[2024-01-24 13:37:27,657] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:37:27,658] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:37:27,659] [INFO] DQC Reference Directory: /var/lib/cwl/stg471c926d-8c40-4a94-be5b-c1c63811392f/dqc_reference
[2024-01-24 13:37:28,913] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:37:28,914] [INFO] Task started: Prodigal
[2024-01-24 13:37:28,914] [INFO] Running command: gunzip -c /var/lib/cwl/stg028199f4-183d-499f-bb54-9d7cb7e04dd3/GCF_000482445.1_ASM48244v1_genomic.fna.gz | prodigal -d GCF_000482445.1_ASM48244v1_genomic.fna/cds.fna -a GCF_000482445.1_ASM48244v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:42,643] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:42,643] [INFO] Task started: HMMsearch
[2024-01-24 13:37:42,643] [INFO] Running command: hmmsearch --tblout GCF_000482445.1_ASM48244v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg471c926d-8c40-4a94-be5b-c1c63811392f/dqc_reference/reference_markers.hmm GCF_000482445.1_ASM48244v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:42,940] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:42,942] [INFO] Found 6/6 markers.
[2024-01-24 13:37:42,979] [INFO] Query marker FASTA was written to GCF_000482445.1_ASM48244v1_genomic.fna/markers.fasta
[2024-01-24 13:37:42,979] [INFO] Task started: Blastn
[2024-01-24 13:37:42,979] [INFO] Running command: blastn -query GCF_000482445.1_ASM48244v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg471c926d-8c40-4a94-be5b-c1c63811392f/dqc_reference/reference_markers.fasta -out GCF_000482445.1_ASM48244v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:43,869] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:43,873] [INFO] Selected 18 target genomes.
[2024-01-24 13:37:43,873] [INFO] Target genome list was writen to GCF_000482445.1_ASM48244v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:44,083] [INFO] Task started: fastANI
[2024-01-24 13:37:44,083] [INFO] Running command: fastANI --query /var/lib/cwl/stg028199f4-183d-499f-bb54-9d7cb7e04dd3/GCF_000482445.1_ASM48244v1_genomic.fna.gz --refList GCF_000482445.1_ASM48244v1_genomic.fna/target_genomes.txt --output GCF_000482445.1_ASM48244v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:38:06,540] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:06,541] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg471c926d-8c40-4a94-be5b-c1c63811392f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:38:06,541] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg471c926d-8c40-4a94-be5b-c1c63811392f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:38:06,559] [INFO] Found 18 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:38:06,559] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:38:06,559] [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 oryzae	strain=ATCC 35933	GCA_000482445.1	347	347	type	True	100.0	1288	1295	95	conclusive
Xanthomonas oryzae	strain=ICMP3125	GCA_004136375.1	347	347	type	True	99.9412	1286	1295	95	conclusive
Xanthomonas oryzae	strain=WHRI 5234	GCA_003064145.1	347	347	pathovar	True	97.6397	1189	1295	95	conclusive
Xanthomonas vasicola	strain=SAM119	GCA_003015715.1	56459	56459	pathovar	True	91.3975	1173	1295	95	below_threshold
Xanthomonas vasicola	strain=SAM119	GCA_002191955.1	56459	56459	pathovar	True	91.3967	1161	1295	95	below_threshold
Xanthomonas vasicola	strain=CFBP2543	GCA_002939925.1	56459	56459	type	True	91.3416	1145	1295	95	below_threshold
Xanthomonas vasicola	strain=NCPPB 2649	GCA_000770355.2	56459	56459	pathovar	True	91.3324	1170	1295	95	below_threshold
Xanthomonas vasicola	strain=NCPPB 2417	GCA_000772705.2	56459	56459	type	True	91.3021	1156	1295	95	below_threshold
Xanthomonas euvesicatoria	strain=ATCC 11633	GCA_020880415.1	456327	456327	type	True	90.1446	1121	1295	95	below_threshold
Xanthomonas citri	strain=ICMP5732	GCA_021474205.1	346	346	pathovar	True	90.1107	1129	1295	95	below_threshold
Xanthomonas cissicola	strain=LMG21719	GCA_002019225.1	86186	86186	suspected-type	True	90.089	1080	1295	95	below_threshold
Xanthomonas citri	strain=LMG9322	GCA_002018575.1	346	346	suspected-type	True	90.0597	1095	1295	95	below_threshold
Xanthomonas citri	strain=CFBP7112	GCA_002218265.1	346	346	pathovar	True	90.0107	1132	1295	95	below_threshold
Xanthomonas hydrangeae	strain=LMG 31884	GCA_905142475.1	2775159	2775159	type	True	86.6751	1087	1295	95	below_threshold
Xanthomonas cassavae	strain=NCPPB 101	GCA_020783895.1	56450	56450	type	True	86.6628	1031	1295	95	below_threshold
Xanthomonas cassavae	strain=CFBP 4642	GCA_000454545.1	56450	56450	type	True	86.536	1071	1295	95	below_threshold
Xanthomonas fragariae	strain=PD 885	GCA_900380235.1	48664	48664	type	True	85.5926	881	1295	95	below_threshold
Xanthomonas fragariae	strain=PD885	GCA_900183975.1	48664	48664	type	True	85.4165	958	1295	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:38:06,561] [INFO] DFAST Taxonomy check result was written to GCF_000482445.1_ASM48244v1_genomic.fna/tc_result.tsv
[2024-01-24 13:38:06,562] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:38:06,562] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:38:06,562] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg471c926d-8c40-4a94-be5b-c1c63811392f/dqc_reference/checkm_data
[2024-01-24 13:38:06,563] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:38:06,622] [INFO] Task started: CheckM
[2024-01-24 13:38:06,622] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000482445.1_ASM48244v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000482445.1_ASM48244v1_genomic.fna/checkm_input GCF_000482445.1_ASM48244v1_genomic.fna/checkm_result
[2024-01-24 13:38:49,181] [INFO] Task succeeded: CheckM
[2024-01-24 13:38:49,182] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:38:49,204] [INFO] ===== Completeness check finished =====
[2024-01-24 13:38:49,204] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:38:49,205] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000482445.1_ASM48244v1_genomic.fna/markers.fasta)
[2024-01-24 13:38:49,205] [INFO] Task started: Blastn
[2024-01-24 13:38:49,205] [INFO] Running command: blastn -query GCF_000482445.1_ASM48244v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg471c926d-8c40-4a94-be5b-c1c63811392f/dqc_reference/reference_markers_gtdb.fasta -out GCF_000482445.1_ASM48244v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:50,845] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:50,849] [INFO] Selected 14 target genomes.
[2024-01-24 13:38:50,850] [INFO] Target genome list was writen to GCF_000482445.1_ASM48244v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:51,202] [INFO] Task started: fastANI
[2024-01-24 13:38:51,203] [INFO] Running command: fastANI --query /var/lib/cwl/stg028199f4-183d-499f-bb54-9d7cb7e04dd3/GCF_000482445.1_ASM48244v1_genomic.fna.gz --refList GCF_000482445.1_ASM48244v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000482445.1_ASM48244v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:39:09,144] [INFO] Task succeeded: fastANI
[2024-01-24 13:39:09,158] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:39:09,159] [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_004136375.1	s__Xanthomonas oryzae	99.9412	1286	1295	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	99.14	96.34	0.95	0.82	364	conclusive
GCF_002846205.1	s__Xanthomonas prunicola	91.312	1152	1295	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	99.99	99.99	1.00	0.99	3	-
GCF_000772705.2	s__Xanthomonas vasicola	91.3085	1156	1295	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	98.75	98.20	0.95	0.92	113	-
GCF_013112235.1	s__Xanthomonas perforans	90.3265	1136	1295	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	99.28	96.72	0.95	0.89	246	-
GCF_008801575.1	s__Xanthomonas cissicola	90.1457	1103	1295	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	97.71	95.83	0.91	0.86	247	-
GCF_003999565.1	s__Xanthomonas phaseoli	89.8071	1130	1295	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	89.7831	1041	1295	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	98.43	97.90	0.94	0.92	5	-
GCF_900092025.1	s__Xanthomonas bromi	89.6807	1123	1295	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	100.00	100.00	0.99	0.99	2	-
GCF_001660815.1	s__Xanthomonas nasturtii	88.9887	1073	1295	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	98.97	98.97	0.95	0.95	2	-
GCF_000802365.1	s__Xanthomonas cannabis	87.1101	993	1295	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	96.66	96.40	0.92	0.89	21	-
GCF_900476395.1	s__Xanthomonas euroxanthea	86.983	1045	1295	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	98.09	97.74	0.93	0.92	25	-
GCF_012848175.1	s__Xanthomonas campestris_C	86.6246	1063	1295	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	86.5479	1068	1295	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	86.387	1073	1295	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 13:39:09,161] [INFO] GTDB search result was written to GCF_000482445.1_ASM48244v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:39:09,161] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:39:09,170] [INFO] DFAST_QC result json was written to GCF_000482445.1_ASM48244v1_genomic.fna/dqc_result.json
[2024-01-24 13:39:09,171] [INFO] DFAST_QC completed!
[2024-01-24 13:39:09,171] [INFO] Total running time: 0h1m42s