[2024-01-24 12:54:05,443] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:54:05,451] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:54:05,451] [INFO] DQC Reference Directory: /var/lib/cwl/stgc07233d7-6f6f-42f6-bd22-183007c8b7f6/dqc_reference
[2024-01-24 12:54:07,724] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:54:07,725] [INFO] Task started: Prodigal
[2024-01-24 12:54:07,725] [INFO] Running command: gunzip -c /var/lib/cwl/stg2f1c8f43-f398-4294-9dcb-7a250d13583b/GCF_002939755.1_XbrCFBP1976_genomic.fna.gz | prodigal -d GCF_002939755.1_XbrCFBP1976_genomic.fna/cds.fna -a GCF_002939755.1_XbrCFBP1976_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:54:26,179] [INFO] Task succeeded: Prodigal
[2024-01-24 12:54:26,179] [INFO] Task started: HMMsearch
[2024-01-24 12:54:26,179] [INFO] Running command: hmmsearch --tblout GCF_002939755.1_XbrCFBP1976_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc07233d7-6f6f-42f6-bd22-183007c8b7f6/dqc_reference/reference_markers.hmm GCF_002939755.1_XbrCFBP1976_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:54:26,532] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:54:26,534] [INFO] Found 6/6 markers.
[2024-01-24 12:54:26,581] [INFO] Query marker FASTA was written to GCF_002939755.1_XbrCFBP1976_genomic.fna/markers.fasta
[2024-01-24 12:54:26,582] [INFO] Task started: Blastn
[2024-01-24 12:54:26,582] [INFO] Running command: blastn -query GCF_002939755.1_XbrCFBP1976_genomic.fna/markers.fasta -db /var/lib/cwl/stgc07233d7-6f6f-42f6-bd22-183007c8b7f6/dqc_reference/reference_markers.fasta -out GCF_002939755.1_XbrCFBP1976_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:27,450] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:27,454] [INFO] Selected 28 target genomes.
[2024-01-24 12:54:27,454] [INFO] Target genome list was writen to GCF_002939755.1_XbrCFBP1976_genomic.fna/target_genomes.txt
[2024-01-24 12:54:27,476] [INFO] Task started: fastANI
[2024-01-24 12:54:27,476] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f1c8f43-f398-4294-9dcb-7a250d13583b/GCF_002939755.1_XbrCFBP1976_genomic.fna.gz --refList GCF_002939755.1_XbrCFBP1976_genomic.fna/target_genomes.txt --output GCF_002939755.1_XbrCFBP1976_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:54:57,391] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:57,392] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc07233d7-6f6f-42f6-bd22-183007c8b7f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:54:57,392] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc07233d7-6f6f-42f6-bd22-183007c8b7f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:54:57,411] [INFO] Found 26 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:54:57,411] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:54:57,412] [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 bromi	strain=CFBP1976	GCA_002939755.1	56449	56449	type	True	100.0	1558	1561	95	conclusive
Xanthomonas bromi		GCA_900092025.1	56449	56449	type	True	99.9773	1516	1561	95	conclusive
Xanthomonas vasicola	strain=SAM119	GCA_003015715.1	56459	56459	pathovar	True	89.6395	1330	1561	95	below_threshold
Xanthomonas vasicola	strain=NCPPB 2649	GCA_000770355.2	56459	56459	pathovar	True	89.6299	1324	1561	95	below_threshold
Xanthomonas vasicola	strain=SAM119	GCA_002191955.1	56459	56459	pathovar	True	89.6289	1312	1561	95	below_threshold
Xanthomonas euvesicatoria	strain=ATCC 11633	GCA_020880415.1	456327	456327	type	True	89.536	1289	1561	95	below_threshold
Xanthomonas citri	strain=CFBP 2913	GCA_002688625.1	346	346	pathovar	True	89.5285	1328	1561	95	below_threshold
Xanthomonas citri	strain=LMG872	GCA_020011215.1	346	346	pathovar	True	89.5243	1229	1561	95	below_threshold
Xanthomonas citri	strain=ICMP5732	GCA_021474205.1	346	346	pathovar	True	89.5158	1332	1561	95	below_threshold
Xanthomonas citri	strain=LMG867	GCA_020011255.1	346	346	pathovar	True	89.4897	1241	1561	95	below_threshold
Xanthomonas phaseoli	strain=CFBP2534	GCA_017745345.1	1985254	1985254	pathovar	True	89.4611	1293	1561	95	below_threshold
Xanthomonas phaseoli	strain=NCPPB 3035	GCA_000774035.2	1985254	1985254	pathovar	True	89.421	1290	1561	95	below_threshold
Xanthomonas citri	strain=CFBP7112	GCA_002218265.1	346	346	pathovar	True	89.4115	1323	1561	95	below_threshold
Xanthomonas nasturtii	strain=WHRI 8853	GCA_001660815.1	1843581	1843581	type	True	89.1286	1272	1561	95	below_threshold
Xanthomonas vesicatoria	strain=LMG911	GCA_001908725.1	56460	56460	type	True	87.2848	1275	1561	95	below_threshold
Xanthomonas vesicatoria	strain=ATCC 35937	GCA_000192025.2	56460	56460	type	True	87.2527	1229	1561	95	below_threshold
Xanthomonas dyei	strain=CFBP7245	GCA_002939865.1	743699	743699	type	True	87.2324	1267	1561	95	below_threshold
Xanthomonas cassavae	strain=NCPPB 101	GCA_020783895.1	56450	56450	type	True	87.1512	1203	1561	95	below_threshold
Xanthomonas cassavae	strain=CFBP 4642	GCA_000454545.1	56450	56450	type	True	87.1456	1243	1561	95	below_threshold
Xanthomonas floridensis	strain=WHRI 8848	GCA_001642575.1	1843580	1843580	type	True	87.1282	1252	1561	95	below_threshold
Xanthomonas hydrangeae	strain=LMG 31884	GCA_905142475.1	2775159	2775159	type	True	86.9303	1276	1561	95	below_threshold
Xanthomonas hortorum	strain=CFBP2533	GCA_012922215.1	56454	56454	pathovar	True	86.9241	1262	1561	95	below_threshold
Xanthomonas hortorum	strain=CFBP 2533	GCA_021353095.1	56454	56454	pathovar	True	86.9152	1249	1561	95	below_threshold
Wenzhouxiangella marina	strain=DSM 103414	GCA_014203035.1	1579979	1579979	type	True	76.6137	97	1561	95	below_threshold
Mesorhizobium composti	strain=CC-YTH430	GCA_004801285.1	2675109	2675109	type	True	76.0465	82	1561	95	below_threshold
Tabrizicola algicola	strain=ETT8	GCA_010915705.1	2709381	2709381	type	True	75.8129	52	1561	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:54:57,413] [INFO] DFAST Taxonomy check result was written to GCF_002939755.1_XbrCFBP1976_genomic.fna/tc_result.tsv
[2024-01-24 12:54:57,414] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:54:57,414] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:54:57,414] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc07233d7-6f6f-42f6-bd22-183007c8b7f6/dqc_reference/checkm_data
[2024-01-24 12:54:57,415] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:54:57,464] [INFO] Task started: CheckM
[2024-01-24 12:54:57,464] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002939755.1_XbrCFBP1976_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002939755.1_XbrCFBP1976_genomic.fna/checkm_input GCF_002939755.1_XbrCFBP1976_genomic.fna/checkm_result
[2024-01-24 12:55:49,872] [INFO] Task succeeded: CheckM
[2024-01-24 12:55:49,874] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:55:49,896] [INFO] ===== Completeness check finished =====
[2024-01-24 12:55:49,896] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:55:49,897] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002939755.1_XbrCFBP1976_genomic.fna/markers.fasta)
[2024-01-24 12:55:49,897] [INFO] Task started: Blastn
[2024-01-24 12:55:49,897] [INFO] Running command: blastn -query GCF_002939755.1_XbrCFBP1976_genomic.fna/markers.fasta -db /var/lib/cwl/stgc07233d7-6f6f-42f6-bd22-183007c8b7f6/dqc_reference/reference_markers_gtdb.fasta -out GCF_002939755.1_XbrCFBP1976_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:55:51,226] [INFO] Task succeeded: Blastn
[2024-01-24 12:55:51,232] [INFO] Selected 20 target genomes.
[2024-01-24 12:55:51,232] [INFO] Target genome list was writen to GCF_002939755.1_XbrCFBP1976_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:55:51,315] [INFO] Task started: fastANI
[2024-01-24 12:55:51,316] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f1c8f43-f398-4294-9dcb-7a250d13583b/GCF_002939755.1_XbrCFBP1976_genomic.fna.gz --refList GCF_002939755.1_XbrCFBP1976_genomic.fna/target_genomes_gtdb.txt --output GCF_002939755.1_XbrCFBP1976_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:56:14,327] [INFO] Task succeeded: fastANI
[2024-01-24 12:56:14,350] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:56:14,350] [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_900092025.1	s__Xanthomonas bromi	99.9773	1516	1561	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	100.00	100.00	0.99	0.99	2	conclusive
GCF_002846205.1	s__Xanthomonas prunicola	89.8877	1350	1561	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	99.99	99.99	1.00	0.99	3	-
GCF_008801575.1	s__Xanthomonas cissicola	89.6163	1283	1561	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	97.71	95.83	0.91	0.86	247	-
GCF_000772705.2	s__Xanthomonas vasicola	89.5999	1305	1561	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	98.75	98.20	0.95	0.92	113	-
GCF_001304695.1	s__Xanthomonas axonopodis	89.5455	1183	1561	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	98.43	97.90	0.94	0.92	5	-
GCF_013112235.1	s__Xanthomonas perforans	89.521	1339	1561	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	99.28	96.72	0.95	0.89	246	-
GCF_003999565.1	s__Xanthomonas phaseoli	89.3999	1327	1561	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	89.2009	1252	1561	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	99.14	96.34	0.95	0.82	364	-
GCF_001660815.1	s__Xanthomonas nasturtii	89.13	1271	1561	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	98.97	98.97	0.95	0.95	2	-
GCF_012848175.1	s__Xanthomonas campestris_C	87.3708	1252	1561	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	87.2748	1276	1561	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	99.30	98.65	0.97	0.94	15	-
GCF_002939865.1	s__Xanthomonas dyei	87.2324	1267	1561	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	87.1636	1241	1561	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001642575.1	s__Xanthomonas floridensis	87.1263	1252	1561	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001423585.1	s__Xanthomonas sp001423585	86.999	1264	1561	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	98.11	97.14	0.95	0.93	10	-
GCF_014197275.1	s__Xanthomonas campestris_B	86.8892	1253	1561	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	98.71	98.71	0.92	0.92	2	-
GCF_004801285.1	s__Mesorhizobium composti	76.0465	82	1561	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	96.99	96.99	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:56:14,352] [INFO] GTDB search result was written to GCF_002939755.1_XbrCFBP1976_genomic.fna/result_gtdb.tsv
[2024-01-24 12:56:14,352] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:56:14,357] [INFO] DFAST_QC result json was written to GCF_002939755.1_XbrCFBP1976_genomic.fna/dqc_result.json
[2024-01-24 12:56:14,357] [INFO] DFAST_QC completed!
[2024-01-24 12:56:14,357] [INFO] Total running time: 0h2m9s