[2024-01-24 15:10:22,206] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:22,209] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:22,209] [INFO] DQC Reference Directory: /var/lib/cwl/stg06727afc-36fd-4c2d-b14a-08663ceb79fd/dqc_reference
[2024-01-24 15:10:23,850] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:23,851] [INFO] Task started: Prodigal
[2024-01-24 15:10:23,851] [INFO] Running command: gunzip -c /var/lib/cwl/stgbe484cc9-282b-4f6c-8816-ead8ad8fa19c/GCF_002803515.1_ASM280351v1_genomic.fna.gz | prodigal -d GCF_002803515.1_ASM280351v1_genomic.fna/cds.fna -a GCF_002803515.1_ASM280351v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:10:40,948] [INFO] Task succeeded: Prodigal
[2024-01-24 15:10:40,948] [INFO] Task started: HMMsearch
[2024-01-24 15:10:40,949] [INFO] Running command: hmmsearch --tblout GCF_002803515.1_ASM280351v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg06727afc-36fd-4c2d-b14a-08663ceb79fd/dqc_reference/reference_markers.hmm GCF_002803515.1_ASM280351v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:10:41,208] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:10:41,209] [INFO] Found 6/6 markers.
[2024-01-24 15:10:41,249] [INFO] Query marker FASTA was written to GCF_002803515.1_ASM280351v1_genomic.fna/markers.fasta
[2024-01-24 15:10:41,249] [INFO] Task started: Blastn
[2024-01-24 15:10:41,250] [INFO] Running command: blastn -query GCF_002803515.1_ASM280351v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg06727afc-36fd-4c2d-b14a-08663ceb79fd/dqc_reference/reference_markers.fasta -out GCF_002803515.1_ASM280351v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:10:42,256] [INFO] Task succeeded: Blastn
[2024-01-24 15:10:42,259] [INFO] Selected 12 target genomes.
[2024-01-24 15:10:42,259] [INFO] Target genome list was writen to GCF_002803515.1_ASM280351v1_genomic.fna/target_genomes.txt
[2024-01-24 15:10:42,264] [INFO] Task started: fastANI
[2024-01-24 15:10:42,264] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe484cc9-282b-4f6c-8816-ead8ad8fa19c/GCF_002803515.1_ASM280351v1_genomic.fna.gz --refList GCF_002803515.1_ASM280351v1_genomic.fna/target_genomes.txt --output GCF_002803515.1_ASM280351v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:10:58,049] [INFO] Task succeeded: fastANI
[2024-01-24 15:10:58,050] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg06727afc-36fd-4c2d-b14a-08663ceb79fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:10:58,050] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg06727afc-36fd-4c2d-b14a-08663ceb79fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:10:58,061] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:10:58,061] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:10:58,061] [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 lactitubi	strain=M15	GCA_002803515.1	2045214	2045214	type	True	100.0	1621	1621	95	conclusive
Stenotrophomonas indicatrix	strain=WS40	GCA_002750975.1	2045451	2045451	type	True	93.8853	1370	1621	95	below_threshold
Stenotrophomonas maltophilia	strain=NBRC 14161	GCA_001591205.1	40324	40324	type	True	88.3708	1242	1621	95	below_threshold
Stenotrophomonas pavanii	strain=DSM 25135	GCA_001431565.1	487698	487698	type	True	88.3634	1193	1621	95	below_threshold
Stenotrophomonas maltophilia	strain=ATCC 13637	GCA_001997185.1	40324	40324	type	True	88.3526	1234	1621	95	below_threshold
Stenotrophomonas sepilia	strain=SM16975	GCA_003244875.1	2860290	2860290	type	True	88.2521	1173	1621	95	below_threshold
Stenotrophomonas maltophilia	strain=MTCC 434	GCA_000597745.1	40324	40324	type	True	88.2511	1156	1621	95	below_threshold
Stenotrophomonas pennii	strain=Sa5BUN4	GCA_014836545.1	2762239	2762239	type	True	84.5971	936	1621	95	below_threshold
Stenotrophomonas acidaminiphila	strain=DSM 13117	GCA_024221815.1	128780	128780	type	True	83.1175	839	1621	95	below_threshold
Stenotrophomonas pictorum	strain=JCM 9942	GCA_001310775.1	86184	86184	type	True	83.0149	504	1621	95	below_threshold
Xanthomonas indica	strain=PPL560	GCA_022669045.1	2912242	2912242	type	True	82.2615	856	1621	95	below_threshold
Xanthomonas translucens	strain=ATCC 19319	GCA_020880735.1	343	343	type	True	82.2428	698	1621	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:10:58,063] [INFO] DFAST Taxonomy check result was written to GCF_002803515.1_ASM280351v1_genomic.fna/tc_result.tsv
[2024-01-24 15:10:58,063] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:10:58,063] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:10:58,064] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg06727afc-36fd-4c2d-b14a-08663ceb79fd/dqc_reference/checkm_data
[2024-01-24 15:10:58,065] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:10:58,114] [INFO] Task started: CheckM
[2024-01-24 15:10:58,115] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002803515.1_ASM280351v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002803515.1_ASM280351v1_genomic.fna/checkm_input GCF_002803515.1_ASM280351v1_genomic.fna/checkm_result
[2024-01-24 15:12:06,656] [INFO] Task succeeded: CheckM
[2024-01-24 15:12:06,657] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:12:06,674] [INFO] ===== Completeness check finished =====
[2024-01-24 15:12:06,674] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:12:06,674] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002803515.1_ASM280351v1_genomic.fna/markers.fasta)
[2024-01-24 15:12:06,674] [INFO] Task started: Blastn
[2024-01-24 15:12:06,674] [INFO] Running command: blastn -query GCF_002803515.1_ASM280351v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg06727afc-36fd-4c2d-b14a-08663ceb79fd/dqc_reference/reference_markers_gtdb.fasta -out GCF_002803515.1_ASM280351v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:12:08,396] [INFO] Task succeeded: Blastn
[2024-01-24 15:12:08,399] [INFO] Selected 14 target genomes.
[2024-01-24 15:12:08,399] [INFO] Target genome list was writen to GCF_002803515.1_ASM280351v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:12:08,409] [INFO] Task started: fastANI
[2024-01-24 15:12:08,409] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe484cc9-282b-4f6c-8816-ead8ad8fa19c/GCF_002803515.1_ASM280351v1_genomic.fna.gz --refList GCF_002803515.1_ASM280351v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002803515.1_ASM280351v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:12:28,797] [INFO] Task succeeded: fastANI
[2024-01-24 15:12:28,809] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:12:28,809] [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_002803515.1	s__Stenotrophomonas lactitubi	100.0	1621	1621	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	96.67	95.60	0.90	0.88	12	conclusive
GCF_002750975.1	s__Stenotrophomonas indicatrix	93.8853	1370	1621	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	97.78	96.47	0.93	0.89	30	-
GCF_013364355.1	s__Stenotrophomonas sp013364355	93.84	1345	1621	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000020665.1	s__Stenotrophomonas maltophilia_L	88.7495	1280	1621	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	98.35	98.00	0.93	0.90	7	-
GCF_006970445.1	s__Stenotrophomonas maltophilia_AU	88.6724	1271	1621	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003028475.1	s__Stenotrophomonas sp003028475	88.6507	1218	1621	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	98.27	96.55	0.95	0.90	3	-
GCF_001274595.1	s__Stenotrophomonas maltophilia_AJ	88.6128	1230	1621	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	97.15	96.26	0.91	0.88	10	-
GCF_006974125.1	s__Stenotrophomonas maltophilia_O	88.5952	1258	1621	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	98.85	98.84	0.92	0.90	5	-
GCF_003086775.1	s__Stenotrophomonas sp003086775	88.5349	1202	1621	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	98.05	97.07	0.94	0.87	8	-
GCF_002799155.1	s__Stenotrophomonas maltophilia_R	88.5103	1253	1621	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	88.4672	1273	1621	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	95.93	95.59	0.89	0.87	14	-
GCF_004684085.1	s__Stenotrophomonas maltophilia_AS	88.4019	1234	1621	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900186865.1	s__Stenotrophomonas maltophilia	88.3843	1301	1621	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	97.99	97.31	0.92	0.87	234	-
GCA_003510825.1	s__Stenotrophomonas sp003086795	87.7601	712	1621	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 15:12:28,811] [INFO] GTDB search result was written to GCF_002803515.1_ASM280351v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:12:28,811] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:12:28,815] [INFO] DFAST_QC result json was written to GCF_002803515.1_ASM280351v1_genomic.fna/dqc_result.json
[2024-01-24 15:12:28,815] [INFO] DFAST_QC completed!
[2024-01-24 15:12:28,815] [INFO] Total running time: 0h2m7s