[2024-01-24 13:35:27,492] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:35:27,494] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:35:27,495] [INFO] DQC Reference Directory: /var/lib/cwl/stgc76bc445-bd6c-4525-a45b-975d3eec0eb7/dqc_reference
[2024-01-24 13:35:28,703] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:35:28,704] [INFO] Task started: Prodigal
[2024-01-24 13:35:28,704] [INFO] Running command: gunzip -c /var/lib/cwl/stg5322d925-1b98-49e9-be4e-a9f8347fa584/GCF_001642575.1_Xfloridensis_v1.0_genomic.fna.gz | prodigal -d GCF_001642575.1_Xfloridensis_v1.0_genomic.fna/cds.fna -a GCF_001642575.1_Xfloridensis_v1.0_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:35:48,108] [INFO] Task succeeded: Prodigal
[2024-01-24 13:35:48,109] [INFO] Task started: HMMsearch
[2024-01-24 13:35:48,109] [INFO] Running command: hmmsearch --tblout GCF_001642575.1_Xfloridensis_v1.0_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc76bc445-bd6c-4525-a45b-975d3eec0eb7/dqc_reference/reference_markers.hmm GCF_001642575.1_Xfloridensis_v1.0_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:35:48,392] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:35:48,394] [INFO] Found 6/6 markers.
[2024-01-24 13:35:48,435] [INFO] Query marker FASTA was written to GCF_001642575.1_Xfloridensis_v1.0_genomic.fna/markers.fasta
[2024-01-24 13:35:48,435] [INFO] Task started: Blastn
[2024-01-24 13:35:48,435] [INFO] Running command: blastn -query GCF_001642575.1_Xfloridensis_v1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stgc76bc445-bd6c-4525-a45b-975d3eec0eb7/dqc_reference/reference_markers.fasta -out GCF_001642575.1_Xfloridensis_v1.0_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:35:49,309] [INFO] Task succeeded: Blastn
[2024-01-24 13:35:49,313] [INFO] Selected 23 target genomes.
[2024-01-24 13:35:49,314] [INFO] Target genome list was writen to GCF_001642575.1_Xfloridensis_v1.0_genomic.fna/target_genomes.txt
[2024-01-24 13:35:49,342] [INFO] Task started: fastANI
[2024-01-24 13:35:49,343] [INFO] Running command: fastANI --query /var/lib/cwl/stg5322d925-1b98-49e9-be4e-a9f8347fa584/GCF_001642575.1_Xfloridensis_v1.0_genomic.fna.gz --refList GCF_001642575.1_Xfloridensis_v1.0_genomic.fna/target_genomes.txt --output GCF_001642575.1_Xfloridensis_v1.0_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:36:15,886] [INFO] Task succeeded: fastANI
[2024-01-24 13:36:15,887] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc76bc445-bd6c-4525-a45b-975d3eec0eb7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:36:15,887] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc76bc445-bd6c-4525-a45b-975d3eec0eb7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:36:15,914] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:36:15,915] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:36:15,915] [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
Xanthomonas floridensis	strain=WHRI 8848	GCA_001642575.1	1843580	1843580	type	True	100.0	1721	1723	95	conclusive
Xanthomonas cassavae	strain=NCPPB 101	GCA_020783895.1	56450	56450	type	True	93.3793	1366	1723	95	below_threshold
Xanthomonas cassavae	strain=CFBP 4642	GCA_000454545.1	56450	56450	type	True	93.2931	1401	1723	95	below_threshold
Xanthomonas cucurbitae	strain=CFBP2542	GCA_002939885.1	56453	56453	type	True	89.798	1212	1723	95	below_threshold
Xanthomonas pisi	strain=DSM 18956	GCA_001010415.1	56457	56457	type	True	89.5774	1137	1723	95	below_threshold
Xanthomonas dyei	strain=CFBP7245	GCA_002939865.1	743699	743699	type	True	88.5766	1429	1723	95	below_threshold
Xanthomonas vesicatoria	strain=LMG911	GCA_001908725.1	56460	56460	type	True	88.4328	1427	1723	95	below_threshold
Xanthomonas vesicatoria	strain=ATCC 35937	GCA_000192025.2	56460	56460	type	True	88.4181	1352	1723	95	below_threshold
Xanthomonas melonis	strain=NCPPB 3434	GCA_020783655.1	56456	56456	type	True	88.1267	1356	1723	95	below_threshold
Xanthomonas phaseoli	strain=CFBP2534	GCA_017745345.1	1985254	1985254	pathovar	True	87.1069	1325	1723	95	below_threshold
Xanthomonas phaseoli	strain=NCPPB 3035	GCA_000774035.2	1985254	1985254	pathovar	True	87.0349	1319	1723	95	below_threshold
Xanthomonas hydrangeae	strain=LMG 31884	GCA_905142475.1	2775159	2775159	type	True	87.0254	1359	1723	95	below_threshold
Xanthomonas euvesicatoria	strain=ATCC 11633	GCA_020880415.1	456327	456327	type	True	86.9982	1329	1723	95	below_threshold
Xanthomonas hortorum	strain=CFBP 2533	GCA_021353095.1	56454	56454	pathovar	True	86.9905	1327	1723	95	below_threshold
Xanthomonas hortorum	strain=CFBP2533	GCA_012922215.1	56454	56454	pathovar	True	86.983	1339	1723	95	below_threshold
Xanthomonas citri	strain=ICMP5732	GCA_021474205.1	346	346	pathovar	True	86.766	1390	1723	95	below_threshold
Xanthomonas campestris	strain=NCPPB 528	GCA_020813135.1	339	339	type	True	86.4339	1307	1723	95	below_threshold
Xanthomonas oryzae	strain=WHRI 5234	GCA_003064145.1	347	347	pathovar	True	86.3135	1141	1723	95	below_threshold
Xanthomonas oryzae	strain=ICMP3125	GCA_004136375.1	347	347	type	True	85.9889	1156	1723	95	below_threshold
Lysobacter silvestris	strain=AM20-91	GCA_002895945.1	1645665	1645665	type	True	78.3536	360	1723	95	below_threshold
Komagataeibacter nataicola	strain=LMG 1536	GCA_003207795.1	265960	265960	type	True	75.592	51	1723	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:36:15,916] [INFO] DFAST Taxonomy check result was written to GCF_001642575.1_Xfloridensis_v1.0_genomic.fna/tc_result.tsv
[2024-01-24 13:36:15,917] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:36:15,917] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:36:15,917] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc76bc445-bd6c-4525-a45b-975d3eec0eb7/dqc_reference/checkm_data
[2024-01-24 13:36:15,918] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:36:15,969] [INFO] Task started: CheckM
[2024-01-24 13:36:15,969] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001642575.1_Xfloridensis_v1.0_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001642575.1_Xfloridensis_v1.0_genomic.fna/checkm_input GCF_001642575.1_Xfloridensis_v1.0_genomic.fna/checkm_result
[2024-01-24 13:37:17,666] [INFO] Task succeeded: CheckM
[2024-01-24 13:37:17,667] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:37:17,687] [INFO] ===== Completeness check finished =====
[2024-01-24 13:37:17,688] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:37:17,688] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001642575.1_Xfloridensis_v1.0_genomic.fna/markers.fasta)
[2024-01-24 13:37:17,689] [INFO] Task started: Blastn
[2024-01-24 13:37:17,689] [INFO] Running command: blastn -query GCF_001642575.1_Xfloridensis_v1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stgc76bc445-bd6c-4525-a45b-975d3eec0eb7/dqc_reference/reference_markers_gtdb.fasta -out GCF_001642575.1_Xfloridensis_v1.0_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:19,134] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:19,141] [INFO] Selected 16 target genomes.
[2024-01-24 13:37:19,141] [INFO] Target genome list was writen to GCF_001642575.1_Xfloridensis_v1.0_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:37:19,194] [INFO] Task started: fastANI
[2024-01-24 13:37:19,194] [INFO] Running command: fastANI --query /var/lib/cwl/stg5322d925-1b98-49e9-be4e-a9f8347fa584/GCF_001642575.1_Xfloridensis_v1.0_genomic.fna.gz --refList GCF_001642575.1_Xfloridensis_v1.0_genomic.fna/target_genomes_gtdb.txt --output GCF_001642575.1_Xfloridensis_v1.0_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:37:41,235] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:41,251] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:37:41,252] [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_001642575.1	s__Xanthomonas floridensis	100.0	1721	1723	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_012848175.1	s__Xanthomonas campestris_C	93.6594	1395	1723	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000454545.1	s__Xanthomonas cassavae	93.3147	1399	1723	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002939785.1	s__Xanthomonas codiaei	92.0246	1448	1723	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002939885.1	s__Xanthomonas cucurbitae	89.7853	1213	1723	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	99.30	99.30	0.96	0.96	2	-
GCF_001010415.1	s__Xanthomonas pisi	89.6174	1134	1723	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002939865.1	s__Xanthomonas dyei	88.5766	1429	1723	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001908725.1	s__Xanthomonas vesicatoria	88.426	1428	1723	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	99.30	98.65	0.97	0.94	15	-
GCF_001423585.1	s__Xanthomonas sp001423585	88.351	1480	1723	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	98.11	97.14	0.95	0.93	10	-
GCF_000802365.1	s__Xanthomonas cannabis	88.2114	1266	1723	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	96.66	96.40	0.92	0.89	21	-
GCF_001013475.1	s__Xanthomonas arboricola	87.5993	1344	1723	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	96.94	96.17	0.91	0.85	117	-
GCF_002939945.1	s__Xanthomonas arboricola_A	87.4854	1293	1723	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	95.91	95.91	0.90	0.90	2	-
GCF_002940665.1	s__Xanthomonas arboricola_B	87.4657	1289	1723	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	97.97	97.84	0.92	0.92	4	-
GCF_003999565.1	s__Xanthomonas phaseoli	86.9862	1369	1723	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	98.19	96.38	0.95	0.90	158	-
GCF_004136375.1	s__Xanthomonas oryzae	85.9778	1158	1723	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	99.14	96.34	0.95	0.82	364	-
GCF_001431645.1	s__Stenotrophomonas_A panacihumi	82.4368	797	1723	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas_A	95.0	99.98	99.98	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:37:41,269] [INFO] GTDB search result was written to GCF_001642575.1_Xfloridensis_v1.0_genomic.fna/result_gtdb.tsv
[2024-01-24 13:37:41,270] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:37:41,274] [INFO] DFAST_QC result json was written to GCF_001642575.1_Xfloridensis_v1.0_genomic.fna/dqc_result.json
[2024-01-24 13:37:41,274] [INFO] DFAST_QC completed!
[2024-01-24 13:37:41,274] [INFO] Total running time: 0h2m14s