[2024-01-24 14:31:30,181] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:31:30,183] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:31:30,183] [INFO] DQC Reference Directory: /var/lib/cwl/stg06ca1f11-336f-4db2-b225-fbea49e843dc/dqc_reference
[2024-01-24 14:31:31,564] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:31:31,565] [INFO] Task started: Prodigal
[2024-01-24 14:31:31,565] [INFO] Running command: gunzip -c /var/lib/cwl/stgc667b0a9-9494-4878-b188-c6f1e389c0ae/GCF_002846205.1_ASM284620v1_genomic.fna.gz | prodigal -d GCF_002846205.1_ASM284620v1_genomic.fna/cds.fna -a GCF_002846205.1_ASM284620v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:31:55,329] [INFO] Task succeeded: Prodigal
[2024-01-24 14:31:55,329] [INFO] Task started: HMMsearch
[2024-01-24 14:31:55,330] [INFO] Running command: hmmsearch --tblout GCF_002846205.1_ASM284620v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg06ca1f11-336f-4db2-b225-fbea49e843dc/dqc_reference/reference_markers.hmm GCF_002846205.1_ASM284620v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:31:55,643] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:31:55,645] [INFO] Found 6/6 markers.
[2024-01-24 14:31:55,706] [INFO] Query marker FASTA was written to GCF_002846205.1_ASM284620v1_genomic.fna/markers.fasta
[2024-01-24 14:31:55,706] [INFO] Task started: Blastn
[2024-01-24 14:31:55,706] [INFO] Running command: blastn -query GCF_002846205.1_ASM284620v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg06ca1f11-336f-4db2-b225-fbea49e843dc/dqc_reference/reference_markers.fasta -out GCF_002846205.1_ASM284620v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:56,666] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:56,669] [INFO] Selected 25 target genomes.
[2024-01-24 14:31:56,670] [INFO] Target genome list was writen to GCF_002846205.1_ASM284620v1_genomic.fna/target_genomes.txt
[2024-01-24 14:31:56,697] [INFO] Task started: fastANI
[2024-01-24 14:31:56,697] [INFO] Running command: fastANI --query /var/lib/cwl/stgc667b0a9-9494-4878-b188-c6f1e389c0ae/GCF_002846205.1_ASM284620v1_genomic.fna.gz --refList GCF_002846205.1_ASM284620v1_genomic.fna/target_genomes.txt --output GCF_002846205.1_ASM284620v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:32:27,146] [INFO] Task succeeded: fastANI
[2024-01-24 14:32:27,147] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg06ca1f11-336f-4db2-b225-fbea49e843dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:32:27,147] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg06ca1f11-336f-4db2-b225-fbea49e843dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:32:27,166] [INFO] Found 25 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:32:27,166] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:32:27,167] [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 prunicola	strain=CFBP 8353	GCA_002846205.1	2053930	2053930	type	True	100.0	1732	1736	95	conclusive
Xanthomonas vasicola	strain=CFBP2543	GCA_002939925.1	56459	56459	type	True	91.1991	1372	1736	95	below_threshold
Xanthomonas oryzae	strain=ATCC 35933	GCA_000482445.1	347	347	type	True	91.1484	1150	1736	95	below_threshold
Xanthomonas vasicola	strain=SAM119	GCA_002191955.1	56459	56459	pathovar	True	91.1377	1372	1736	95	below_threshold
Xanthomonas vasicola	strain=SAM119	GCA_003015715.1	56459	56459	pathovar	True	91.124	1372	1736	95	below_threshold
Xanthomonas oryzae	strain=WHRI 5234	GCA_003064145.1	347	347	pathovar	True	91.1193	1243	1736	95	below_threshold
Xanthomonas vasicola	strain=NCPPB 2649	GCA_000770355.2	56459	56459	pathovar	True	91.0921	1402	1736	95	below_threshold
Xanthomonas oryzae	strain=ICMP3125	GCA_004136375.1	347	347	type	True	90.762	1249	1736	95	below_threshold
Xanthomonas citri	strain=LMG 941	GCA_000263335.1	346	346	pathovar	True	90.1259	1350	1736	95	below_threshold
Xanthomonas cissicola	strain=CCUG 18839	GCA_008801575.1	86186	86186	suspected-type	True	90.1166	1386	1736	95	below_threshold
Xanthomonas cissicola	strain=LMG21719	GCA_002019225.1	86186	86186	suspected-type	True	90.1108	1334	1736	95	below_threshold
Xanthomonas citri	strain=ICMP5732	GCA_021474205.1	346	346	pathovar	True	90.0437	1470	1736	95	below_threshold
Xanthomonas euvesicatoria	strain=ATCC 11633	GCA_020880415.1	456327	456327	type	True	90.0332	1397	1736	95	below_threshold
Xanthomonas citri	strain=LMG9322	GCA_002018575.1	346	346	suspected-type	True	90.0326	1371	1736	95	below_threshold
Xanthomonas euvesicatoria pv. alfalfae	strain=CFBP3836	GCA_017724035.1	359387	456327	pathovar	True	90.0098	1445	1736	95	below_threshold
Xanthomonas euvesicatoria pv. alfalfae	strain=CFBP 3836	GCA_000488955.1	359387	456327	pathovar	True	89.969	1442	1736	95	below_threshold
Xanthomonas axonopodis	strain=DSM 3585	GCA_001304695.1	53413	53413	suspected-type	True	89.6694	1212	1736	95	below_threshold
Xanthomonas pisi	strain=DSM 18956	GCA_001010415.1	56457	56457	type	True	88.3589	1053	1736	95	below_threshold
Xanthomonas dyei	strain=CFBP7245	GCA_002939865.1	743699	743699	type	True	87.1736	1389	1736	95	below_threshold
Xanthomonas floridensis	strain=WHRI 8848	GCA_001642575.1	1843580	1843580	type	True	87.1318	1347	1736	95	below_threshold
Xanthomonas vesicatoria	strain=ATCC 35937	GCA_000192025.2	56460	56460	type	True	86.9165	1295	1736	95	below_threshold
Xanthomonas vesicatoria	strain=LMG911	GCA_001908725.1	56460	56460	type	True	86.8497	1369	1736	95	below_threshold
Xanthomonas hortorum	strain=CFBP 2533	GCA_021353095.1	56454	56454	pathovar	True	86.8422	1333	1736	95	below_threshold
Xanthomonas hydrangeae	strain=LMG 31884	GCA_905142475.1	2775159	2775159	type	True	86.8416	1351	1736	95	below_threshold
Xanthomonas hortorum	strain=CFBP2533	GCA_012922215.1	56454	56454	pathovar	True	86.8333	1339	1736	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:32:27,168] [INFO] DFAST Taxonomy check result was written to GCF_002846205.1_ASM284620v1_genomic.fna/tc_result.tsv
[2024-01-24 14:32:27,169] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:32:27,169] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:32:27,169] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg06ca1f11-336f-4db2-b225-fbea49e843dc/dqc_reference/checkm_data
[2024-01-24 14:32:27,171] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:32:27,223] [INFO] Task started: CheckM
[2024-01-24 14:32:27,223] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002846205.1_ASM284620v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002846205.1_ASM284620v1_genomic.fna/checkm_input GCF_002846205.1_ASM284620v1_genomic.fna/checkm_result
[2024-01-24 14:33:31,348] [INFO] Task succeeded: CheckM
[2024-01-24 14:33:31,350] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:33:31,372] [INFO] ===== Completeness check finished =====
[2024-01-24 14:33:31,373] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:33:31,373] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002846205.1_ASM284620v1_genomic.fna/markers.fasta)
[2024-01-24 14:33:31,374] [INFO] Task started: Blastn
[2024-01-24 14:33:31,374] [INFO] Running command: blastn -query GCF_002846205.1_ASM284620v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg06ca1f11-336f-4db2-b225-fbea49e843dc/dqc_reference/reference_markers_gtdb.fasta -out GCF_002846205.1_ASM284620v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:33:33,167] [INFO] Task succeeded: Blastn
[2024-01-24 14:33:33,171] [INFO] Selected 15 target genomes.
[2024-01-24 14:33:33,171] [INFO] Target genome list was writen to GCF_002846205.1_ASM284620v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:33:33,183] [INFO] Task started: fastANI
[2024-01-24 14:33:33,184] [INFO] Running command: fastANI --query /var/lib/cwl/stgc667b0a9-9494-4878-b188-c6f1e389c0ae/GCF_002846205.1_ASM284620v1_genomic.fna.gz --refList GCF_002846205.1_ASM284620v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002846205.1_ASM284620v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:33:51,966] [INFO] Task succeeded: fastANI
[2024-01-24 14:33:51,992] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:33:51,992] [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_002846205.1	s__Xanthomonas prunicola	100.0	1733	1736	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	99.99	99.99	1.00	0.99	3	conclusive
GCF_000772705.2	s__Xanthomonas vasicola	91.2048	1375	1736	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	98.75	98.20	0.95	0.92	113	-
GCF_004136375.1	s__Xanthomonas oryzae	90.7751	1248	1736	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	99.14	96.34	0.95	0.82	364	-
GCF_008801575.1	s__Xanthomonas cissicola	90.1177	1386	1736	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	97.71	95.83	0.91	0.86	247	-
GCF_900092025.1	s__Xanthomonas bromi	89.8379	1353	1736	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003999565.1	s__Xanthomonas phaseoli	89.6876	1418	1736	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	98.19	96.38	0.95	0.90	158	-
GCF_001304695.1	s__Xanthomonas axonopodis	89.6694	1212	1736	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	98.43	97.90	0.94	0.92	5	-
GCF_001660815.1	s__Xanthomonas nasturtii	89.0844	1339	1736	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	98.97	98.97	0.95	0.95	2	-
GCF_001010415.1	s__Xanthomonas pisi	88.3812	1051	1736	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000802365.1	s__Xanthomonas cannabis	87.2024	1235	1736	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	96.66	96.40	0.92	0.89	21	-
GCF_002939865.1	s__Xanthomonas dyei	87.1617	1391	1736	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	87.1257	1348	1736	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	87.0779	1365	1736	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	98.11	97.14	0.95	0.93	10	-
GCF_001908725.1	s__Xanthomonas vesicatoria	86.8447	1370	1736	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	99.30	98.65	0.97	0.94	15	-
GCF_002939785.1	s__Xanthomonas codiaei	86.6745	1326	1736	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:33:51,994] [INFO] GTDB search result was written to GCF_002846205.1_ASM284620v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:33:51,994] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:33:51,999] [INFO] DFAST_QC result json was written to GCF_002846205.1_ASM284620v1_genomic.fna/dqc_result.json
[2024-01-24 14:33:51,999] [INFO] DFAST_QC completed!
[2024-01-24 14:33:51,999] [INFO] Total running time: 0h2m22s