[2024-01-24 13:45:45,447] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:45:45,451] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:45:45,451] [INFO] DQC Reference Directory: /var/lib/cwl/stgc3048c68-25d7-43d0-b0ce-3ebddc57e574/dqc_reference
[2024-01-24 13:45:46,822] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:45:46,825] [INFO] Task started: Prodigal
[2024-01-24 13:45:46,826] [INFO] Running command: gunzip -c /var/lib/cwl/stgfb51b415-ff15-4a6f-9977-b0c8236b16fa/GCF_020813135.1_ASM2081313v1_genomic.fna.gz | prodigal -d GCF_020813135.1_ASM2081313v1_genomic.fna/cds.fna -a GCF_020813135.1_ASM2081313v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:05,264] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:05,265] [INFO] Task started: HMMsearch
[2024-01-24 13:46:05,265] [INFO] Running command: hmmsearch --tblout GCF_020813135.1_ASM2081313v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc3048c68-25d7-43d0-b0ce-3ebddc57e574/dqc_reference/reference_markers.hmm GCF_020813135.1_ASM2081313v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:05,585] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:05,587] [INFO] Found 6/6 markers.
[2024-01-24 13:46:05,635] [INFO] Query marker FASTA was written to GCF_020813135.1_ASM2081313v1_genomic.fna/markers.fasta
[2024-01-24 13:46:05,635] [INFO] Task started: Blastn
[2024-01-24 13:46:05,635] [INFO] Running command: blastn -query GCF_020813135.1_ASM2081313v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc3048c68-25d7-43d0-b0ce-3ebddc57e574/dqc_reference/reference_markers.fasta -out GCF_020813135.1_ASM2081313v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:06,580] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:06,584] [INFO] Selected 16 target genomes.
[2024-01-24 13:46:06,584] [INFO] Target genome list was writen to GCF_020813135.1_ASM2081313v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:06,595] [INFO] Task started: fastANI
[2024-01-24 13:46:06,595] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb51b415-ff15-4a6f-9977-b0c8236b16fa/GCF_020813135.1_ASM2081313v1_genomic.fna.gz --refList GCF_020813135.1_ASM2081313v1_genomic.fna/target_genomes.txt --output GCF_020813135.1_ASM2081313v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:29,590] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:29,591] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc3048c68-25d7-43d0-b0ce-3ebddc57e574/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:29,592] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc3048c68-25d7-43d0-b0ce-3ebddc57e574/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:29,606] [INFO] Found 16 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:46:29,606] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:29,607] [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 campestris	strain=NCPPB 528	GCA_020813135.1	339	339	type	True	100.0	1629	1631	95	conclusive
Xanthomonas campestris	strain=ATCC 33913	GCA_000007145.1	339	339	type	True	99.9922	1628	1631	95	conclusive
Xanthomonas campestris	strain=NCPPB 347	GCA_020731405.1	339	339	pathovar	True	98.2769	1507	1631	95	conclusive
Xanthomonas euroxanthea	strain=CPBF 424	GCA_900476395.1	2259622	2259622	type	True	86.9824	1337	1631	95	below_threshold
Xanthomonas hydrangeae	strain=LMG 31884	GCA_905142475.1	2775159	2775159	type	True	86.8447	1376	1631	95	below_threshold
Xanthomonas hortorum	strain=CFBP2533	GCA_012922215.1	56454	56454	pathovar	True	86.7568	1347	1631	95	below_threshold
Xanthomonas hortorum	strain=CFBP 2533	GCA_021353095.1	56454	56454	pathovar	True	86.7186	1344	1631	95	below_threshold
Xanthomonas floridensis	strain=WHRI 8848	GCA_001642575.1	1843580	1843580	type	True	86.4237	1335	1631	95	below_threshold
Xanthomonas cassavae	strain=NCPPB 101	GCA_020783895.1	56450	56450	type	True	86.3731	1230	1631	95	below_threshold
Xanthomonas vesicatoria	strain=LMG911	GCA_001908725.1	56460	56460	type	True	86.0744	1340	1631	95	below_threshold
Xanthomonas vesicatoria	strain=ATCC 35937	GCA_000192025.2	56460	56460	type	True	85.9987	1282	1631	95	below_threshold
Xanthomonas euvesicatoria	strain=ATCC 11633	GCA_020880415.1	456327	456327	type	True	85.9369	1281	1631	95	below_threshold
Xanthomonas cucurbitae	strain=CFBP2542	GCA_002939885.1	56453	56453	type	True	85.8488	1150	1631	95	below_threshold
Xanthomonas citri	strain=LMG867	GCA_020011255.1	346	346	pathovar	True	85.7779	1243	1631	95	below_threshold
Xanthomonas citri	strain=CFBP7112	GCA_002218265.1	346	346	pathovar	True	85.7658	1315	1631	95	below_threshold
Xanthomonas citri	strain=ICMP5732	GCA_021474205.1	346	346	pathovar	True	85.7337	1306	1631	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:29,611] [INFO] DFAST Taxonomy check result was written to GCF_020813135.1_ASM2081313v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:29,612] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:29,613] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:29,616] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc3048c68-25d7-43d0-b0ce-3ebddc57e574/dqc_reference/checkm_data
[2024-01-24 13:46:29,618] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:29,671] [INFO] Task started: CheckM
[2024-01-24 13:46:29,672] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020813135.1_ASM2081313v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020813135.1_ASM2081313v1_genomic.fna/checkm_input GCF_020813135.1_ASM2081313v1_genomic.fna/checkm_result
[2024-01-24 13:47:30,428] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:30,429] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:30,463] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:30,463] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:30,464] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020813135.1_ASM2081313v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:30,464] [INFO] Task started: Blastn
[2024-01-24 13:47:30,464] [INFO] Running command: blastn -query GCF_020813135.1_ASM2081313v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc3048c68-25d7-43d0-b0ce-3ebddc57e574/dqc_reference/reference_markers_gtdb.fasta -out GCF_020813135.1_ASM2081313v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:32,208] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:32,211] [INFO] Selected 19 target genomes.
[2024-01-24 13:47:32,212] [INFO] Target genome list was writen to GCF_020813135.1_ASM2081313v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:32,234] [INFO] Task started: fastANI
[2024-01-24 13:47:32,235] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb51b415-ff15-4a6f-9977-b0c8236b16fa/GCF_020813135.1_ASM2081313v1_genomic.fna.gz --refList GCF_020813135.1_ASM2081313v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020813135.1_ASM2081313v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:56,669] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:56,688] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:56,689] [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_000007145.1	s__Xanthomonas campestris	99.9922	1628	1631	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	98.22	96.56	0.94	0.87	68	conclusive
GCF_003353015.1	s__Xanthomonas arboricola_E	86.9861	1335	1631	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900476395.1	s__Xanthomonas euroxanthea	86.9613	1341	1631	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	98.09	97.74	0.93	0.92	25	-
GCF_002940205.1	s__Xanthomonas arboricola_C	86.9346	1316	1631	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	99.99	99.99	0.99	0.99	2	-
GCF_002940665.1	s__Xanthomonas arboricola_B	86.7926	1242	1631	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	97.97	97.84	0.92	0.92	4	-
GCF_002939985.1	s__Xanthomonas hortorum_A	86.7853	1314	1631	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	96.0883	98.80	97.51	0.93	0.89	28	-
GCF_905142465.1	s__Xanthomonas sp905142465	86.7791	1346	1631	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.1927	99.49	99.23	0.97	0.96	4	-
GCF_001423495.1	s__Xanthomonas sp001423495	86.5517	1320	1631	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012848175.1	s__Xanthomonas campestris_C	86.4767	1292	1631	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	86.4171	1337	1631	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001010415.1	s__Xanthomonas pisi	86.417	1028	1631	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002939785.1	s__Xanthomonas codiaei	86.3647	1304	1631	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	86.0733	1340	1631	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	99.30	98.65	0.97	0.94	15	-
GCF_002939885.1	s__Xanthomonas cucurbitae	85.8293	1152	1631	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	99.30	99.30	0.96	0.96	2	-
GCF_008801575.1	s__Xanthomonas cissicola	85.8029	1262	1631	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	85.7289	1205	1631	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	100.00	100.00	0.99	0.99	2	-
GCF_009192945.1	s__Xanthomonas maliensis	83.5368	1127	1631	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	99.91	99.91	0.98	0.98	2	-
GCA_002429615.1	s__Stenotrophomonas_A sp002429615	82.0468	717	1631	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001431405.1	s__Pseudoxanthomonas_A dokdonensis	79.3598	548	1631	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:56,691] [INFO] GTDB search result was written to GCF_020813135.1_ASM2081313v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:56,692] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:56,700] [INFO] DFAST_QC result json was written to GCF_020813135.1_ASM2081313v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:56,701] [INFO] DFAST_QC completed!
[2024-01-24 13:47:56,701] [INFO] Total running time: 0h2m11s