[2023-06-27 20:38:45,654] [INFO] DFAST_QC pipeline started.
[2023-06-27 20:38:45,656] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 20:38:45,656] [INFO] DQC Reference Directory: /var/lib/cwl/stgb1493b0e-8f95-4f3d-aad7-083e5f2d9184/dqc_reference
[2023-06-27 20:38:46,830] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 20:38:46,831] [INFO] Task started: Prodigal
[2023-06-27 20:38:46,831] [INFO] Running command: gunzip -c /var/lib/cwl/stg99ee9c3b-dfa8-4e9e-9b8b-68b58a62bc17/GCA_002345545.1_ASM234554v1_genomic.fna.gz | prodigal -d GCA_002345545.1_ASM234554v1_genomic.fna/cds.fna -a GCA_002345545.1_ASM234554v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 20:38:57,501] [INFO] Task succeeded: Prodigal
[2023-06-27 20:38:57,501] [INFO] Task started: HMMsearch
[2023-06-27 20:38:57,501] [INFO] Running command: hmmsearch --tblout GCA_002345545.1_ASM234554v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb1493b0e-8f95-4f3d-aad7-083e5f2d9184/dqc_reference/reference_markers.hmm GCA_002345545.1_ASM234554v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 20:38:57,699] [INFO] Task succeeded: HMMsearch
[2023-06-27 20:38:57,700] [INFO] Found 6/6 markers.
[2023-06-27 20:38:57,729] [INFO] Query marker FASTA was written to GCA_002345545.1_ASM234554v1_genomic.fna/markers.fasta
[2023-06-27 20:38:57,730] [INFO] Task started: Blastn
[2023-06-27 20:38:57,730] [INFO] Running command: blastn -query GCA_002345545.1_ASM234554v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb1493b0e-8f95-4f3d-aad7-083e5f2d9184/dqc_reference/reference_markers.fasta -out GCA_002345545.1_ASM234554v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 20:38:58,625] [INFO] Task succeeded: Blastn
[2023-06-27 20:38:58,629] [INFO] Selected 14 target genomes.
[2023-06-27 20:38:58,630] [INFO] Target genome list was writen to GCA_002345545.1_ASM234554v1_genomic.fna/target_genomes.txt
[2023-06-27 20:38:58,631] [INFO] Task started: fastANI
[2023-06-27 20:38:58,631] [INFO] Running command: fastANI --query /var/lib/cwl/stg99ee9c3b-dfa8-4e9e-9b8b-68b58a62bc17/GCA_002345545.1_ASM234554v1_genomic.fna.gz --refList GCA_002345545.1_ASM234554v1_genomic.fna/target_genomes.txt --output GCA_002345545.1_ASM234554v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 20:39:10,558] [INFO] Task succeeded: fastANI
[2023-06-27 20:39:10,559] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb1493b0e-8f95-4f3d-aad7-083e5f2d9184/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 20:39:10,559] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb1493b0e-8f95-4f3d-aad7-083e5f2d9184/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 20:39:10,570] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 20:39:10,570] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 20:39:10,571] [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 pictorum	strain=JCM 9942	GCA_001431585.1	86184	86184	type	True	87.1723	848	1085	95	below_threshold
Stenotrophomonas pictorum	strain=JCM 9942	GCA_001310775.1	86184	86184	type	True	86.8997	566	1085	95	below_threshold
Stenotrophomonas nitritireducens	strain=DSM 12575	GCA_001431425.1	83617	83617	type	True	85.9702	798	1085	95	below_threshold
Stenotrophomonas acidaminiphila	strain=DSM 13117	GCA_024221815.1	128780	128780	type	True	85.8619	814	1085	95	below_threshold
Stenotrophomonas acidaminiphila	strain=JCM 13310	GCA_001431595.1	128780	128780	type	True	85.6765	778	1085	95	below_threshold
Stenotrophomonas daejeonensis	strain=JCM 16244	GCA_001431505.1	659018	659018	type	True	85.6647	723	1085	95	below_threshold
Stenotrophomonas terrae	strain=DSM 18941	GCA_001431465.1	405446	405446	type	True	84.632	776	1085	95	below_threshold
Stenotrophomonas pavanii	strain=DSM 25135	GCA_001431565.1	487698	487698	type	True	83.179	669	1085	95	below_threshold
Stenotrophomonas lactitubi	strain=M15	GCA_002803515.1	2045214	2045214	type	True	82.9388	688	1085	95	below_threshold
Stenotrophomonas indicatrix	strain=WS40	GCA_002750975.1	2045451	2045451	type	True	82.8177	680	1085	95	below_threshold
Xanthomonas indica	strain=PPL560	GCA_022669045.1	2912242	2912242	type	True	82.582	698	1085	95	below_threshold
Stenotrophomonas pennii	strain=Sa5BUN4	GCA_014836545.1	2762239	2762239	type	True	82.2502	644	1085	95	below_threshold
Xanthomonas hydrangeae	strain=LMG 31884	GCA_905142475.1	2775159	2775159	type	True	81.1426	609	1085	95	below_threshold
Xanthomonas euvesicatoria	strain=ATCC 11633	GCA_020880415.1	456327	456327	type	True	81.1119	596	1085	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 20:39:10,572] [INFO] DFAST Taxonomy check result was written to GCA_002345545.1_ASM234554v1_genomic.fna/tc_result.tsv
[2023-06-27 20:39:10,573] [INFO] ===== Taxonomy check completed =====
[2023-06-27 20:39:10,573] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 20:39:10,573] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb1493b0e-8f95-4f3d-aad7-083e5f2d9184/dqc_reference/checkm_data
[2023-06-27 20:39:10,574] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 20:39:10,607] [INFO] Task started: CheckM
[2023-06-27 20:39:10,607] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002345545.1_ASM234554v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002345545.1_ASM234554v1_genomic.fna/checkm_input GCA_002345545.1_ASM234554v1_genomic.fna/checkm_result
[2023-06-27 20:39:49,904] [INFO] Task succeeded: CheckM
[2023-06-27 20:39:49,905] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 20:39:49,924] [INFO] ===== Completeness check finished =====
[2023-06-27 20:39:49,924] [INFO] ===== Start GTDB Search =====
[2023-06-27 20:39:49,924] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002345545.1_ASM234554v1_genomic.fna/markers.fasta)
[2023-06-27 20:39:49,924] [INFO] Task started: Blastn
[2023-06-27 20:39:49,924] [INFO] Running command: blastn -query GCA_002345545.1_ASM234554v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb1493b0e-8f95-4f3d-aad7-083e5f2d9184/dqc_reference/reference_markers_gtdb.fasta -out GCA_002345545.1_ASM234554v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 20:39:51,600] [INFO] Task succeeded: Blastn
[2023-06-27 20:39:51,604] [INFO] Selected 17 target genomes.
[2023-06-27 20:39:51,604] [INFO] Target genome list was writen to GCA_002345545.1_ASM234554v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 20:39:51,615] [INFO] Task started: fastANI
[2023-06-27 20:39:51,615] [INFO] Running command: fastANI --query /var/lib/cwl/stg99ee9c3b-dfa8-4e9e-9b8b-68b58a62bc17/GCA_002345545.1_ASM234554v1_genomic.fna.gz --refList GCA_002345545.1_ASM234554v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002345545.1_ASM234554v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 20:40:05,217] [INFO] Task succeeded: fastANI
[2023-06-27 20:40:05,231] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 20:40:05,232] [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
GCA_002345545.1	s__Stenotrophomonas sp002345545	100.0	1083	1085	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001310775.1	s__Stenotrophomonas pictorum	86.8997	566	1085	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	99.94	99.94	0.99	0.99	2	-
GCF_001431425.1	s__Stenotrophomonas nitritireducens	85.996	796	1085	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	98.94	98.42	0.92	0.89	3	-
GCF_009496535.1	s__Stenotrophomonas sp003504055	85.9781	808	1085	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	96.53	96.53	0.92	0.92	2	-
GCF_004348115.1	s__Stenotrophomonas sp004348115	85.8156	805	1085	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	98.00	98.00	0.94	0.94	2	-
GCF_002951995.1	s__Stenotrophomonas acidaminiphila_A	85.781	806	1085	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	98.50	98.36	0.92	0.88	13	-
GCF_001431595.1	s__Stenotrophomonas acidaminiphila	85.6579	779	1085	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	98.49	97.05	0.89	0.86	11	-
GCF_001431505.1	s__Stenotrophomonas daejeonensis	85.6305	725	1085	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	85.4478	771	1085	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002471015.1	s__Stenotrophomonas sp002471015	84.9244	787	1085	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	96.17	95.12	0.84	0.81	4	-
GCF_001700965.1	s__Stenotrophomonas nitritireducens_A	84.916	842	1085	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002329155.1	s__Stenotrophomonas sp002329155	84.8955	797	1085	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001431465.1	s__Stenotrophomonas terrae	84.6165	778	1085	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003248565.1	s__Stenotrophomonas sp003248565	84.133	591	1085	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002750975.1	s__Stenotrophomonas indicatrix	82.8262	679	1085	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	97.78	96.47	0.93	0.89	30	-
GCF_004920835.1	s__Stenotrophomonas maltophilia_AQ	82.8086	681	1085	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	99.58	99.16	0.97	0.95	3	-
GCA_003510825.1	s__Stenotrophomonas sp003086795	82.4695	413	1085	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	95.73	95.09	0.81	0.78	6	-
--------------------------------------------------------------------------------
[2023-06-27 20:40:05,234] [INFO] GTDB search result was written to GCA_002345545.1_ASM234554v1_genomic.fna/result_gtdb.tsv
[2023-06-27 20:40:05,234] [INFO] ===== GTDB Search completed =====
[2023-06-27 20:40:05,238] [INFO] DFAST_QC result json was written to GCA_002345545.1_ASM234554v1_genomic.fna/dqc_result.json
[2023-06-27 20:40:05,238] [INFO] DFAST_QC completed!
[2023-06-27 20:40:05,238] [INFO] Total running time: 0h1m20s