[2024-01-24 11:34:54,721] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:54,730] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:54,730] [INFO] DQC Reference Directory: /var/lib/cwl/stgcbe7ab92-f94b-46d5-8092-bb4d43031663/dqc_reference
[2024-01-24 11:34:56,423] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:56,424] [INFO] Task started: Prodigal
[2024-01-24 11:34:56,424] [INFO] Running command: gunzip -c /var/lib/cwl/stgef205b2c-44e3-4c00-a00f-905ab7eb49b3/GCF_024221815.1_ASM2422181v1_genomic.fna.gz | prodigal -d GCF_024221815.1_ASM2422181v1_genomic.fna/cds.fna -a GCF_024221815.1_ASM2422181v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:08,741] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:08,742] [INFO] Task started: HMMsearch
[2024-01-24 11:35:08,742] [INFO] Running command: hmmsearch --tblout GCF_024221815.1_ASM2422181v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcbe7ab92-f94b-46d5-8092-bb4d43031663/dqc_reference/reference_markers.hmm GCF_024221815.1_ASM2422181v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:09,012] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:09,013] [INFO] Found 6/6 markers.
[2024-01-24 11:35:09,052] [INFO] Query marker FASTA was written to GCF_024221815.1_ASM2422181v1_genomic.fna/markers.fasta
[2024-01-24 11:35:09,052] [INFO] Task started: Blastn
[2024-01-24 11:35:09,052] [INFO] Running command: blastn -query GCF_024221815.1_ASM2422181v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcbe7ab92-f94b-46d5-8092-bb4d43031663/dqc_reference/reference_markers.fasta -out GCF_024221815.1_ASM2422181v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:10,067] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:10,071] [INFO] Selected 13 target genomes.
[2024-01-24 11:35:10,072] [INFO] Target genome list was writen to GCF_024221815.1_ASM2422181v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:10,080] [INFO] Task started: fastANI
[2024-01-24 11:35:10,080] [INFO] Running command: fastANI --query /var/lib/cwl/stgef205b2c-44e3-4c00-a00f-905ab7eb49b3/GCF_024221815.1_ASM2422181v1_genomic.fna.gz --refList GCF_024221815.1_ASM2422181v1_genomic.fna/target_genomes.txt --output GCF_024221815.1_ASM2422181v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:22,452] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:22,453] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcbe7ab92-f94b-46d5-8092-bb4d43031663/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:22,453] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcbe7ab92-f94b-46d5-8092-bb4d43031663/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:22,470] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:35:22,470] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:22,470] [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	100.0	1284	1285	95	conclusive
Stenotrophomonas acidaminiphila	strain=JCM 13310	GCA_001431595.1	128780	128780	type	True	98.7799	1092	1285	95	conclusive
Stenotrophomonas nitritireducens	strain=DSM 12575	GCA_001431425.1	83617	83617	type	True	91.1946	982	1285	95	below_threshold
Stenotrophomonas daejeonensis	strain=JCM 16244	GCA_001431505.1	659018	659018	type	True	88.4141	855	1285	95	below_threshold
Stenotrophomonas pictorum	strain=JCM 9942	GCA_001310775.1	86184	86184	type	True	85.5651	563	1285	95	below_threshold
Stenotrophomonas pictorum	strain=JCM 9942	GCA_001431585.1	86184	86184	type	True	85.4705	878	1285	95	below_threshold
Stenotrophomonas pavanii	strain=DSM 25135	GCA_001431565.1	487698	487698	type	True	83.9465	791	1285	95	below_threshold
Stenotrophomonas pavanii	strain=LMG 25348	GCA_900101175.1	487698	487698	type	True	83.8831	818	1285	95	below_threshold
Stenotrophomonas nematodicola	strain=CPCC 101271	GCA_009467805.1	2656746	2656746	type	True	83.8606	822	1285	95	below_threshold
Pseudoxanthomonas suwonensis	strain=DSM 17175	GCA_010093235.1	314722	314722	suspected-type	True	82.9279	695	1285	95	below_threshold
Xanthomonas hydrangeae	strain=LMG 31884	GCA_905142475.1	2775159	2775159	type	True	81.2206	709	1285	95	below_threshold
Xanthomonas hortorum	strain=CFBP2533	GCA_012922215.1	56454	56454	pathovar	True	80.9906	714	1285	95	below_threshold
Xanthomonas hortorum	strain=CFBP 2533	GCA_021353095.1	56454	56454	pathovar	True	80.9446	720	1285	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:22,472] [INFO] DFAST Taxonomy check result was written to GCF_024221815.1_ASM2422181v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:22,473] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:22,473] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:22,473] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcbe7ab92-f94b-46d5-8092-bb4d43031663/dqc_reference/checkm_data
[2024-01-24 11:35:22,474] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:22,514] [INFO] Task started: CheckM
[2024-01-24 11:35:22,515] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024221815.1_ASM2422181v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024221815.1_ASM2422181v1_genomic.fna/checkm_input GCF_024221815.1_ASM2422181v1_genomic.fna/checkm_result
[2024-01-24 11:36:12,440] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:12,441] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:12,462] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:12,463] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:12,463] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024221815.1_ASM2422181v1_genomic.fna/markers.fasta)
[2024-01-24 11:36:12,464] [INFO] Task started: Blastn
[2024-01-24 11:36:12,464] [INFO] Running command: blastn -query GCF_024221815.1_ASM2422181v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcbe7ab92-f94b-46d5-8092-bb4d43031663/dqc_reference/reference_markers_gtdb.fasta -out GCF_024221815.1_ASM2422181v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:14,597] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:14,601] [INFO] Selected 7 target genomes.
[2024-01-24 11:36:14,602] [INFO] Target genome list was writen to GCF_024221815.1_ASM2422181v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:14,622] [INFO] Task started: fastANI
[2024-01-24 11:36:14,622] [INFO] Running command: fastANI --query /var/lib/cwl/stgef205b2c-44e3-4c00-a00f-905ab7eb49b3/GCF_024221815.1_ASM2422181v1_genomic.fna.gz --refList GCF_024221815.1_ASM2422181v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024221815.1_ASM2422181v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:21,901] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:21,911] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:36:21,911] [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_001431595.1	s__Stenotrophomonas acidaminiphila	98.7799	1092	1285	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	98.49	97.05	0.89	0.86	11	conclusive
GCF_002951995.1	s__Stenotrophomonas acidaminiphila_A	93.6661	1112	1285	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	98.50	98.36	0.92	0.88	13	-
GCF_001431425.1	s__Stenotrophomonas nitritireducens	91.1775	983	1285	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	91.1726	1032	1285	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	96.53	96.53	0.92	0.92	2	-
GCF_001431505.1	s__Stenotrophomonas daejeonensis	88.3977	856	1285	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	87.7144	900	1285	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004216795.1	s__Stenotrophomonas_A sp004216795	83.602	794	1285	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:36:21,913] [INFO] GTDB search result was written to GCF_024221815.1_ASM2422181v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:21,914] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:21,918] [INFO] DFAST_QC result json was written to GCF_024221815.1_ASM2422181v1_genomic.fna/dqc_result.json
[2024-01-24 11:36:21,918] [INFO] DFAST_QC completed!
[2024-01-24 11:36:21,919] [INFO] Total running time: 0h1m27s