[2024-01-24 15:14:52,124] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:14:52,125] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:14:52,126] [INFO] DQC Reference Directory: /var/lib/cwl/stgb9faaedc-76f7-404a-b1c7-9dd1914aac08/dqc_reference
[2024-01-24 15:14:53,377] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:14:53,378] [INFO] Task started: Prodigal
[2024-01-24 15:14:53,378] [INFO] Running command: gunzip -c /var/lib/cwl/stg401c0bab-0b38-4028-b037-38e69a809f62/GCF_010093165.1_ASM1009316v1_genomic.fna.gz | prodigal -d GCF_010093165.1_ASM1009316v1_genomic.fna/cds.fna -a GCF_010093165.1_ASM1009316v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:15:03,888] [INFO] Task succeeded: Prodigal
[2024-01-24 15:15:03,888] [INFO] Task started: HMMsearch
[2024-01-24 15:15:03,888] [INFO] Running command: hmmsearch --tblout GCF_010093165.1_ASM1009316v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb9faaedc-76f7-404a-b1c7-9dd1914aac08/dqc_reference/reference_markers.hmm GCF_010093165.1_ASM1009316v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:15:04,171] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:15:04,172] [INFO] Found 6/6 markers.
[2024-01-24 15:15:04,205] [INFO] Query marker FASTA was written to GCF_010093165.1_ASM1009316v1_genomic.fna/markers.fasta
[2024-01-24 15:15:04,205] [INFO] Task started: Blastn
[2024-01-24 15:15:04,205] [INFO] Running command: blastn -query GCF_010093165.1_ASM1009316v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb9faaedc-76f7-404a-b1c7-9dd1914aac08/dqc_reference/reference_markers.fasta -out GCF_010093165.1_ASM1009316v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:15:05,215] [INFO] Task succeeded: Blastn
[2024-01-24 15:15:05,219] [INFO] Selected 13 target genomes.
[2024-01-24 15:15:05,220] [INFO] Target genome list was writen to GCF_010093165.1_ASM1009316v1_genomic.fna/target_genomes.txt
[2024-01-24 15:15:05,227] [INFO] Task started: fastANI
[2024-01-24 15:15:05,227] [INFO] Running command: fastANI --query /var/lib/cwl/stg401c0bab-0b38-4028-b037-38e69a809f62/GCF_010093165.1_ASM1009316v1_genomic.fna.gz --refList GCF_010093165.1_ASM1009316v1_genomic.fna/target_genomes.txt --output GCF_010093165.1_ASM1009316v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:15:17,254] [INFO] Task succeeded: fastANI
[2024-01-24 15:15:17,255] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb9faaedc-76f7-404a-b1c7-9dd1914aac08/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:15:17,255] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb9faaedc-76f7-404a-b1c7-9dd1914aac08/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:15:17,267] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:15:17,267] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:15:17,267] [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 broegbernensis	strain=DSM 12573	GCA_010093165.1	83619	83619	type	True	100.0	1138	1138	95	conclusive
Pseudoxanthomonas broegbernensis	strain=DSM 12573	GCA_014202435.1	83619	83619	type	True	99.9865	1128	1138	95	conclusive
Pseudoxanthomonas jiangsuensis	strain=DSM 22398	GCA_010093185.1	619688	619688	type	True	87.5976	840	1138	95	below_threshold
Pseudoxanthomonas koreensis	strain=KCTC 12208	GCA_010093225.1	266061	266061	type	True	86.8209	710	1138	95	below_threshold
Pseudoxanthomonas kaohsiungensis	strain=DSM 17583	GCA_010211765.1	283923	283923	type	True	86.1561	802	1138	95	below_threshold
Pseudoxanthomonas suwonensis	strain=DSM 17175	GCA_010093235.1	314722	314722	suspected-type	True	85.8165	785	1138	95	below_threshold
Pseudoxanthomonas daejeonensis	strain=DSM 17801	GCA_010093205.1	266062	266062	type	True	85.2169	785	1138	95	below_threshold
Xanthomonas indica	strain=PPL560	GCA_022669045.1	2912242	2912242	type	True	82.9277	742	1138	95	below_threshold
Xanthomonas hyacinthi	strain=CFBP 1156	GCA_009769165.1	56455	56455	type	True	82.7672	744	1138	95	below_threshold
Xanthomonas translucens	strain=ATCC 19319	GCA_020880735.1	343	343	type	True	82.6352	623	1138	95	below_threshold
Luteimonas weifangensis	strain=WF-2	GCA_003416885.1	2303539	2303539	type	True	82.1464	560	1138	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	81.8844	513	1138	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	81.7078	632	1138	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:15:17,269] [INFO] DFAST Taxonomy check result was written to GCF_010093165.1_ASM1009316v1_genomic.fna/tc_result.tsv
[2024-01-24 15:15:17,269] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:15:17,269] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:15:17,270] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb9faaedc-76f7-404a-b1c7-9dd1914aac08/dqc_reference/checkm_data
[2024-01-24 15:15:17,271] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:15:17,310] [INFO] Task started: CheckM
[2024-01-24 15:15:17,310] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010093165.1_ASM1009316v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010093165.1_ASM1009316v1_genomic.fna/checkm_input GCF_010093165.1_ASM1009316v1_genomic.fna/checkm_result
[2024-01-24 15:15:55,624] [INFO] Task succeeded: CheckM
[2024-01-24 15:15:55,625] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:15:55,647] [INFO] ===== Completeness check finished =====
[2024-01-24 15:15:55,648] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:15:55,648] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010093165.1_ASM1009316v1_genomic.fna/markers.fasta)
[2024-01-24 15:15:55,649] [INFO] Task started: Blastn
[2024-01-24 15:15:55,649] [INFO] Running command: blastn -query GCF_010093165.1_ASM1009316v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb9faaedc-76f7-404a-b1c7-9dd1914aac08/dqc_reference/reference_markers_gtdb.fasta -out GCF_010093165.1_ASM1009316v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:15:57,588] [INFO] Task succeeded: Blastn
[2024-01-24 15:15:57,592] [INFO] Selected 13 target genomes.
[2024-01-24 15:15:57,593] [INFO] Target genome list was writen to GCF_010093165.1_ASM1009316v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:15:57,604] [INFO] Task started: fastANI
[2024-01-24 15:15:57,604] [INFO] Running command: fastANI --query /var/lib/cwl/stg401c0bab-0b38-4028-b037-38e69a809f62/GCF_010093165.1_ASM1009316v1_genomic.fna.gz --refList GCF_010093165.1_ASM1009316v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010093165.1_ASM1009316v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:16:09,290] [INFO] Task succeeded: fastANI
[2024-01-24 15:16:09,305] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:16:09,305] [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_014202435.1	s__Pseudoxanthomonas broegbernensis	99.9865	1128	1138	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCF_010093185.1	s__Pseudoxanthomonas jiangsuensis	87.5717	841	1138	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000972865.1	s__Pseudoxanthomonas suwonensis_B	87.0242	831	1138	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	86.7982	712	1138	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	86.5861	794	1138	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	99.33	99.13	0.95	0.92	5	-
GCF_000513995.1	s__Pseudoxanthomonas sp000513995	86.2758	796	1138	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	86.2107	798	1138	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000185965.1	s__Pseudoxanthomonas suwonensis_A	85.9235	803	1138	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010093235.1	s__Pseudoxanthomonas suwonensis	85.802	786	1138	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	85.7534	620	1138	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	99.26	99.26	0.94	0.94	2	-
GCA_018060215.1	s__Pseudoxanthomonas sp018060215	85.4668	521	1138	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	99.22	98.87	0.83	0.81	6	-
GCF_009769165.1	s__Xanthomonas_A hyacinthi	82.8795	734	1138	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas_A	95.0	100.00	100.00	1.00	1.00	2	-
GCA_004297225.1	s__Luteimonas_B sp004297225	80.8586	442	1138	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:16:09,307] [INFO] GTDB search result was written to GCF_010093165.1_ASM1009316v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:16:09,307] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:16:09,311] [INFO] DFAST_QC result json was written to GCF_010093165.1_ASM1009316v1_genomic.fna/dqc_result.json
[2024-01-24 15:16:09,311] [INFO] DFAST_QC completed!
[2024-01-24 15:16:09,311] [INFO] Total running time: 0h1m17s