[2023-03-15 08:09:45,436] [INFO] DFAST_QC pipeline started.
[2023-03-15 08:09:45,436] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 08:09:45,436] [INFO] DQC Reference Directory: /var/lib/cwl/stg48d4c5f0-1d87-44fe-ae8b-73372c44bb1f/dqc_reference
[2023-03-15 08:09:46,699] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 08:09:46,700] [INFO] Task started: Prodigal
[2023-03-15 08:09:46,700] [INFO] Running command: cat /var/lib/cwl/stg6f081203-e3aa-4af0-8684-69003b14c3fe/OceanDNA-b44694.fa | prodigal -d OceanDNA-b44694/cds.fna -a OceanDNA-b44694/protein.faa -g 11 -q > /dev/null
[2023-03-15 08:10:17,248] [INFO] Task succeeded: Prodigal
[2023-03-15 08:10:17,248] [INFO] Task started: HMMsearch
[2023-03-15 08:10:17,248] [INFO] Running command: hmmsearch --tblout OceanDNA-b44694/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg48d4c5f0-1d87-44fe-ae8b-73372c44bb1f/dqc_reference/reference_markers.hmm OceanDNA-b44694/protein.faa > /dev/null
[2023-03-15 08:10:17,513] [INFO] Task succeeded: HMMsearch
[2023-03-15 08:10:17,514] [INFO] Found 6/6 markers.
[2023-03-15 08:10:17,543] [INFO] Query marker FASTA was written to OceanDNA-b44694/markers.fasta
[2023-03-15 08:10:17,544] [INFO] Task started: Blastn
[2023-03-15 08:10:17,544] [INFO] Running command: blastn -query OceanDNA-b44694/markers.fasta -db /var/lib/cwl/stg48d4c5f0-1d87-44fe-ae8b-73372c44bb1f/dqc_reference/reference_markers.fasta -out OceanDNA-b44694/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:10:18,507] [INFO] Task succeeded: Blastn
[2023-03-15 08:10:18,508] [INFO] Selected 13 target genomes.
[2023-03-15 08:10:18,508] [INFO] Target genome list was writen to OceanDNA-b44694/target_genomes.txt
[2023-03-15 08:10:18,516] [INFO] Task started: fastANI
[2023-03-15 08:10:18,516] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f081203-e3aa-4af0-8684-69003b14c3fe/OceanDNA-b44694.fa --refList OceanDNA-b44694/target_genomes.txt --output OceanDNA-b44694/fastani_result.tsv --threads 1
[2023-03-15 08:10:33,770] [INFO] Task succeeded: fastANI
[2023-03-15 08:10:33,771] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg48d4c5f0-1d87-44fe-ae8b-73372c44bb1f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 08:10:33,771] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg48d4c5f0-1d87-44fe-ae8b-73372c44bb1f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 08:10:33,780] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 08:10:33,780] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 08:10:33,780] [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	91.2368	1205	1546	95	below_threshold
Stenotrophomonas maltophilia	strain=NCTC10257	GCA_900186865.1	40324	40324	type	True	91.236	1249	1546	95	below_threshold
Stenotrophomonas maltophilia	strain=ATCC 13637	GCA_001997185.1	40324	40324	type	True	91.2349	1203	1546	95	below_threshold
Stenotrophomonas maltophilia	strain=MTCC 434	GCA_000597745.1	40324	40324	type	True	91.116	1129	1546	95	below_threshold
Stenotrophomonas pavanii	strain=DSM 25135	GCA_001431565.1	487698	487698	type	True	90.9003	1125	1546	95	below_threshold
Stenotrophomonas sepilia	strain=SM16975	GCA_003244875.1	2860290	2860290	type	True	90.8739	1154	1546	95	below_threshold
[Pseudomonas] hibiscicola	strain=ATCC 19867	GCA_000382065.1	86189	86189	type	True	90.862	1192	1546	95	below_threshold
Stenotrophomonas pavanii	strain=LMG 25348	GCA_900101175.1	487698	487698	type	True	90.8344	1196	1546	95	below_threshold
Stenotrophomonas pennii	strain=Sa5BUN4	GCA_014836545.1	2762239	2762239	type	True	84.5373	864	1546	95	below_threshold
Stenotrophomonas acidaminiphila	strain=DSM 13117	GCA_024221815.1	128780	128780	type	True	83.7238	790	1546	95	below_threshold
Stenotrophomonas pictorum	strain=JCM 9942	GCA_001310775.1	86184	86184	type	True	83.134	485	1546	95	below_threshold
Xanthomonas indica	strain=PPL560	GCA_022669045.1	2912242	2912242	type	True	82.5356	819	1546	95	below_threshold
Xanthomonas translucens	strain=ATCC 19319	GCA_020880735.1	343	343	type	True	82.4489	669	1546	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 08:10:33,780] [INFO] DFAST Taxonomy check result was written to OceanDNA-b44694/tc_result.tsv
[2023-03-15 08:10:33,780] [INFO] ===== Taxonomy check completed =====
[2023-03-15 08:10:33,780] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 08:10:33,781] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg48d4c5f0-1d87-44fe-ae8b-73372c44bb1f/dqc_reference/checkm_data
[2023-03-15 08:10:33,781] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 08:10:33,788] [INFO] Task started: CheckM
[2023-03-15 08:10:33,788] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b44694/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b44694/checkm_input OceanDNA-b44694/checkm_result
[2023-03-15 08:12:02,105] [INFO] Task succeeded: CheckM
[2023-03-15 08:12:02,106] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 08:12:02,109] [INFO] ===== Completeness check finished =====
[2023-03-15 08:12:02,109] [INFO] ===== Start GTDB Search =====
[2023-03-15 08:12:02,109] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b44694/markers.fasta)
[2023-03-15 08:12:02,110] [INFO] Task started: Blastn
[2023-03-15 08:12:02,110] [INFO] Running command: blastn -query OceanDNA-b44694/markers.fasta -db /var/lib/cwl/stg48d4c5f0-1d87-44fe-ae8b-73372c44bb1f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b44694/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:12:03,907] [INFO] Task succeeded: Blastn
[2023-03-15 08:12:03,907] [INFO] Selected 15 target genomes.
[2023-03-15 08:12:03,908] [INFO] Target genome list was writen to OceanDNA-b44694/target_genomes_gtdb.txt
[2023-03-15 08:12:03,914] [INFO] Task started: fastANI
[2023-03-15 08:12:03,914] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f081203-e3aa-4af0-8684-69003b14c3fe/OceanDNA-b44694.fa --refList OceanDNA-b44694/target_genomes_gtdb.txt --output OceanDNA-b44694/fastani_result_gtdb.tsv --threads 1
[2023-03-15 08:12:24,094] [INFO] Task succeeded: fastANI
[2023-03-15 08:12:24,103] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 08:12:24,104] [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_001274595.1	s__Stenotrophomonas maltophilia_AJ	96.226	1334	1546	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	97.15	96.26	0.91	0.88	10	conclusive
GCF_003205835.1	s__Stenotrophomonas maltophilia_AL	91.681	1263	1546	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	98.59	98.33	0.89	0.86	7	-
GCF_002192255.1	s__Stenotrophomonas sp002192255	91.6313	1210	1546	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	95.64	95.45	0.89	0.84	9	-
GCF_013464915.1	s__Stenotrophomonas maltophilia_AT	91.5013	1200	1546	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	99.65	98.65	0.97	0.93	5	-
GCF_003970865.1	s__Stenotrophomonas maltophilia_AR	91.4271	1179	1546	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	91.4138	1242	1546	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	95.93	95.59	0.89	0.87	14	-
GCF_002799245.1	s__Stenotrophomonas maltophilia_S	91.4003	1225	1546	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004346925.1	s__Stenotrophomonas maltophilia_A	91.3931	1230	1546	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	97.29	95.44	0.89	0.84	41	-
GCF_006970445.1	s__Stenotrophomonas maltophilia_AU	91.366	1235	1546	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002799155.1	s__Stenotrophomonas maltophilia_R	91.3357	1216	1546	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	91.2438	1249	1546	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	97.99	97.31	0.92	0.87	234	-
GCF_002799165.1	s__Stenotrophomonas maltophilia_Q	91.2152	1235	1546	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	97.69	95.30	0.93	0.83	9	-
GCA_001431625.1	s__Stenotrophomonas geniculata	91.0272	1191	1546	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	97.51	96.26	0.87	0.77	45	-
GCF_013464485.1	s__Stenotrophomonas maltophilia_AW	90.9216	1225	1546	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	90.8444	1219	1546	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	98.27	96.55	0.95	0.90	3	-
--------------------------------------------------------------------------------
[2023-03-15 08:12:24,104] [INFO] GTDB search result was written to OceanDNA-b44694/result_gtdb.tsv
[2023-03-15 08:12:24,104] [INFO] ===== GTDB Search completed =====
[2023-03-15 08:12:24,106] [INFO] DFAST_QC result json was written to OceanDNA-b44694/dqc_result.json
[2023-03-15 08:12:24,106] [INFO] DFAST_QC completed!
[2023-03-15 08:12:24,106] [INFO] Total running time: 0h2m39s