[2024-01-25 19:51:35,689] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:51:35,690] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:51:35,691] [INFO] DQC Reference Directory: /var/lib/cwl/stg5afea4ee-fb2d-421b-b2c5-e375b629f587/dqc_reference
[2024-01-25 19:51:36,880] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:51:36,881] [INFO] Task started: Prodigal
[2024-01-25 19:51:36,881] [INFO] Running command: gunzip -c /var/lib/cwl/stgc53eef03-6753-4200-8bcc-7b6456f92885/GCF_003244875.1_ASM324487v1_genomic.fna.gz | prodigal -d GCF_003244875.1_ASM324487v1_genomic.fna/cds.fna -a GCF_003244875.1_ASM324487v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:51:50,740] [INFO] Task succeeded: Prodigal
[2024-01-25 19:51:50,740] [INFO] Task started: HMMsearch
[2024-01-25 19:51:50,740] [INFO] Running command: hmmsearch --tblout GCF_003244875.1_ASM324487v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5afea4ee-fb2d-421b-b2c5-e375b629f587/dqc_reference/reference_markers.hmm GCF_003244875.1_ASM324487v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:51:51,057] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:51:51,058] [INFO] Found 6/6 markers.
[2024-01-25 19:51:51,099] [INFO] Query marker FASTA was written to GCF_003244875.1_ASM324487v1_genomic.fna/markers.fasta
[2024-01-25 19:51:51,100] [INFO] Task started: Blastn
[2024-01-25 19:51:51,100] [INFO] Running command: blastn -query GCF_003244875.1_ASM324487v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5afea4ee-fb2d-421b-b2c5-e375b629f587/dqc_reference/reference_markers.fasta -out GCF_003244875.1_ASM324487v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:51:52,095] [INFO] Task succeeded: Blastn
[2024-01-25 19:51:52,098] [INFO] Selected 13 target genomes.
[2024-01-25 19:51:52,098] [INFO] Target genome list was writen to GCF_003244875.1_ASM324487v1_genomic.fna/target_genomes.txt
[2024-01-25 19:51:52,106] [INFO] Task started: fastANI
[2024-01-25 19:51:52,107] [INFO] Running command: fastANI --query /var/lib/cwl/stgc53eef03-6753-4200-8bcc-7b6456f92885/GCF_003244875.1_ASM324487v1_genomic.fna.gz --refList GCF_003244875.1_ASM324487v1_genomic.fna/target_genomes.txt --output GCF_003244875.1_ASM324487v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:52:06,705] [INFO] Task succeeded: fastANI
[2024-01-25 19:52:06,706] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5afea4ee-fb2d-421b-b2c5-e375b629f587/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:52:06,706] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5afea4ee-fb2d-421b-b2c5-e375b629f587/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:52:06,715] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:52:06,715] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:52:06,715] [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 sepilia	strain=SM16975	GCA_003244875.1	2860290	2860290	type	True	100.0	1466	1471	95	conclusive
[Pseudomonas] hibiscicola	strain=ATCC 19867	GCA_000382065.1	86189	86189	type	True	92.7836	1232	1471	95	below_threshold
Stenotrophomonas pavanii	strain=LMG 25348	GCA_900101175.1	487698	487698	type	True	92.7097	1248	1471	95	below_threshold
Stenotrophomonas pavanii	strain=DSM 25135	GCA_001431565.1	487698	487698	type	True	92.6948	1198	1471	95	below_threshold
Stenotrophomonas maltophilia	strain=NCTC10257	GCA_900186865.1	40324	40324	type	True	91.9602	1297	1471	95	below_threshold
Stenotrophomonas maltophilia	strain=ATCC 13637	GCA_001997185.1	40324	40324	type	True	91.9343	1241	1471	95	below_threshold
Stenotrophomonas maltophilia	strain=NBRC 14161	GCA_001591205.1	40324	40324	type	True	91.9307	1235	1471	95	below_threshold
Stenotrophomonas maltophilia	strain=MTCC 434	GCA_000597745.1	40324	40324	type	True	91.8292	1185	1471	95	below_threshold
Stenotrophomonas pennii	strain=Sa5BUN4	GCA_014836545.1	2762239	2762239	type	True	84.3565	885	1471	95	below_threshold
Stenotrophomonas acidaminiphila	strain=DSM 13117	GCA_024221815.1	128780	128780	type	True	83.6482	779	1471	95	below_threshold
Stenotrophomonas pictorum	strain=JCM 9942	GCA_001310775.1	86184	86184	type	True	83.1146	483	1471	95	below_threshold
Xanthomonas indica	strain=PPL560	GCA_022669045.1	2912242	2912242	type	True	82.5947	825	1471	95	below_threshold
Xanthomonas translucens	strain=ATCC 19319	GCA_020880735.1	343	343	type	True	82.3521	663	1471	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:52:06,717] [INFO] DFAST Taxonomy check result was written to GCF_003244875.1_ASM324487v1_genomic.fna/tc_result.tsv
[2024-01-25 19:52:06,717] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:52:06,717] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:52:06,718] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5afea4ee-fb2d-421b-b2c5-e375b629f587/dqc_reference/checkm_data
[2024-01-25 19:52:06,718] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:52:06,767] [INFO] Task started: CheckM
[2024-01-25 19:52:06,767] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003244875.1_ASM324487v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003244875.1_ASM324487v1_genomic.fna/checkm_input GCF_003244875.1_ASM324487v1_genomic.fna/checkm_result
[2024-01-25 19:53:04,475] [INFO] Task succeeded: CheckM
[2024-01-25 19:53:04,476] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:53:04,505] [INFO] ===== Completeness check finished =====
[2024-01-25 19:53:04,506] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:53:04,506] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003244875.1_ASM324487v1_genomic.fna/markers.fasta)
[2024-01-25 19:53:04,506] [INFO] Task started: Blastn
[2024-01-25 19:53:04,506] [INFO] Running command: blastn -query GCF_003244875.1_ASM324487v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5afea4ee-fb2d-421b-b2c5-e375b629f587/dqc_reference/reference_markers_gtdb.fasta -out GCF_003244875.1_ASM324487v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:53:06,382] [INFO] Task succeeded: Blastn
[2024-01-25 19:53:06,385] [INFO] Selected 16 target genomes.
[2024-01-25 19:53:06,385] [INFO] Target genome list was writen to GCF_003244875.1_ASM324487v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:53:06,424] [INFO] Task started: fastANI
[2024-01-25 19:53:06,424] [INFO] Running command: fastANI --query /var/lib/cwl/stgc53eef03-6753-4200-8bcc-7b6456f92885/GCF_003244875.1_ASM324487v1_genomic.fna.gz --refList GCF_003244875.1_ASM324487v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003244875.1_ASM324487v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:53:26,996] [INFO] Task succeeded: fastANI
[2024-01-25 19:53:27,006] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:53:27,006] [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
GCA_014171555.1	s__Stenotrophomonas maltophilia_AK	96.1137	1268	1471	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	97.10	95.71	0.92	0.85	90	conclusive
GCF_000284595.1	s__Stenotrophomonas maltophilia_F	93.2692	1275	1471	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	98.76	98.38	0.92	0.88	60	-
GCF_006970445.1	s__Stenotrophomonas maltophilia_AU	93.2388	1228	1471	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	92.816	1237	1471	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	95.64	95.45	0.89	0.84	9	-
GCF_000382065.1	s__Stenotrophomonas maltophilia_B	92.7885	1231	1471	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	97.83	97.17	0.91	0.87	24	-
GCF_002799245.1	s__Stenotrophomonas maltophilia_S	92.7845	1202	1471	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	92.7097	1248	1471	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	92.4163	1241	1471	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001431625.1	s__Stenotrophomonas geniculata	92.013	1205	1471	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	91.984	1295	1471	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	91.803	1273	1471	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	97.69	95.30	0.93	0.83	9	-
GCF_002138415.1	s__Stenotrophomonas maltophilia_G	91.7402	1226	1471	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	91.7354	1217	1471	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	91.6661	1191	1471	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	98.85	98.84	0.92	0.90	5	-
GCF_013464915.1	s__Stenotrophomonas maltophilia_AT	91.3255	1194	1471	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	90.8041	1167	1471	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	98.27	96.55	0.95	0.90	3	-
--------------------------------------------------------------------------------
[2024-01-25 19:53:27,008] [INFO] GTDB search result was written to GCF_003244875.1_ASM324487v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:53:27,008] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:53:27,012] [INFO] DFAST_QC result json was written to GCF_003244875.1_ASM324487v1_genomic.fna/dqc_result.json
[2024-01-25 19:53:27,013] [INFO] DFAST_QC completed!
[2024-01-25 19:53:27,013] [INFO] Total running time: 0h1m51s