[2023-03-15 10:49:28,605] [INFO] DFAST_QC pipeline started.
[2023-03-15 10:49:28,606] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 10:49:28,606] [INFO] DQC Reference Directory: /var/lib/cwl/stg2fcd0f59-7a66-4d0c-a2a7-ed0592ef3014/dqc_reference
[2023-03-15 10:49:29,728] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 10:49:29,729] [INFO] Task started: Prodigal
[2023-03-15 10:49:29,729] [INFO] Running command: cat /var/lib/cwl/stga3960876-b350-427c-973d-008e4651c6f4/OceanDNA-b44698.fa | prodigal -d OceanDNA-b44698/cds.fna -a OceanDNA-b44698/protein.faa -g 11 -q > /dev/null
[2023-03-15 10:49:58,509] [INFO] Task succeeded: Prodigal
[2023-03-15 10:49:58,509] [INFO] Task started: HMMsearch
[2023-03-15 10:49:58,509] [INFO] Running command: hmmsearch --tblout OceanDNA-b44698/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2fcd0f59-7a66-4d0c-a2a7-ed0592ef3014/dqc_reference/reference_markers.hmm OceanDNA-b44698/protein.faa > /dev/null
[2023-03-15 10:49:58,827] [INFO] Task succeeded: HMMsearch
[2023-03-15 10:49:58,827] [INFO] Found 6/6 markers.
[2023-03-15 10:49:58,855] [INFO] Query marker FASTA was written to OceanDNA-b44698/markers.fasta
[2023-03-15 10:49:58,856] [INFO] Task started: Blastn
[2023-03-15 10:49:58,856] [INFO] Running command: blastn -query OceanDNA-b44698/markers.fasta -db /var/lib/cwl/stg2fcd0f59-7a66-4d0c-a2a7-ed0592ef3014/dqc_reference/reference_markers.fasta -out OceanDNA-b44698/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:49:59,798] [INFO] Task succeeded: Blastn
[2023-03-15 10:49:59,800] [INFO] Selected 14 target genomes.
[2023-03-15 10:49:59,800] [INFO] Target genome list was writen to OceanDNA-b44698/target_genomes.txt
[2023-03-15 10:49:59,810] [INFO] Task started: fastANI
[2023-03-15 10:49:59,810] [INFO] Running command: fastANI --query /var/lib/cwl/stga3960876-b350-427c-973d-008e4651c6f4/OceanDNA-b44698.fa --refList OceanDNA-b44698/target_genomes.txt --output OceanDNA-b44698/fastani_result.tsv --threads 1
[2023-03-15 10:50:16,745] [INFO] Task succeeded: fastANI
[2023-03-15 10:50:16,745] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2fcd0f59-7a66-4d0c-a2a7-ed0592ef3014/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 10:50:16,745] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2fcd0f59-7a66-4d0c-a2a7-ed0592ef3014/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 10:50:16,755] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 10:50:16,755] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 10:50:16,755] [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	93.7394	1244	1448	95	below_threshold
Stenotrophomonas pavanii	strain=DSM 25135	GCA_001431565.1	487698	487698	type	True	93.7025	1207	1448	95	below_threshold
Stenotrophomonas sepilia	strain=SM16975	GCA_003244875.1	2860290	2860290	type	True	93.1164	1192	1448	95	below_threshold
Stenotrophomonas maltophilia	strain=NCTC10257	GCA_900186865.1	40324	40324	type	True	92.4301	1269	1448	95	below_threshold
Stenotrophomonas maltophilia	strain=ATCC 13637	GCA_001997185.1	40324	40324	type	True	92.3916	1216	1448	95	below_threshold
[Pseudomonas] hibiscicola	strain=ATCC 19867	GCA_000382065.1	86189	86189	type	True	92.3905	1225	1448	95	below_threshold
Stenotrophomonas maltophilia	strain=NBRC 14161	GCA_001591205.1	40324	40324	type	True	92.3895	1210	1448	95	below_threshold
Stenotrophomonas maltophilia	strain=MTCC 434	GCA_000597745.1	40324	40324	type	True	92.2689	1149	1448	95	below_threshold
Stenotrophomonas lactitubi	strain=M15	GCA_002803515.1	2045214	2045214	type	True	88.4788	1188	1448	95	below_threshold
Stenotrophomonas pennii	strain=Sa5BUN4	GCA_014836545.1	2762239	2762239	type	True	84.5484	878	1448	95	below_threshold
Stenotrophomonas acidaminiphila	strain=DSM 13117	GCA_024221815.1	128780	128780	type	True	83.7925	775	1448	95	below_threshold
Stenotrophomonas pictorum	strain=JCM 9942	GCA_001310775.1	86184	86184	type	True	83.1202	482	1448	95	below_threshold
Xanthomonas indica	strain=PPL560	GCA_022669045.1	2912242	2912242	type	True	82.5855	837	1448	95	below_threshold
Xanthomonas translucens	strain=ATCC 19319	GCA_020880735.1	343	343	type	True	82.2064	680	1448	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 10:50:16,756] [INFO] DFAST Taxonomy check result was written to OceanDNA-b44698/tc_result.tsv
[2023-03-15 10:50:16,756] [INFO] ===== Taxonomy check completed =====
[2023-03-15 10:50:16,756] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 10:50:16,756] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2fcd0f59-7a66-4d0c-a2a7-ed0592ef3014/dqc_reference/checkm_data
[2023-03-15 10:50:16,757] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 10:50:16,764] [INFO] Task started: CheckM
[2023-03-15 10:50:16,764] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b44698/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b44698/checkm_input OceanDNA-b44698/checkm_result
[2023-03-15 10:51:34,475] [INFO] Task succeeded: CheckM
[2023-03-15 10:51:34,475] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 71.35%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 10:51:34,479] [INFO] ===== Completeness check finished =====
[2023-03-15 10:51:34,479] [INFO] ===== Start GTDB Search =====
[2023-03-15 10:51:34,479] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b44698/markers.fasta)
[2023-03-15 10:51:34,480] [INFO] Task started: Blastn
[2023-03-15 10:51:34,480] [INFO] Running command: blastn -query OceanDNA-b44698/markers.fasta -db /var/lib/cwl/stg2fcd0f59-7a66-4d0c-a2a7-ed0592ef3014/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b44698/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:51:36,283] [INFO] Task succeeded: Blastn
[2023-03-15 10:51:36,284] [INFO] Selected 14 target genomes.
[2023-03-15 10:51:36,284] [INFO] Target genome list was writen to OceanDNA-b44698/target_genomes_gtdb.txt
[2023-03-15 10:51:36,301] [INFO] Task started: fastANI
[2023-03-15 10:51:36,301] [INFO] Running command: fastANI --query /var/lib/cwl/stga3960876-b350-427c-973d-008e4651c6f4/OceanDNA-b44698.fa --refList OceanDNA-b44698/target_genomes_gtdb.txt --output OceanDNA-b44698/fastani_result_gtdb.tsv --threads 1
[2023-03-15 10:51:55,005] [INFO] Task succeeded: fastANI
[2023-03-15 10:51:55,014] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 10:51:55,014] [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	98.7908	1356	1448	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	93.9948	1282	1448	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	93.9234	1267	1448	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	93.7394	1244	1448	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	93.4854	1231	1448	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	93.2578	1256	1448	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	92.4363	1268	1448	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	97.99	97.31	0.92	0.87	234	-
GCF_002138415.1	s__Stenotrophomonas maltophilia_G	92.3128	1237	1448	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	92.195	1223	1448	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	91.9556	1217	1448	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	91.724	1228	1448	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	91.586	1182	1448	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	99.65	98.65	0.97	0.93	5	-
GCF_001274595.1	s__Stenotrophomonas maltophilia_AJ	91.5337	1208	1448	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	97.15	96.26	0.91	0.88	10	-
GCF_003028475.1	s__Stenotrophomonas sp003028475	90.9593	1180	1448	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 10:51:55,014] [INFO] GTDB search result was written to OceanDNA-b44698/result_gtdb.tsv
[2023-03-15 10:51:55,015] [INFO] ===== GTDB Search completed =====
[2023-03-15 10:51:55,016] [INFO] DFAST_QC result json was written to OceanDNA-b44698/dqc_result.json
[2023-03-15 10:51:55,017] [INFO] DFAST_QC completed!
[2023-03-15 10:51:55,017] [INFO] Total running time: 0h2m26s