[2024-01-24 13:17:13,863] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:13,865] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:13,865] [INFO] DQC Reference Directory: /var/lib/cwl/stg8f90a61f-f8d7-482c-9a38-84573b225dfd/dqc_reference
[2024-01-24 13:17:15,162] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:15,163] [INFO] Task started: Prodigal
[2024-01-24 13:17:15,163] [INFO] Running command: gunzip -c /var/lib/cwl/stge6e11831-e10a-49b4-9ed0-36df88e01004/GCF_008710035.1_ASM871003v1_genomic.fna.gz | prodigal -d GCF_008710035.1_ASM871003v1_genomic.fna/cds.fna -a GCF_008710035.1_ASM871003v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:28,654] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:28,654] [INFO] Task started: HMMsearch
[2024-01-24 13:17:28,654] [INFO] Running command: hmmsearch --tblout GCF_008710035.1_ASM871003v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8f90a61f-f8d7-482c-9a38-84573b225dfd/dqc_reference/reference_markers.hmm GCF_008710035.1_ASM871003v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:28,946] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:28,947] [INFO] Found 6/6 markers.
[2024-01-24 13:17:28,989] [INFO] Query marker FASTA was written to GCF_008710035.1_ASM871003v1_genomic.fna/markers.fasta
[2024-01-24 13:17:28,990] [INFO] Task started: Blastn
[2024-01-24 13:17:28,990] [INFO] Running command: blastn -query GCF_008710035.1_ASM871003v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8f90a61f-f8d7-482c-9a38-84573b225dfd/dqc_reference/reference_markers.fasta -out GCF_008710035.1_ASM871003v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:30,019] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:30,024] [INFO] Selected 15 target genomes.
[2024-01-24 13:17:30,025] [INFO] Target genome list was writen to GCF_008710035.1_ASM871003v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:30,040] [INFO] Task started: fastANI
[2024-01-24 13:17:30,040] [INFO] Running command: fastANI --query /var/lib/cwl/stge6e11831-e10a-49b4-9ed0-36df88e01004/GCF_008710035.1_ASM871003v1_genomic.fna.gz --refList GCF_008710035.1_ASM871003v1_genomic.fna/target_genomes.txt --output GCF_008710035.1_ASM871003v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:46,936] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:46,936] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8f90a61f-f8d7-482c-9a38-84573b225dfd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:46,937] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8f90a61f-f8d7-482c-9a38-84573b225dfd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:46,954] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:17:46,954] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:17:46,954] [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 maltophilia	strain=NBRC 14161	GCA_001591205.1	40324	40324	type	True	89.0141	1069	1379	95	below_threshold
Stenotrophomonas maltophilia	strain=NCTC10257	GCA_900186865.1	40324	40324	type	True	88.9957	1113	1379	95	below_threshold
Stenotrophomonas maltophilia	strain=MTCC 434	GCA_000597745.1	40324	40324	type	True	88.9718	1021	1379	95	below_threshold
Stenotrophomonas maltophilia	strain=ATCC 13637	GCA_001997185.1	40324	40324	type	True	88.9121	1078	1379	95	below_threshold
Stenotrophomonas pavanii	strain=LMG 25348	GCA_900101175.1	487698	487698	type	True	88.9032	1110	1379	95	below_threshold
Stenotrophomonas pavanii	strain=DSM 25135	GCA_001431565.1	487698	487698	type	True	88.8066	1088	1379	95	below_threshold
[Pseudomonas] hibiscicola	strain=ATCC 19867	GCA_000382065.1	86189	86189	type	True	88.702	1145	1379	95	below_threshold
Stenotrophomonas sepilia	strain=SM16975	GCA_003244875.1	2860290	2860290	type	True	88.679	1077	1379	95	below_threshold
Stenotrophomonas indicatrix	strain=WS40	GCA_002750975.1	2045451	2045451	type	True	88.5185	1147	1379	95	below_threshold
Stenotrophomonas lactitubi	strain=M15	GCA_002803515.1	2045214	2045214	type	True	88.444	1141	1379	95	below_threshold
Stenotrophomonas pennii	strain=Sa5BUN4	GCA_014836545.1	2762239	2762239	type	True	84.823	949	1379	95	below_threshold
Stenotrophomonas acidaminiphila	strain=DSM 13117	GCA_024221815.1	128780	128780	type	True	83.7608	811	1379	95	below_threshold
Stenotrophomonas pictorum	strain=JCM 9942	GCA_001310775.1	86184	86184	type	True	83.392	479	1379	95	below_threshold
Xanthomonas indica	strain=PPL560	GCA_022669045.1	2912242	2912242	type	True	82.5911	865	1379	95	below_threshold
Xanthomonas translucens	strain=ATCC 19319	GCA_020880735.1	343	343	type	True	82.5108	686	1379	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:17:46,956] [INFO] DFAST Taxonomy check result was written to GCF_008710035.1_ASM871003v1_genomic.fna/tc_result.tsv
[2024-01-24 13:17:46,957] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:46,957] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:46,957] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8f90a61f-f8d7-482c-9a38-84573b225dfd/dqc_reference/checkm_data
[2024-01-24 13:17:46,958] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:47,000] [INFO] Task started: CheckM
[2024-01-24 13:17:47,000] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008710035.1_ASM871003v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008710035.1_ASM871003v1_genomic.fna/checkm_input GCF_008710035.1_ASM871003v1_genomic.fna/checkm_result
[2024-01-24 13:18:34,022] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:34,023] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:34,044] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:34,045] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:34,045] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008710035.1_ASM871003v1_genomic.fna/markers.fasta)
[2024-01-24 13:18:34,046] [INFO] Task started: Blastn
[2024-01-24 13:18:34,046] [INFO] Running command: blastn -query GCF_008710035.1_ASM871003v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8f90a61f-f8d7-482c-9a38-84573b225dfd/dqc_reference/reference_markers_gtdb.fasta -out GCF_008710035.1_ASM871003v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:35,999] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:36,004] [INFO] Selected 7 target genomes.
[2024-01-24 13:18:36,004] [INFO] Target genome list was writen to GCF_008710035.1_ASM871003v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:36,011] [INFO] Task started: fastANI
[2024-01-24 13:18:36,011] [INFO] Running command: fastANI --query /var/lib/cwl/stge6e11831-e10a-49b4-9ed0-36df88e01004/GCF_008710035.1_ASM871003v1_genomic.fna.gz --refList GCF_008710035.1_ASM871003v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008710035.1_ASM871003v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:18:48,220] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:48,230] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:18:48,231] [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_008710035.1	s__Stenotrophomonas cyclobalanopsidis	100.0	1374	1379	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	95.26	95.20	0.90	0.87	5	conclusive
GCA_002364755.1	s__Stenotrophomonas maltophilia_AX	94.9239	1216	1379	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	97.19	95.30	0.93	0.90	3	-
GCA_003510825.1	s__Stenotrophomonas sp003086795	93.9474	744	1379	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	95.73	95.09	0.81	0.78	6	-
GCF_003086775.1	s__Stenotrophomonas sp003086775	93.2829	1248	1379	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	98.05	97.07	0.94	0.87	8	-
GCF_003086895.1	s__Stenotrophomonas sp003086895	91.402	1231	1379	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	89.15	1105	1379	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	98.27	96.55	0.95	0.90	3	-
GCF_002138415.1	s__Stenotrophomonas maltophilia_G	89.0032	1140	1379	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	95.93	95.59	0.89	0.87	14	-
--------------------------------------------------------------------------------
[2024-01-24 13:18:48,232] [INFO] GTDB search result was written to GCF_008710035.1_ASM871003v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:18:48,233] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:18:48,236] [INFO] DFAST_QC result json was written to GCF_008710035.1_ASM871003v1_genomic.fna/dqc_result.json
[2024-01-24 13:18:48,236] [INFO] DFAST_QC completed!
[2024-01-24 13:18:48,237] [INFO] Total running time: 0h1m34s