[2024-01-24 11:26:28,069] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:28,072] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:28,072] [INFO] DQC Reference Directory: /var/lib/cwl/stgbaeab163-489c-4159-928b-67e2e548d90c/dqc_reference
[2024-01-24 11:26:29,566] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:29,567] [INFO] Task started: Prodigal
[2024-01-24 11:26:29,568] [INFO] Running command: gunzip -c /var/lib/cwl/stg0f5a3f93-199e-414c-bd89-5b49fc0f36c3/GCF_024621935.1_ASM2462193v1_genomic.fna.gz | prodigal -d GCF_024621935.1_ASM2462193v1_genomic.fna/cds.fna -a GCF_024621935.1_ASM2462193v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:45,523] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:45,523] [INFO] Task started: HMMsearch
[2024-01-24 11:26:45,523] [INFO] Running command: hmmsearch --tblout GCF_024621935.1_ASM2462193v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbaeab163-489c-4159-928b-67e2e548d90c/dqc_reference/reference_markers.hmm GCF_024621935.1_ASM2462193v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:45,871] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:45,873] [INFO] Found 6/6 markers.
[2024-01-24 11:26:45,919] [INFO] Query marker FASTA was written to GCF_024621935.1_ASM2462193v1_genomic.fna/markers.fasta
[2024-01-24 11:26:45,919] [INFO] Task started: Blastn
[2024-01-24 11:26:45,919] [INFO] Running command: blastn -query GCF_024621935.1_ASM2462193v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbaeab163-489c-4159-928b-67e2e548d90c/dqc_reference/reference_markers.fasta -out GCF_024621935.1_ASM2462193v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:46,955] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:46,967] [INFO] Selected 14 target genomes.
[2024-01-24 11:26:46,968] [INFO] Target genome list was writen to GCF_024621935.1_ASM2462193v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:46,974] [INFO] Task started: fastANI
[2024-01-24 11:26:46,974] [INFO] Running command: fastANI --query /var/lib/cwl/stg0f5a3f93-199e-414c-bd89-5b49fc0f36c3/GCF_024621935.1_ASM2462193v1_genomic.fna.gz --refList GCF_024621935.1_ASM2462193v1_genomic.fna/target_genomes.txt --output GCF_024621935.1_ASM2462193v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:06,405] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:06,405] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbaeab163-489c-4159-928b-67e2e548d90c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:06,405] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbaeab163-489c-4159-928b-67e2e548d90c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:06,417] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:27:06,417] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:27:06,418] [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 pavanii	strain=LMG 25348	GCA_900101175.1	487698	487698	type	True	93.7944	1289	1561	95	below_threshold
Stenotrophomonas pavanii	strain=DSM 25135	GCA_001431565.1	487698	487698	type	True	93.7429	1245	1561	95	below_threshold
Stenotrophomonas sepilia	strain=SM16975	GCA_003244875.1	2860290	2860290	type	True	93.1056	1253	1561	95	below_threshold
Stenotrophomonas maltophilia	strain=NCTC10257	GCA_900186865.1	40324	40324	type	True	92.4722	1337	1561	95	below_threshold
[Pseudomonas] hibiscicola	strain=ATCC 19867	GCA_000382065.1	86189	86189	type	True	92.4718	1262	1561	95	below_threshold
Stenotrophomonas maltophilia	strain=ATCC 13637	GCA_001997185.1	40324	40324	type	True	92.4658	1270	1561	95	below_threshold
Stenotrophomonas maltophilia	strain=NBRC 14161	GCA_001591205.1	40324	40324	type	True	92.3964	1276	1561	95	below_threshold
Stenotrophomonas maltophilia	strain=MTCC 434	GCA_000597745.1	40324	40324	type	True	92.3541	1197	1561	95	below_threshold
Stenotrophomonas lactitubi	strain=M15	GCA_002803515.1	2045214	2045214	type	True	88.6461	1273	1561	95	below_threshold
Stenotrophomonas pennii	strain=Sa5BUN4	GCA_014836545.1	2762239	2762239	type	True	84.7121	910	1561	95	below_threshold
Stenotrophomonas acidaminiphila	strain=DSM 13117	GCA_024221815.1	128780	128780	type	True	84.232	841	1561	95	below_threshold
Stenotrophomonas pictorum	strain=JCM 9942	GCA_001310775.1	86184	86184	type	True	83.5744	504	1561	95	below_threshold
Xanthomonas indica	strain=PPL560	GCA_022669045.1	2912242	2912242	type	True	82.7064	863	1561	95	below_threshold
Xanthomonas translucens	strain=ATCC 19319	GCA_020880735.1	343	343	type	True	82.5325	681	1561	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:06,419] [INFO] DFAST Taxonomy check result was written to GCF_024621935.1_ASM2462193v1_genomic.fna/tc_result.tsv
[2024-01-24 11:27:06,420] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:06,420] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:06,420] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbaeab163-489c-4159-928b-67e2e548d90c/dqc_reference/checkm_data
[2024-01-24 11:27:06,421] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:06,469] [INFO] Task started: CheckM
[2024-01-24 11:27:06,469] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024621935.1_ASM2462193v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024621935.1_ASM2462193v1_genomic.fna/checkm_input GCF_024621935.1_ASM2462193v1_genomic.fna/checkm_result
[2024-01-24 11:28:05,443] [INFO] Task succeeded: CheckM
[2024-01-24 11:28:05,444] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:28:05,466] [INFO] ===== Completeness check finished =====
[2024-01-24 11:28:05,466] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:28:05,467] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024621935.1_ASM2462193v1_genomic.fna/markers.fasta)
[2024-01-24 11:28:05,467] [INFO] Task started: Blastn
[2024-01-24 11:28:05,467] [INFO] Running command: blastn -query GCF_024621935.1_ASM2462193v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbaeab163-489c-4159-928b-67e2e548d90c/dqc_reference/reference_markers_gtdb.fasta -out GCF_024621935.1_ASM2462193v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:28:07,451] [INFO] Task succeeded: Blastn
[2024-01-24 11:28:07,456] [INFO] Selected 14 target genomes.
[2024-01-24 11:28:07,456] [INFO] Target genome list was writen to GCF_024621935.1_ASM2462193v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:28:07,468] [INFO] Task started: fastANI
[2024-01-24 11:28:07,468] [INFO] Running command: fastANI --query /var/lib/cwl/stg0f5a3f93-199e-414c-bd89-5b49fc0f36c3/GCF_024621935.1_ASM2462193v1_genomic.fna.gz --refList GCF_024621935.1_ASM2462193v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024621935.1_ASM2462193v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:28:28,099] [INFO] Task succeeded: fastANI
[2024-01-24 11:28:28,116] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:28:28,116] [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_000284595.1	s__Stenotrophomonas maltophilia_F	98.5841	1402	1561	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	98.76	98.38	0.92	0.88	60	conclusive
GCF_002192255.1	s__Stenotrophomonas sp002192255	94.0503	1333	1561	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	95.64	95.45	0.89	0.84	9	-
GCF_006970445.1	s__Stenotrophomonas maltophilia_AU	94.0131	1319	1561	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101175.1	s__Stenotrophomonas pavanii	93.7944	1289	1561	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	98.59	98.08	0.91	0.84	20	-
GCF_002799155.1	s__Stenotrophomonas maltophilia_R	93.5117	1288	1561	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002799245.1	s__Stenotrophomonas maltophilia_S	93.2817	1321	1561	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	92.4722	1337	1561	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	97.99	97.31	0.92	0.87	234	-
GCF_003205835.1	s__Stenotrophomonas maltophilia_AL	92.4371	1299	1561	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	98.59	98.33	0.89	0.86	7	-
GCF_002138415.1	s__Stenotrophomonas maltophilia_G	92.3859	1292	1561	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	95.93	95.59	0.89	0.87	14	-
GCF_004346925.1	s__Stenotrophomonas maltophilia_A	92.3112	1269	1561	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	97.29	95.44	0.89	0.84	41	-
GCF_006974125.1	s__Stenotrophomonas maltophilia_O	92.0098	1272	1561	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	98.85	98.84	0.92	0.90	5	-
GCF_002799165.1	s__Stenotrophomonas maltophilia_Q	91.6913	1327	1561	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	91.5879	1237	1561	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	99.65	98.65	0.97	0.93	5	-
GCF_003028475.1	s__Stenotrophomonas sp003028475	90.9562	1240	1561	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	98.27	96.55	0.95	0.90	3	-
--------------------------------------------------------------------------------
[2024-01-24 11:28:28,118] [INFO] GTDB search result was written to GCF_024621935.1_ASM2462193v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:28:28,118] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:28:28,122] [INFO] DFAST_QC result json was written to GCF_024621935.1_ASM2462193v1_genomic.fna/dqc_result.json
[2024-01-24 11:28:28,122] [INFO] DFAST_QC completed!
[2024-01-24 11:28:28,122] [INFO] Total running time: 0h2m0s