[2024-01-24 13:28:27,243] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:27,245] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:27,245] [INFO] DQC Reference Directory: /var/lib/cwl/stg49abc0a6-8efa-4024-b132-32b59752be72/dqc_reference
[2024-01-24 13:28:28,528] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:28,529] [INFO] Task started: Prodigal
[2024-01-24 13:28:28,530] [INFO] Running command: gunzip -c /var/lib/cwl/stge4235704-22ef-46a7-86b4-fa34b428fd30/GCF_014596295.1_ASM1459629v1_genomic.fna.gz | prodigal -d GCF_014596295.1_ASM1459629v1_genomic.fna/cds.fna -a GCF_014596295.1_ASM1459629v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:41,639] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:41,640] [INFO] Task started: HMMsearch
[2024-01-24 13:28:41,640] [INFO] Running command: hmmsearch --tblout GCF_014596295.1_ASM1459629v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg49abc0a6-8efa-4024-b132-32b59752be72/dqc_reference/reference_markers.hmm GCF_014596295.1_ASM1459629v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:41,929] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:41,930] [INFO] Found 6/6 markers.
[2024-01-24 13:28:41,972] [INFO] Query marker FASTA was written to GCF_014596295.1_ASM1459629v1_genomic.fna/markers.fasta
[2024-01-24 13:28:41,972] [INFO] Task started: Blastn
[2024-01-24 13:28:41,972] [INFO] Running command: blastn -query GCF_014596295.1_ASM1459629v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg49abc0a6-8efa-4024-b132-32b59752be72/dqc_reference/reference_markers.fasta -out GCF_014596295.1_ASM1459629v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:42,919] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:42,922] [INFO] Selected 15 target genomes.
[2024-01-24 13:28:42,922] [INFO] Target genome list was writen to GCF_014596295.1_ASM1459629v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:42,931] [INFO] Task started: fastANI
[2024-01-24 13:28:42,931] [INFO] Running command: fastANI --query /var/lib/cwl/stge4235704-22ef-46a7-86b4-fa34b428fd30/GCF_014596295.1_ASM1459629v1_genomic.fna.gz --refList GCF_014596295.1_ASM1459629v1_genomic.fna/target_genomes.txt --output GCF_014596295.1_ASM1459629v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:57,795] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:57,795] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg49abc0a6-8efa-4024-b132-32b59752be72/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:57,795] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg49abc0a6-8efa-4024-b132-32b59752be72/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:57,809] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:28:57,809] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:57,809] [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
Stenotrophomonas pennii	strain=Sa5BUN4	GCA_014836545.1	2762239	2762239	type	True	97.2161	1182	1313	95	conclusive
Stenotrophomonas chelatiphaga	strain=DSM 21508	GCA_001431535.1	517011	517011	type	True	92.3505	1083	1313	95	below_threshold
Stenotrophomonas tumulicola	strain=JCM 30961	GCA_014117215.1	1685415	1685415	type	True	85.9113	962	1313	95	below_threshold
Stenotrophomonas indicatrix	strain=WS40	GCA_002750975.1	2045451	2045451	type	True	84.8775	946	1313	95	below_threshold
Stenotrophomonas pavanii	strain=DSM 25135	GCA_001431565.1	487698	487698	type	True	84.7606	906	1313	95	below_threshold
Stenotrophomonas pavanii	strain=LMG 25348	GCA_900101175.1	487698	487698	type	True	84.7193	946	1313	95	below_threshold
Stenotrophomonas lactitubi	strain=M15	GCA_002803515.1	2045214	2045214	type	True	84.6876	952	1313	95	below_threshold
Stenotrophomonas maltophilia	strain=NBRC 14161	GCA_001591205.1	40324	40324	type	True	84.6408	905	1313	95	below_threshold
Stenotrophomonas maltophilia	strain=MTCC 434	GCA_000597745.1	40324	40324	type	True	84.5808	857	1313	95	below_threshold
Stenotrophomonas rhizophila	strain=DSM14405	GCA_000661955.1	216778	216778	suspected-type	True	84.1976	959	1313	95	below_threshold
Stenotrophomonas bentonitica	strain=DSM 103927	GCA_013185915.1	1450134	1450134	type	True	84.027	926	1313	95	below_threshold
Stenotrophomonas acidaminiphila	strain=DSM 13117	GCA_024221815.1	128780	128780	type	True	82.6783	762	1313	95	below_threshold
Stenotrophomonas pictorum	strain=JCM 9942	GCA_001310775.1	86184	86184	type	True	82.4536	481	1313	95	below_threshold
Xanthomonas indica	strain=PPL560	GCA_022669045.1	2912242	2912242	type	True	82.0061	783	1313	95	below_threshold
Xanthomonas translucens	strain=ATCC 19319	GCA_020880735.1	343	343	type	True	81.7935	652	1313	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:57,811] [INFO] DFAST Taxonomy check result was written to GCF_014596295.1_ASM1459629v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:57,811] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:57,812] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:57,812] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg49abc0a6-8efa-4024-b132-32b59752be72/dqc_reference/checkm_data
[2024-01-24 13:28:57,813] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:57,855] [INFO] Task started: CheckM
[2024-01-24 13:28:57,855] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014596295.1_ASM1459629v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014596295.1_ASM1459629v1_genomic.fna/checkm_input GCF_014596295.1_ASM1459629v1_genomic.fna/checkm_result
[2024-01-24 13:29:47,018] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:47,019] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:47,038] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:47,038] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:47,039] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014596295.1_ASM1459629v1_genomic.fna/markers.fasta)
[2024-01-24 13:29:47,039] [INFO] Task started: Blastn
[2024-01-24 13:29:47,039] [INFO] Running command: blastn -query GCF_014596295.1_ASM1459629v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg49abc0a6-8efa-4024-b132-32b59752be72/dqc_reference/reference_markers_gtdb.fasta -out GCF_014596295.1_ASM1459629v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:48,839] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:48,844] [INFO] Selected 13 target genomes.
[2024-01-24 13:29:48,844] [INFO] Target genome list was writen to GCF_014596295.1_ASM1459629v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:48,853] [INFO] Task started: fastANI
[2024-01-24 13:29:48,853] [INFO] Running command: fastANI --query /var/lib/cwl/stge4235704-22ef-46a7-86b4-fa34b428fd30/GCF_014596295.1_ASM1459629v1_genomic.fna.gz --refList GCF_014596295.1_ASM1459629v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014596295.1_ASM1459629v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:30:03,372] [INFO] Task succeeded: fastANI
[2024-01-24 13:30:03,387] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:30:03,388] [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_002836635.1	s__Stenotrophomonas sp002836635	98.5543	1190	1313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	97.91	95.43	0.91	0.85	8	conclusive
GCF_001431535.1	s__Stenotrophomonas chelatiphaga	92.3532	1082	1313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	99.00	99.00	0.96	0.96	2	-
GCF_014621775.1	s__Stenotrophomonas sp014621775	86.3704	1059	1313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	97.53	97.52	0.92	0.91	3	-
GCF_014117215.1	s__Stenotrophomonas tumulicola	85.9056	962	1313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003086775.1	s__Stenotrophomonas sp003086775	85.1508	973	1313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	98.05	97.07	0.94	0.87	8	-
GCF_003028475.1	s__Stenotrophomonas sp003028475	84.9891	921	1313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	98.27	96.55	0.95	0.90	3	-
GCF_013464915.1	s__Stenotrophomonas maltophilia_AT	84.9174	896	1313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	99.65	98.65	0.97	0.93	5	-
GCA_009912235.1	s__Stenotrophomonas maltophilia_AV	84.8344	811	1313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001274595.1	s__Stenotrophomonas maltophilia_AJ	84.718	950	1313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	97.15	96.26	0.91	0.88	10	-
GCF_013464485.1	s__Stenotrophomonas maltophilia_AW	84.5465	897	1313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011761925.1	s__Stenotrophomonas sp011761925	84.3671	923	1313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018612915.1	s__Stenotrophomonas sp018612915	83.9907	678	1313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002387845.1	s__Stenotrophomonas maltophilia_AG	83.5184	833	1313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:30:03,389] [INFO] GTDB search result was written to GCF_014596295.1_ASM1459629v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:30:03,390] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:30:03,393] [INFO] DFAST_QC result json was written to GCF_014596295.1_ASM1459629v1_genomic.fna/dqc_result.json
[2024-01-24 13:30:03,393] [INFO] DFAST_QC completed!
[2024-01-24 13:30:03,393] [INFO] Total running time: 0h1m36s