[2024-01-24 11:22:49,119] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:22:49,121] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:22:49,121] [INFO] DQC Reference Directory: /var/lib/cwl/stgfcaa7746-a651-4a92-956b-009138086463/dqc_reference
[2024-01-24 11:22:50,310] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:22:50,311] [INFO] Task started: Prodigal
[2024-01-24 11:22:50,311] [INFO] Running command: gunzip -c /var/lib/cwl/stg3f7f82b7-f521-468d-b488-0eaf62bbbf9c/GCF_014836545.1_ASM1483654v1_genomic.fna.gz | prodigal -d GCF_014836545.1_ASM1483654v1_genomic.fna/cds.fna -a GCF_014836545.1_ASM1483654v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:23:03,194] [INFO] Task succeeded: Prodigal
[2024-01-24 11:23:03,195] [INFO] Task started: HMMsearch
[2024-01-24 11:23:03,195] [INFO] Running command: hmmsearch --tblout GCF_014836545.1_ASM1483654v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfcaa7746-a651-4a92-956b-009138086463/dqc_reference/reference_markers.hmm GCF_014836545.1_ASM1483654v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:23:03,446] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:23:03,447] [INFO] Found 6/6 markers.
[2024-01-24 11:23:03,495] [INFO] Query marker FASTA was written to GCF_014836545.1_ASM1483654v1_genomic.fna/markers.fasta
[2024-01-24 11:23:03,495] [INFO] Task started: Blastn
[2024-01-24 11:23:03,496] [INFO] Running command: blastn -query GCF_014836545.1_ASM1483654v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfcaa7746-a651-4a92-956b-009138086463/dqc_reference/reference_markers.fasta -out GCF_014836545.1_ASM1483654v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:23:04,465] [INFO] Task succeeded: Blastn
[2024-01-24 11:23:04,468] [INFO] Selected 15 target genomes.
[2024-01-24 11:23:04,468] [INFO] Target genome list was writen to GCF_014836545.1_ASM1483654v1_genomic.fna/target_genomes.txt
[2024-01-24 11:23:04,474] [INFO] Task started: fastANI
[2024-01-24 11:23:04,475] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f7f82b7-f521-468d-b488-0eaf62bbbf9c/GCF_014836545.1_ASM1483654v1_genomic.fna.gz --refList GCF_014836545.1_ASM1483654v1_genomic.fna/target_genomes.txt --output GCF_014836545.1_ASM1483654v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:23:19,931] [INFO] Task succeeded: fastANI
[2024-01-24 11:23:19,931] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfcaa7746-a651-4a92-956b-009138086463/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:23:19,931] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfcaa7746-a651-4a92-956b-009138086463/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:23:19,945] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:23:19,946] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:23:19,946] [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 pennii	strain=Sa5BUN4	GCA_014836545.1	2762239	2762239	type	True	100.0	1291	1292	95	conclusive
Stenotrophomonas chelatiphaga	strain=DSM 21508	GCA_001431535.1	517011	517011	type	True	92.2781	1083	1292	95	below_threshold
Stenotrophomonas tumulicola	strain=JCM 30961	GCA_014117215.1	1685415	1685415	type	True	85.9186	939	1292	95	below_threshold
Stenotrophomonas pavanii	strain=LMG 25348	GCA_900101175.1	487698	487698	type	True	84.8883	928	1292	95	below_threshold
Stenotrophomonas pavanii	strain=DSM 25135	GCA_001431565.1	487698	487698	type	True	84.8459	906	1292	95	below_threshold
Stenotrophomonas indicatrix	strain=WS40	GCA_002750975.1	2045451	2045451	type	True	84.8244	956	1292	95	below_threshold
Stenotrophomonas maltophilia	strain=NBRC 14161	GCA_001591205.1	40324	40324	type	True	84.7542	892	1292	95	below_threshold
Stenotrophomonas maltophilia	strain=MTCC 434	GCA_000597745.1	40324	40324	type	True	84.7206	855	1292	95	below_threshold
Stenotrophomonas lactitubi	strain=M15	GCA_002803515.1	2045214	2045214	type	True	84.7066	932	1292	95	below_threshold
Stenotrophomonas rhizophila	strain=DSM14405	GCA_000661955.1	216778	216778	suspected-type	True	84.2998	958	1292	95	below_threshold
Stenotrophomonas bentonitica	strain=DSM 103927	GCA_013185915.1	1450134	1450134	type	True	84.1669	907	1292	95	below_threshold
Stenotrophomonas acidaminiphila	strain=DSM 13117	GCA_024221815.1	128780	128780	type	True	82.7079	748	1292	95	below_threshold
Xanthomonas indica	strain=PPL560	GCA_022669045.1	2912242	2912242	type	True	82.0525	787	1292	95	below_threshold
Xanthomonas translucens	strain=ATCC 19319	GCA_020880735.1	343	343	type	True	81.6855	647	1292	95	below_threshold
Xanthomonas citri	strain=ICMP5732	GCA_021474205.1	346	346	pathovar	True	80.4547	701	1292	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:23:19,948] [INFO] DFAST Taxonomy check result was written to GCF_014836545.1_ASM1483654v1_genomic.fna/tc_result.tsv
[2024-01-24 11:23:19,948] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:23:19,948] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:23:19,949] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfcaa7746-a651-4a92-956b-009138086463/dqc_reference/checkm_data
[2024-01-24 11:23:19,950] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:23:19,988] [INFO] Task started: CheckM
[2024-01-24 11:23:19,988] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014836545.1_ASM1483654v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014836545.1_ASM1483654v1_genomic.fna/checkm_input GCF_014836545.1_ASM1483654v1_genomic.fna/checkm_result
[2024-01-24 11:24:04,271] [INFO] Task succeeded: CheckM
[2024-01-24 11:24:04,272] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:24:04,293] [INFO] ===== Completeness check finished =====
[2024-01-24 11:24:04,293] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:24:04,294] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014836545.1_ASM1483654v1_genomic.fna/markers.fasta)
[2024-01-24 11:24:04,294] [INFO] Task started: Blastn
[2024-01-24 11:24:04,294] [INFO] Running command: blastn -query GCF_014836545.1_ASM1483654v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfcaa7746-a651-4a92-956b-009138086463/dqc_reference/reference_markers_gtdb.fasta -out GCF_014836545.1_ASM1483654v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:24:06,168] [INFO] Task succeeded: Blastn
[2024-01-24 11:24:06,172] [INFO] Selected 15 target genomes.
[2024-01-24 11:24:06,172] [INFO] Target genome list was writen to GCF_014836545.1_ASM1483654v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:24:06,211] [INFO] Task started: fastANI
[2024-01-24 11:24:06,212] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f7f82b7-f521-468d-b488-0eaf62bbbf9c/GCF_014836545.1_ASM1483654v1_genomic.fna.gz --refList GCF_014836545.1_ASM1483654v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014836545.1_ASM1483654v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:24:21,640] [INFO] Task succeeded: fastANI
[2024-01-24 11:24:21,657] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:24:21,657] [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_002836635.1	s__Stenotrophomonas sp002836635	97.2413	1138	1292	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	97.91	95.43	0.91	0.85	8	conclusive
GCF_001431535.1	s__Stenotrophomonas chelatiphaga	92.2781	1083	1292	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	99.00	99.00	0.96	0.96	2	-
GCF_014621775.1	s__Stenotrophomonas sp014621775	86.555	1048	1292	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	97.53	97.52	0.92	0.91	3	-
GCF_014117215.1	s__Stenotrophomonas tumulicola	85.9155	940	1292	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003086775.1	s__Stenotrophomonas sp003086775	85.1868	968	1292	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	98.05	97.07	0.94	0.87	8	-
GCF_003028475.1	s__Stenotrophomonas sp003028475	84.9283	932	1292	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	98.27	96.55	0.95	0.90	3	-
GCF_001274595.1	s__Stenotrophomonas maltophilia_AJ	84.9015	916	1292	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	97.15	96.26	0.91	0.88	10	-
GCF_006974125.1	s__Stenotrophomonas maltophilia_O	84.7559	918	1292	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	98.85	98.84	0.92	0.90	5	-
GCA_009912235.1	s__Stenotrophomonas maltophilia_AV	84.7407	819	1292	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	84.6267	937	1292	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	95.93	95.59	0.89	0.87	14	-
GCF_011761925.1	s__Stenotrophomonas sp011761925	84.4236	901	1292	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013387485.1	s__Stenotrophomonas maltophilia_AA	84.0937	923	1292	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	97.19	96.54	0.90	0.89	3	-
GCF_018612915.1	s__Stenotrophomonas sp018612915	83.9975	667	1292	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003751305.1	s__Stenotrophomonas rhizophila_B	83.9401	916	1292	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002387845.1	s__Stenotrophomonas maltophilia_AG	83.5394	831	1292	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:24:21,659] [INFO] GTDB search result was written to GCF_014836545.1_ASM1483654v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:24:21,659] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:24:21,663] [INFO] DFAST_QC result json was written to GCF_014836545.1_ASM1483654v1_genomic.fna/dqc_result.json
[2024-01-24 11:24:21,663] [INFO] DFAST_QC completed!
[2024-01-24 11:24:21,663] [INFO] Total running time: 0h1m33s