[2024-01-24 11:19:55,037] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:19:55,040] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:19:55,040] [INFO] DQC Reference Directory: /var/lib/cwl/stge3dff056-ed88-44c8-a406-08263b17cd87/dqc_reference
[2024-01-24 11:19:56,399] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:19:56,399] [INFO] Task started: Prodigal
[2024-01-24 11:19:56,400] [INFO] Running command: gunzip -c /var/lib/cwl/stga9168470-111f-4d3a-bca8-1b755180fea8/GCF_010093185.1_ASM1009318v1_genomic.fna.gz | prodigal -d GCF_010093185.1_ASM1009318v1_genomic.fna/cds.fna -a GCF_010093185.1_ASM1009318v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:20:07,024] [INFO] Task succeeded: Prodigal
[2024-01-24 11:20:07,025] [INFO] Task started: HMMsearch
[2024-01-24 11:20:07,025] [INFO] Running command: hmmsearch --tblout GCF_010093185.1_ASM1009318v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge3dff056-ed88-44c8-a406-08263b17cd87/dqc_reference/reference_markers.hmm GCF_010093185.1_ASM1009318v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:20:07,313] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:20:07,315] [INFO] Found 6/6 markers.
[2024-01-24 11:20:07,352] [INFO] Query marker FASTA was written to GCF_010093185.1_ASM1009318v1_genomic.fna/markers.fasta
[2024-01-24 11:20:07,353] [INFO] Task started: Blastn
[2024-01-24 11:20:07,353] [INFO] Running command: blastn -query GCF_010093185.1_ASM1009318v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge3dff056-ed88-44c8-a406-08263b17cd87/dqc_reference/reference_markers.fasta -out GCF_010093185.1_ASM1009318v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:08,323] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:08,327] [INFO] Selected 20 target genomes.
[2024-01-24 11:20:08,328] [INFO] Target genome list was writen to GCF_010093185.1_ASM1009318v1_genomic.fna/target_genomes.txt
[2024-01-24 11:20:08,337] [INFO] Task started: fastANI
[2024-01-24 11:20:08,338] [INFO] Running command: fastANI --query /var/lib/cwl/stga9168470-111f-4d3a-bca8-1b755180fea8/GCF_010093185.1_ASM1009318v1_genomic.fna.gz --refList GCF_010093185.1_ASM1009318v1_genomic.fna/target_genomes.txt --output GCF_010093185.1_ASM1009318v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:20:26,779] [INFO] Task succeeded: fastANI
[2024-01-24 11:20:26,780] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge3dff056-ed88-44c8-a406-08263b17cd87/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:20:26,780] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge3dff056-ed88-44c8-a406-08263b17cd87/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:20:26,797] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:20:26,797] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:20:26,797] [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
Pseudoxanthomonas jiangsuensis	strain=DSM 22398	GCA_010093185.1	619688	619688	type	True	100.0	1213	1215	95	conclusive
Pseudoxanthomonas koreensis	strain=KCTC 12208	GCA_010093225.1	266061	266061	type	True	87.8012	772	1215	95	below_threshold
Pseudoxanthomonas broegbernensis	strain=DSM 12573	GCA_010093165.1	83619	83619	type	True	87.6739	846	1215	95	below_threshold
Pseudoxanthomonas broegbernensis	strain=DSM 12573	GCA_014202435.1	83619	83619	type	True	87.6594	867	1215	95	below_threshold
Pseudoxanthomonas kaohsiungensis	strain=DSM 17583	GCA_010211765.1	283923	283923	type	True	87.2982	916	1215	95	below_threshold
Pseudoxanthomonas suwonensis	strain=DSM 17175	GCA_010093235.1	314722	314722	suspected-type	True	86.6259	850	1215	95	below_threshold
Pseudoxanthomonas taiwanensis	strain=DSM 22914	GCA_010093135.1	176598	176598	type	True	86.4198	758	1215	95	below_threshold
Pseudoxanthomonas daejeonensis	strain=DSM 17801	GCA_010093205.1	266062	266062	type	True	86.1148	881	1215	95	below_threshold
Xanthomonas massiliensis	strain=SN8	GCA_900018785.1	1720302	1720302	type	True	83.1974	687	1215	95	below_threshold
Xanthomonas theicola	strain=CFBP 4691	GCA_002940605.1	56464	56464	type	True	83.1609	677	1215	95	below_threshold
Stenotrophomonas acidaminiphila	strain=DSM 13117	GCA_024221815.1	128780	128780	type	True	83.159	757	1215	95	below_threshold
Xanthomonas sacchari	strain=CFBP4641	GCA_002940085.1	56458	56458	suspected-type	True	83.119	785	1215	95	below_threshold
Xanthomonas indica	strain=PPL560	GCA_022669045.1	2912242	2912242	type	True	83.1119	800	1215	95	below_threshold
Xanthomonas theicola	strain=CFBP 4691	GCA_014236795.1	56464	56464	type	True	83.0245	702	1215	95	below_threshold
Pseudoxanthomonas sangjuensis	strain=DSM 28345	GCA_010211755.1	1503750	1503750	type	True	82.9983	683	1215	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	81.8688	662	1215	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	81.8562	532	1215	95	below_threshold
Luteimonas salinisoli	strain=SJ-92	GCA_013425525.1	2752307	2752307	type	True	81.5514	699	1215	95	below_threshold
Stenotrophomonas koreensis	strain=DSM 17805	GCA_001431525.1	266128	266128	type	True	80.7483	530	1215	95	below_threshold
Arenimonas caeni	strain=z29	GCA_003024235.1	2058085	2058085	type	True	80.5039	554	1215	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:20:26,799] [INFO] DFAST Taxonomy check result was written to GCF_010093185.1_ASM1009318v1_genomic.fna/tc_result.tsv
[2024-01-24 11:20:26,800] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:20:26,800] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:20:26,800] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge3dff056-ed88-44c8-a406-08263b17cd87/dqc_reference/checkm_data
[2024-01-24 11:20:26,802] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:20:26,846] [INFO] Task started: CheckM
[2024-01-24 11:20:26,846] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010093185.1_ASM1009318v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010093185.1_ASM1009318v1_genomic.fna/checkm_input GCF_010093185.1_ASM1009318v1_genomic.fna/checkm_result
[2024-01-24 11:21:03,908] [INFO] Task succeeded: CheckM
[2024-01-24 11:21:03,910] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:21:03,931] [INFO] ===== Completeness check finished =====
[2024-01-24 11:21:03,931] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:21:03,931] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010093185.1_ASM1009318v1_genomic.fna/markers.fasta)
[2024-01-24 11:21:03,932] [INFO] Task started: Blastn
[2024-01-24 11:21:03,932] [INFO] Running command: blastn -query GCF_010093185.1_ASM1009318v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge3dff056-ed88-44c8-a406-08263b17cd87/dqc_reference/reference_markers_gtdb.fasta -out GCF_010093185.1_ASM1009318v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:21:05,583] [INFO] Task succeeded: Blastn
[2024-01-24 11:21:05,587] [INFO] Selected 14 target genomes.
[2024-01-24 11:21:05,588] [INFO] Target genome list was writen to GCF_010093185.1_ASM1009318v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:21:05,606] [INFO] Task started: fastANI
[2024-01-24 11:21:05,606] [INFO] Running command: fastANI --query /var/lib/cwl/stga9168470-111f-4d3a-bca8-1b755180fea8/GCF_010093185.1_ASM1009318v1_genomic.fna.gz --refList GCF_010093185.1_ASM1009318v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010093185.1_ASM1009318v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:21:19,459] [INFO] Task succeeded: fastANI
[2024-01-24 11:21:19,476] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:21:19,476] [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_010093185.1	s__Pseudoxanthomonas jiangsuensis	100.0	1213	1215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000972865.1	s__Pseudoxanthomonas suwonensis_B	87.9332	912	1215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010093225.1	s__Pseudoxanthomonas koreensis	87.7672	774	1215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014202435.1	s__Pseudoxanthomonas broegbernensis	87.6672	867	1215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000513955.1	s__Pseudoxanthomonas suwonensis_C	87.4839	865	1215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	98.37	96.94	0.95	0.91	3	-
GCF_000513995.1	s__Pseudoxanthomonas sp000513995	87.387	869	1215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010211765.1	s__Pseudoxanthomonas kaohsiungensis	87.3119	915	1215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000510725.1	s__Pseudoxanthomonas sp000510725	87.2073	857	1215	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	86.7685	895	1215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017302035.1	s__Pseudoxanthomonas sp017302035	86.7104	648	1215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	99.26	99.26	0.94	0.94	2	-
GCA_017745195.1	s__Pseudoxanthomonas sp017745195	86.6608	795	1215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013004645.1	s__Stenotrophomonas maltophilia_AM	81.4205	670	1215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	98.04	97.65	0.90	0.83	20	-
GCA_009912395.1	s__Luteibacter sp009912395	77.9169	318	1215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900099835.1	s__Paraburkholderia fungorum_A	75.4833	117	1215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:21:19,478] [INFO] GTDB search result was written to GCF_010093185.1_ASM1009318v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:21:19,478] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:21:19,482] [INFO] DFAST_QC result json was written to GCF_010093185.1_ASM1009318v1_genomic.fna/dqc_result.json
[2024-01-24 11:21:19,483] [INFO] DFAST_QC completed!
[2024-01-24 11:21:19,483] [INFO] Total running time: 0h1m24s