[2023-06-17 18:03:53,553] [INFO] DFAST_QC pipeline started.
[2023-06-17 18:03:53,556] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 18:03:53,556] [INFO] DQC Reference Directory: /var/lib/cwl/stg0d47bb13-7389-4703-a994-a1453fd3ca64/dqc_reference
[2023-06-17 18:03:54,847] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 18:03:54,848] [INFO] Task started: Prodigal
[2023-06-17 18:03:54,848] [INFO] Running command: gunzip -c /var/lib/cwl/stg47b32172-97b9-4fa7-b802-e3cbc58b4757/GCA_009360425.1_ASM936042v1_genomic.fna.gz | prodigal -d GCA_009360425.1_ASM936042v1_genomic.fna/cds.fna -a GCA_009360425.1_ASM936042v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 18:04:06,021] [INFO] Task succeeded: Prodigal
[2023-06-17 18:04:06,021] [INFO] Task started: HMMsearch
[2023-06-17 18:04:06,021] [INFO] Running command: hmmsearch --tblout GCA_009360425.1_ASM936042v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0d47bb13-7389-4703-a994-a1453fd3ca64/dqc_reference/reference_markers.hmm GCA_009360425.1_ASM936042v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 18:04:06,284] [INFO] Task succeeded: HMMsearch
[2023-06-17 18:04:06,286] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg47b32172-97b9-4fa7-b802-e3cbc58b4757/GCA_009360425.1_ASM936042v1_genomic.fna.gz]
[2023-06-17 18:04:06,318] [INFO] Query marker FASTA was written to GCA_009360425.1_ASM936042v1_genomic.fna/markers.fasta
[2023-06-17 18:04:06,319] [INFO] Task started: Blastn
[2023-06-17 18:04:06,319] [INFO] Running command: blastn -query GCA_009360425.1_ASM936042v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d47bb13-7389-4703-a994-a1453fd3ca64/dqc_reference/reference_markers.fasta -out GCA_009360425.1_ASM936042v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 18:04:07,256] [INFO] Task succeeded: Blastn
[2023-06-17 18:04:07,260] [INFO] Selected 15 target genomes.
[2023-06-17 18:04:07,260] [INFO] Target genome list was writen to GCA_009360425.1_ASM936042v1_genomic.fna/target_genomes.txt
[2023-06-17 18:04:07,263] [INFO] Task started: fastANI
[2023-06-17 18:04:07,263] [INFO] Running command: fastANI --query /var/lib/cwl/stg47b32172-97b9-4fa7-b802-e3cbc58b4757/GCA_009360425.1_ASM936042v1_genomic.fna.gz --refList GCA_009360425.1_ASM936042v1_genomic.fna/target_genomes.txt --output GCA_009360425.1_ASM936042v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 18:04:21,224] [INFO] Task succeeded: fastANI
[2023-06-17 18:04:21,225] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0d47bb13-7389-4703-a994-a1453fd3ca64/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 18:04:21,225] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0d47bb13-7389-4703-a994-a1453fd3ca64/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 18:04:21,238] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 18:04:21,238] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 18:04:21,238] [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 acidaminiphila	strain=DSM 13117	GCA_024221815.1	128780	128780	type	True	93.5667	1012	1182	95	below_threshold
Stenotrophomonas acidaminiphila	strain=JCM 13310	GCA_001431595.1	128780	128780	type	True	93.4903	938	1182	95	below_threshold
Stenotrophomonas nitritireducens	strain=DSM 12575	GCA_001431425.1	83617	83617	type	True	90.8637	896	1182	95	below_threshold
Stenotrophomonas daejeonensis	strain=JCM 16244	GCA_001431505.1	659018	659018	type	True	88.5254	765	1182	95	below_threshold
Stenotrophomonas pictorum	strain=JCM 9942	GCA_001310775.1	86184	86184	type	True	85.2462	520	1182	95	below_threshold
Stenotrophomonas pavanii	strain=DSM 25135	GCA_001431565.1	487698	487698	type	True	84.2931	702	1182	95	below_threshold
Stenotrophomonas maltophilia	strain=NBRC 14161	GCA_001591205.1	40324	40324	type	True	84.0367	729	1182	95	below_threshold
Stenotrophomonas maltophilia	strain=MTCC 434	GCA_000597745.1	40324	40324	type	True	84.0039	699	1182	95	below_threshold
Stenotrophomonas maltophilia	strain=ATCC 13637	GCA_001997185.1	40324	40324	type	True	83.9954	731	1182	95	below_threshold
Stenotrophomonas maltophilia	strain=NCTC10257	GCA_900186865.1	40324	40324	type	True	83.9517	755	1182	95	below_threshold
Stenotrophomonas bentonitica	strain=DSM 103927	GCA_013185915.1	1450134	1450134	type	True	83.7442	724	1182	95	below_threshold
Stenotrophomonas nematodicola	strain=CPCC 101271	GCA_009467805.1	2656746	2656746	type	True	83.5695	736	1182	95	below_threshold
Stenotrophomonas pennii	strain=Sa5BUN4	GCA_014836545.1	2762239	2762239	type	True	82.6233	693	1182	95	below_threshold
Xanthomonas hydrangeae	strain=LMG 31884	GCA_905142475.1	2775159	2775159	type	True	81.4058	636	1182	95	below_threshold
Xanthomonas hortorum	strain=CFBP 2533	GCA_021353095.1	56454	56454	pathovar	True	81.1298	638	1182	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 18:04:21,240] [INFO] DFAST Taxonomy check result was written to GCA_009360425.1_ASM936042v1_genomic.fna/tc_result.tsv
[2023-06-17 18:04:21,241] [INFO] ===== Taxonomy check completed =====
[2023-06-17 18:04:21,241] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 18:04:21,241] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0d47bb13-7389-4703-a994-a1453fd3ca64/dqc_reference/checkm_data
[2023-06-17 18:04:21,243] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 18:04:21,287] [INFO] Task started: CheckM
[2023-06-17 18:04:21,287] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_009360425.1_ASM936042v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_009360425.1_ASM936042v1_genomic.fna/checkm_input GCA_009360425.1_ASM936042v1_genomic.fna/checkm_result
[2023-06-17 18:05:03,318] [INFO] Task succeeded: CheckM
[2023-06-17 18:05:03,319] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-17 18:05:03,343] [INFO] ===== Completeness check finished =====
[2023-06-17 18:05:03,344] [INFO] ===== Start GTDB Search =====
[2023-06-17 18:05:03,344] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_009360425.1_ASM936042v1_genomic.fna/markers.fasta)
[2023-06-17 18:05:03,344] [INFO] Task started: Blastn
[2023-06-17 18:05:03,345] [INFO] Running command: blastn -query GCA_009360425.1_ASM936042v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d47bb13-7389-4703-a994-a1453fd3ca64/dqc_reference/reference_markers_gtdb.fasta -out GCA_009360425.1_ASM936042v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 18:05:05,095] [INFO] Task succeeded: Blastn
[2023-06-17 18:05:05,100] [INFO] Selected 15 target genomes.
[2023-06-17 18:05:05,100] [INFO] Target genome list was writen to GCA_009360425.1_ASM936042v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 18:05:05,132] [INFO] Task started: fastANI
[2023-06-17 18:05:05,132] [INFO] Running command: fastANI --query /var/lib/cwl/stg47b32172-97b9-4fa7-b802-e3cbc58b4757/GCA_009360425.1_ASM936042v1_genomic.fna.gz --refList GCA_009360425.1_ASM936042v1_genomic.fna/target_genomes_gtdb.txt --output GCA_009360425.1_ASM936042v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 18:05:19,739] [INFO] Task succeeded: fastANI
[2023-06-17 18:05:19,752] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 18:05:19,753] [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_002951995.1	s__Stenotrophomonas acidaminiphila_A	98.6808	1037	1182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	98.50	98.36	0.92	0.88	13	conclusive
GCF_001431595.1	s__Stenotrophomonas acidaminiphila	93.4903	938	1182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	98.49	97.05	0.89	0.86	11	-
GCF_009496535.1	s__Stenotrophomonas sp003504055	91.2139	943	1182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	96.53	96.53	0.92	0.92	2	-
GCF_001431425.1	s__Stenotrophomonas nitritireducens	90.8456	897	1182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	98.94	98.42	0.92	0.89	3	-
GCF_001431505.1	s__Stenotrophomonas daejeonensis	88.5078	766	1182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900078405.1	s__Stenotrophomonas sp900078405	87.6989	827	1182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002138415.1	s__Stenotrophomonas maltophilia_G	84.0891	746	1182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	95.93	95.59	0.89	0.87	14	-
GCF_013004645.1	s__Stenotrophomonas maltophilia_AM	84.068	723	1182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	98.04	97.65	0.90	0.83	20	-
GCF_003205835.1	s__Stenotrophomonas maltophilia_AL	84.015	752	1182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	98.59	98.33	0.89	0.86	7	-
GCF_013464915.1	s__Stenotrophomonas maltophilia_AT	83.993	736	1182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	99.65	98.65	0.97	0.93	5	-
GCF_900186865.1	s__Stenotrophomonas maltophilia	83.9766	753	1182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	97.99	97.31	0.92	0.87	234	-
GCF_002893095.1	s__Stenotrophomonas sp002893095	83.9098	708	1182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	97.47	97.41	0.90	0.90	3	-
GCF_001676385.1	s__Stenotrophomonas maltophilia_J	83.742	728	1182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013464485.1	s__Stenotrophomonas maltophilia_AW	83.7051	735	1182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001043115.1	s__Xanthomonas_A sp001043115	83.3073	766	1182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas_A	95.0	96.72	96.71	0.90	0.90	3	-
--------------------------------------------------------------------------------
[2023-06-17 18:05:19,755] [INFO] GTDB search result was written to GCA_009360425.1_ASM936042v1_genomic.fna/result_gtdb.tsv
[2023-06-17 18:05:19,755] [INFO] ===== GTDB Search completed =====
[2023-06-17 18:05:19,759] [INFO] DFAST_QC result json was written to GCA_009360425.1_ASM936042v1_genomic.fna/dqc_result.json
[2023-06-17 18:05:19,760] [INFO] DFAST_QC completed!
[2023-06-17 18:05:19,760] [INFO] Total running time: 0h1m26s