True	80.5825	557	1328	95	below_threshold
Vulcaniibacterium gelatinicum	strain=R-5-52-3	GCA_008033445.1	2598725	2598725	type	True	80.5255	520	1328	95	below_threshold
Vulcaniibacterium thermophilum	strain=KCTC 32020	GCA_007923255.1	1169913	1169913	type	True	80.5108	556	1328	95	below_threshold
Vulcaniibacterium thermophilum	strain=KCTC 32020	GCA_014656335.1	1169913	1169913	type	True	80.4497	573	1328	95	below_threshold
Luteimonas wenzhouensis	strain=YD-1	GCA_007859305.1	2599615	2599615	type	True	80.4393	556	1328	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:37:33,262] [INFO] DFAST Taxonomy check result was written to GCF_020511115.1_ASM2051111v1_genomic.fna/tc_result.tsv
[2024-01-25 19:37:33,262] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:37:33,262] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:37:33,262] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf28a703a-e98d-4de7-a38d-752713c2177b/dqc_reference/checkm_data
[2024-01-25 19:37:33,263] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:37:33,312] [INFO] Task started: CheckM
[2024-01-25 19:37:33,312] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020511115.1_ASM2051111v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020511115.1_ASM2051111v1_genomic.fna/checkm_input GCF_020511115.1_ASM2051111v1_genomic.fna/checkm_result
[2024-01-25 19:38:12,508] [INFO] Task succeeded: CheckM
[2024-01-25 19:38:12,509] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:38:12,535] [INFO] ===== Completeness check finished =====
[2024-01-25 19:38:12,535] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:38:12,536] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020511115.1_ASM2051111v1_genomic.fna/markers.fasta)
[2024-01-25 19:38:12,537] [INFO] Task started: Blastn
[2024-01-25 19:38:12,537] [INFO] Running command: blastn -query GCF_020511115.1_ASM2051111v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf28a703a-e98d-4de7-a38d-752713c2177b/dqc_reference/reference_markers_gtdb.fasta -out GCF_020511115.1_ASM2051111v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:38:14,375] [INFO] Task succeeded: Blastn
[2024-01-25 19:38:14,378] [INFO] Selected 24 target genomes.
[2024-01-25 19:38:14,378] [INFO] Target genome list was writen to GCF_020511115.1_ASM2051111v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:38:14,399] [INFO] Task started: fastANI
[2024-01-25 19:38:14,399] [INFO] Running command: fastANI --query /var/lib/cwl/stga3ff4d51-34d3-459b-99cd-31fa289e013b/GCF_020511115.1_ASM2051111v1_genomic.fna.gz --refList GCF_020511115.1_ASM2051111v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020511115.1_ASM2051111v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:38:31,437] [INFO] Task succeeded: fastANI
[2024-01-25 19:38:31,451] [INFO] Found 24 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:38:31,451] [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_000422305.1	s__Luteimonas mephitis	81.7052	651	1328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859325.1	s__Luteimonas marina	81.3832	666	1328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004352825.1	s__Luteimonas arsenica	81.0908	556	1328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005239095.1	s__Luteimonas_C gilva	81.0063	695	1328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003814555.1	s__Lysobacter tengchongensis	80.8385	663	1328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	99.99	99.99	0.99	0.99	2	-
GCF_006337105.1	s__Thermomonas sp006337105	80.8256	551	1328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902825775.1	s__Luteimonas_C sp902825775	80.7285	619	1328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008244685.1	s__Luteimonas sp008244685	80.7096	616	1328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014836665.1	s__Luteimonas sp014836665	80.6903	545	1328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016774335.1	s__Luteimonas sp016774335	80.6722	617	1328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016615955.1	s__Luteimonas sp016615955	80.6503	509	1328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	99.39	98.78	0.97	0.95	3	-
GCF_008312895.1	s__Luteimonas sp008312895	80.6447	633	1328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013362405.1	s__JABFWF01 sp013362405	80.5818	436	1328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__JABFWF01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004357985.1	s__Luteimonas aestuarii	80.5604	559	1328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016615815.1	s__Luteimonas sp016615815	80.5507	559	1328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	99.14	98.29	0.98	0.95	3	-
GCF_008033445.1	s__Vulcaniibacterium_B gelatinicum	80.5328	519	1328	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_007923255.1	s__Lysobacter thermophilus	80.5279	554	1328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	99.99	99.99	0.98	0.98	2	-
GCF_007859305.1	s__Luteimonas wenzhouensis	80.4081	559	1328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	99.47	99.47	0.98	0.98	2	-
GCF_001014645.1	s__Luteimonas sp001014645	80.2342	570	1328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017302075.1	s__Thermomonas sp017302075	80.1046	435	1328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016789405.1	s__SCMT01 sp016789405	80.0983	535	1328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__SCMT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017302095.1	s__Thermomonas sp017302095	79.9687	339	1328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014202825.1	s__Chiayiivirga flava	79.0361	457	1328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Chiayiivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240435.1	s__SZAS-103 sp018240435	78.907	355	1328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__SZAS-103	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:38:31,452] [INFO] GTDB search result was written to GCF_020511115.1_ASM2051111v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:38:31,453] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:38:31,456] [INFO] DFAST_QC result json was written to GCF_020511115.1_ASM2051111v1_genomic.fna/dqc_result.json
[2024-01-25 19:38:31,456] [INFO] DFAST_QC completed!
[2024-01-25 19:38:31,456] [INFO] Total running time: 0h1m26s