[2024-01-24 11:43:25,073] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:25,078] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:25,078] [INFO] DQC Reference Directory: /var/lib/cwl/stga28990e6-316d-4ca0-89d1-58c936a8dfeb/dqc_reference
[2024-01-24 11:43:30,058] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:30,059] [INFO] Task started: Prodigal
[2024-01-24 11:43:30,059] [INFO] Running command: gunzip -c /var/lib/cwl/stg12739cbd-b182-45af-844e-d79fc9d628e3/GCF_010093135.1_ASM1009313v1_genomic.fna.gz | prodigal -d GCF_010093135.1_ASM1009313v1_genomic.fna/cds.fna -a GCF_010093135.1_ASM1009313v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:43:38,558] [INFO] Task succeeded: Prodigal
[2024-01-24 11:43:38,559] [INFO] Task started: HMMsearch
[2024-01-24 11:43:38,559] [INFO] Running command: hmmsearch --tblout GCF_010093135.1_ASM1009313v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga28990e6-316d-4ca0-89d1-58c936a8dfeb/dqc_reference/reference_markers.hmm GCF_010093135.1_ASM1009313v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:43:38,831] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:43:38,832] [INFO] Found 6/6 markers.
[2024-01-24 11:43:38,861] [INFO] Query marker FASTA was written to GCF_010093135.1_ASM1009313v1_genomic.fna/markers.fasta
[2024-01-24 11:43:38,862] [INFO] Task started: Blastn
[2024-01-24 11:43:38,862] [INFO] Running command: blastn -query GCF_010093135.1_ASM1009313v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga28990e6-316d-4ca0-89d1-58c936a8dfeb/dqc_reference/reference_markers.fasta -out GCF_010093135.1_ASM1009313v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:43:39,909] [INFO] Task succeeded: Blastn
[2024-01-24 11:43:39,913] [INFO] Selected 16 target genomes.
[2024-01-24 11:43:39,914] [INFO] Target genome list was writen to GCF_010093135.1_ASM1009313v1_genomic.fna/target_genomes.txt
[2024-01-24 11:43:39,939] [INFO] Task started: fastANI
[2024-01-24 11:43:39,940] [INFO] Running command: fastANI --query /var/lib/cwl/stg12739cbd-b182-45af-844e-d79fc9d628e3/GCF_010093135.1_ASM1009313v1_genomic.fna.gz --refList GCF_010093135.1_ASM1009313v1_genomic.fna/target_genomes.txt --output GCF_010093135.1_ASM1009313v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:43:53,543] [INFO] Task succeeded: fastANI
[2024-01-24 11:43:53,544] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga28990e6-316d-4ca0-89d1-58c936a8dfeb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:43:53,544] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga28990e6-316d-4ca0-89d1-58c936a8dfeb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:43:53,558] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:43:53,558] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:43:53,559] [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 taiwanensis	strain=DSM 22914	GCA_010093135.1	176598	176598	type	True	100.0	933	941	95	conclusive
Pseudoxanthomonas suwonensis	strain=DSM 17175	GCA_010093235.1	314722	314722	suspected-type	True	87.1864	752	941	95	below_threshold
Pseudoxanthomonas jiangsuensis	strain=DSM 22398	GCA_010093185.1	619688	619688	type	True	86.6692	755	941	95	below_threshold
Pseudoxanthomonas broegbernensis	strain=DSM 12573	GCA_010093165.1	83619	83619	type	True	86.2502	717	941	95	below_threshold
Pseudoxanthomonas broegbernensis	strain=DSM 12573	GCA_014202435.1	83619	83619	type	True	86.1498	730	941	95	below_threshold
Pseudoxanthomonas koreensis	strain=KCTC 12208	GCA_010093225.1	266061	266061	type	True	85.8127	677	941	95	below_threshold
Pseudoxanthomonas kaohsiungensis	strain=DSM 17583	GCA_010211765.1	283923	283923	type	True	85.4981	764	941	95	below_threshold
Xanthomonas massiliensis	strain=SN8	GCA_900018785.1	1720302	1720302	type	True	83.4823	619	941	95	below_threshold
Stenotrophomonas acidaminiphila	strain=DSM 13117	GCA_024221815.1	128780	128780	type	True	83.1047	660	941	95	below_threshold
Xanthomonas sacchari	strain=CFBP4641	GCA_002940085.1	56458	56458	suspected-type	True	82.9992	683	941	95	below_threshold
Stenotrophomonas nitritireducens	strain=DSM 12575	GCA_001431425.1	83617	83617	type	True	82.7192	656	941	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	82.0049	524	941	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	81.9389	620	941	95	below_threshold
Luteimonas salinisoli	strain=SJ-92	GCA_013425525.1	2752307	2752307	type	True	81.6272	640	941	95	below_threshold
Stenotrophomonas maltophilia	strain=NBRC 14161	GCA_001591205.1	40324	40324	type	True	81.5085	609	941	95	below_threshold
Arenimonas caeni	strain=z29	GCA_003024235.1	2058085	2058085	type	True	81.1996	519	941	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:43:53,560] [INFO] DFAST Taxonomy check result was written to GCF_010093135.1_ASM1009313v1_genomic.fna/tc_result.tsv
[2024-01-24 11:43:53,561] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:43:53,561] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:43:53,561] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga28990e6-316d-4ca0-89d1-58c936a8dfeb/dqc_reference/checkm_data
[2024-01-24 11:43:53,563] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:43:53,595] [INFO] Task started: CheckM
[2024-01-24 11:43:53,595] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010093135.1_ASM1009313v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010093135.1_ASM1009313v1_genomic.fna/checkm_input GCF_010093135.1_ASM1009313v1_genomic.fna/checkm_result
[2024-01-24 11:44:37,059] [INFO] Task succeeded: CheckM
[2024-01-24 11:44:37,060] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:44:37,077] [INFO] ===== Completeness check finished =====
[2024-01-24 11:44:37,078] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:44:37,079] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010093135.1_ASM1009313v1_genomic.fna/markers.fasta)
[2024-01-24 11:44:37,079] [INFO] Task started: Blastn
[2024-01-24 11:44:37,079] [INFO] Running command: blastn -query GCF_010093135.1_ASM1009313v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga28990e6-316d-4ca0-89d1-58c936a8dfeb/dqc_reference/reference_markers_gtdb.fasta -out GCF_010093135.1_ASM1009313v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:39,166] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:39,169] [INFO] Selected 13 target genomes.
[2024-01-24 11:44:39,169] [INFO] Target genome list was writen to GCF_010093135.1_ASM1009313v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:44:39,178] [INFO] Task started: fastANI
[2024-01-24 11:44:39,178] [INFO] Running command: fastANI --query /var/lib/cwl/stg12739cbd-b182-45af-844e-d79fc9d628e3/GCF_010093135.1_ASM1009313v1_genomic.fna.gz --refList GCF_010093135.1_ASM1009313v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010093135.1_ASM1009313v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:44:50,323] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:50,338] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:44:50,338] [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_010093135.1	s__Pseudoxanthomonas taiwanensis	100.0	933	941	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	99.04	99.04	0.90	0.90	2	conclusive
GCF_000510725.1	s__Pseudoxanthomonas sp000510725	88.3761	777	941	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	99.33	99.13	0.95	0.92	5	-
GCF_010093235.1	s__Pseudoxanthomonas suwonensis	87.1864	752	941	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000513995.1	s__Pseudoxanthomonas sp000513995	87.0347	775	941	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	86.9484	771	941	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000513955.1	s__Pseudoxanthomonas suwonensis_C	86.7565	776	941	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	98.37	96.94	0.95	0.91	3	-
GCF_010093185.1	s__Pseudoxanthomonas jiangsuensis	86.6851	754	941	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	86.3077	772	941	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	86.1345	731	941	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	99.99	99.99	0.99	0.99	2	-
GCF_010093225.1	s__Pseudoxanthomonas koreensis	85.8125	677	941	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	85.5298	762	941	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009912235.1	s__Stenotrophomonas maltophilia_AV	81.5662	578	941	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003510825.1	s__Stenotrophomonas sp003086795	81.0575	396	941	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	95.73	95.09	0.81	0.78	6	-
--------------------------------------------------------------------------------
[2024-01-24 11:44:50,339] [INFO] GTDB search result was written to GCF_010093135.1_ASM1009313v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:44:50,340] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:44:50,343] [INFO] DFAST_QC result json was written to GCF_010093135.1_ASM1009313v1_genomic.fna/dqc_result.json
[2024-01-24 11:44:50,344] [INFO] DFAST_QC completed!
[2024-01-24 11:44:50,344] [INFO] Total running time: 0h1m25s