[2023-06-28 03:25:01,455] [INFO] DFAST_QC pipeline started.
[2023-06-28 03:25:01,462] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 03:25:01,462] [INFO] DQC Reference Directory: /var/lib/cwl/stg0b384231-837c-487c-8453-66db12c54ce5/dqc_reference
[2023-06-28 03:25:02,793] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 03:25:02,794] [INFO] Task started: Prodigal
[2023-06-28 03:25:02,794] [INFO] Running command: gunzip -c /var/lib/cwl/stgc6cdfe07-d99e-4078-8613-a322a3096ac8/GCA_913776385.1_S3C1435_SP48_genomic.fna.gz | prodigal -d GCA_913776385.1_S3C1435_SP48_genomic.fna/cds.fna -a GCA_913776385.1_S3C1435_SP48_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 03:25:17,864] [INFO] Task succeeded: Prodigal
[2023-06-28 03:25:17,865] [INFO] Task started: HMMsearch
[2023-06-28 03:25:17,865] [INFO] Running command: hmmsearch --tblout GCA_913776385.1_S3C1435_SP48_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0b384231-837c-487c-8453-66db12c54ce5/dqc_reference/reference_markers.hmm GCA_913776385.1_S3C1435_SP48_genomic.fna/protein.faa > /dev/null
[2023-06-28 03:25:18,196] [INFO] Task succeeded: HMMsearch
[2023-06-28 03:25:18,197] [INFO] Found 6/6 markers.
[2023-06-28 03:25:18,237] [INFO] Query marker FASTA was written to GCA_913776385.1_S3C1435_SP48_genomic.fna/markers.fasta
[2023-06-28 03:25:18,238] [INFO] Task started: Blastn
[2023-06-28 03:25:18,238] [INFO] Running command: blastn -query GCA_913776385.1_S3C1435_SP48_genomic.fna/markers.fasta -db /var/lib/cwl/stg0b384231-837c-487c-8453-66db12c54ce5/dqc_reference/reference_markers.fasta -out GCA_913776385.1_S3C1435_SP48_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 03:25:19,202] [INFO] Task succeeded: Blastn
[2023-06-28 03:25:19,206] [INFO] Selected 13 target genomes.
[2023-06-28 03:25:19,206] [INFO] Target genome list was writen to GCA_913776385.1_S3C1435_SP48_genomic.fna/target_genomes.txt
[2023-06-28 03:25:19,209] [INFO] Task started: fastANI
[2023-06-28 03:25:19,209] [INFO] Running command: fastANI --query /var/lib/cwl/stgc6cdfe07-d99e-4078-8613-a322a3096ac8/GCA_913776385.1_S3C1435_SP48_genomic.fna.gz --refList GCA_913776385.1_S3C1435_SP48_genomic.fna/target_genomes.txt --output GCA_913776385.1_S3C1435_SP48_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 03:25:37,046] [INFO] Task succeeded: fastANI
[2023-06-28 03:25:37,047] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0b384231-837c-487c-8453-66db12c54ce5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 03:25:37,047] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0b384231-837c-487c-8453-66db12c54ce5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 03:25:37,060] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 03:25:37,060] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 03:25:37,060] [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=NCTC10257	GCA_900186865.1	40324	40324	type	True	92.2171	1283	1450	95	below_threshold
Stenotrophomonas maltophilia	strain=NBRC 14161	GCA_001591205.1	40324	40324	type	True	92.1326	1230	1450	95	below_threshold
Stenotrophomonas maltophilia	strain=ATCC 13637	GCA_001997185.1	40324	40324	type	True	92.1243	1235	1450	95	below_threshold
Stenotrophomonas maltophilia	strain=MTCC 434	GCA_000597745.1	40324	40324	type	True	92.0805	1153	1450	95	below_threshold
[Pseudomonas] hibiscicola	strain=ATCC 19867	GCA_000382065.1	86189	86189	type	True	91.7986	1274	1450	95	below_threshold
Stenotrophomonas pavanii	strain=LMG 25348	GCA_900101175.1	487698	487698	type	True	91.0482	1251	1450	95	below_threshold
Stenotrophomonas pavanii	strain=DSM 25135	GCA_001431565.1	487698	487698	type	True	91.0125	1208	1450	95	below_threshold
Stenotrophomonas lactitubi	strain=M15	GCA_002803515.1	2045214	2045214	type	True	88.3717	1241	1450	95	below_threshold
Stenotrophomonas pennii	strain=Sa5BUN4	GCA_014836545.1	2762239	2762239	type	True	84.4166	931	1450	95	below_threshold
Stenotrophomonas acidaminiphila	strain=DSM 13117	GCA_024221815.1	128780	128780	type	True	83.6737	817	1450	95	below_threshold
Stenotrophomonas pictorum	strain=JCM 9942	GCA_001310775.1	86184	86184	type	True	83.1619	484	1450	95	below_threshold
Xanthomonas indica	strain=PPL560	GCA_022669045.1	2912242	2912242	type	True	82.5326	848	1450	95	below_threshold
Xanthomonas translucens	strain=ATCC 19319	GCA_020880735.1	343	343	type	True	82.3604	685	1450	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 03:25:37,063] [INFO] DFAST Taxonomy check result was written to GCA_913776385.1_S3C1435_SP48_genomic.fna/tc_result.tsv
[2023-06-28 03:25:37,063] [INFO] ===== Taxonomy check completed =====
[2023-06-28 03:25:37,063] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 03:25:37,064] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0b384231-837c-487c-8453-66db12c54ce5/dqc_reference/checkm_data
[2023-06-28 03:25:37,065] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 03:25:37,110] [INFO] Task started: CheckM
[2023-06-28 03:25:37,110] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_913776385.1_S3C1435_SP48_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_913776385.1_S3C1435_SP48_genomic.fna/checkm_input GCA_913776385.1_S3C1435_SP48_genomic.fna/checkm_result
[2023-06-28 03:26:33,618] [INFO] Task succeeded: CheckM
[2023-06-28 03:26:33,620] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 03:26:33,642] [INFO] ===== Completeness check finished =====
[2023-06-28 03:26:33,642] [INFO] ===== Start GTDB Search =====
[2023-06-28 03:26:33,642] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_913776385.1_S3C1435_SP48_genomic.fna/markers.fasta)
[2023-06-28 03:26:33,643] [INFO] Task started: Blastn
[2023-06-28 03:26:33,643] [INFO] Running command: blastn -query GCA_913776385.1_S3C1435_SP48_genomic.fna/markers.fasta -db /var/lib/cwl/stg0b384231-837c-487c-8453-66db12c54ce5/dqc_reference/reference_markers_gtdb.fasta -out GCA_913776385.1_S3C1435_SP48_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 03:26:35,161] [INFO] Task succeeded: Blastn
[2023-06-28 03:26:35,166] [INFO] Selected 15 target genomes.
[2023-06-28 03:26:35,166] [INFO] Target genome list was writen to GCA_913776385.1_S3C1435_SP48_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 03:26:35,177] [INFO] Task started: fastANI
[2023-06-28 03:26:35,178] [INFO] Running command: fastANI --query /var/lib/cwl/stgc6cdfe07-d99e-4078-8613-a322a3096ac8/GCA_913776385.1_S3C1435_SP48_genomic.fna.gz --refList GCA_913776385.1_S3C1435_SP48_genomic.fna/target_genomes_gtdb.txt --output GCA_913776385.1_S3C1435_SP48_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 03:26:52,760] [INFO] Task succeeded: fastANI
[2023-06-28 03:26:52,774] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 03:26:52,774] [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_002799165.1	s__Stenotrophomonas maltophilia_Q	93.6414	1289	1450	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	97.69	95.30	0.93	0.83	9	-
GCF_013464915.1	s__Stenotrophomonas maltophilia_AT	92.7042	1223	1450	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	99.65	98.65	0.97	0.93	5	-
GCF_006974125.1	s__Stenotrophomonas maltophilia_O	92.5505	1262	1450	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	98.85	98.84	0.92	0.90	5	-
GCA_001431625.1	s__Stenotrophomonas geniculata	92.5309	1194	1450	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	97.51	96.26	0.87	0.77	45	-
GCF_900186865.1	s__Stenotrophomonas maltophilia	92.2171	1283	1450	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	97.99	97.31	0.92	0.87	234	-
GCF_013464485.1	s__Stenotrophomonas maltophilia_AW	91.9077	1227	1450	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000382065.1	s__Stenotrophomonas maltophilia_B	91.785	1275	1450	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	97.83	97.17	0.91	0.87	24	-
GCF_004346925.1	s__Stenotrophomonas maltophilia_A	91.5113	1264	1450	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	97.29	95.44	0.89	0.84	41	-
GCF_002799245.1	s__Stenotrophomonas maltophilia_S	91.3864	1238	1450	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006970445.1	s__Stenotrophomonas maltophilia_AU	91.373	1266	1450	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002192255.1	s__Stenotrophomonas sp002192255	91.3644	1264	1450	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	95.64	95.45	0.89	0.84	9	-
GCF_001431665.1	s__Stenotrophomonas maltophilia_K	90.9793	1174	1450	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 03:26:52,776] [INFO] GTDB search result was written to GCA_913776385.1_S3C1435_SP48_genomic.fna/result_gtdb.tsv
[2023-06-28 03:26:52,777] [INFO] ===== GTDB Search completed =====
[2023-06-28 03:26:52,780] [INFO] DFAST_QC result json was written to GCA_913776385.1_S3C1435_SP48_genomic.fna/dqc_result.json
[2023-06-28 03:26:52,781] [INFO] DFAST_QC completed!
[2023-06-28 03:26:52,781] [INFO] Total running time: 0h1m51s