[2024-01-24 12:54:05,370] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:54:05,374] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:54:05,375] [INFO] DQC Reference Directory: /var/lib/cwl/stg8e3b08f6-4dee-4373-9b30-ed6e1533d0b4/dqc_reference
[2024-01-24 12:54:07,723] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:54:07,724] [INFO] Task started: Prodigal
[2024-01-24 12:54:07,724] [INFO] Running command: gunzip -c /var/lib/cwl/stgb9083a9f-01fc-448c-8d97-62fb742dcdd1/GCF_000454545.1_20120625_genomic.fna.gz | prodigal -d GCF_000454545.1_20120625_genomic.fna/cds.fna -a GCF_000454545.1_20120625_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:54:26,633] [INFO] Task succeeded: Prodigal
[2024-01-24 12:54:26,634] [INFO] Task started: HMMsearch
[2024-01-24 12:54:26,634] [INFO] Running command: hmmsearch --tblout GCF_000454545.1_20120625_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8e3b08f6-4dee-4373-9b30-ed6e1533d0b4/dqc_reference/reference_markers.hmm GCF_000454545.1_20120625_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:54:26,990] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:54:26,992] [INFO] Found 6/6 markers.
[2024-01-24 12:54:27,035] [INFO] Query marker FASTA was written to GCF_000454545.1_20120625_genomic.fna/markers.fasta
[2024-01-24 12:54:27,036] [INFO] Task started: Blastn
[2024-01-24 12:54:27,036] [INFO] Running command: blastn -query GCF_000454545.1_20120625_genomic.fna/markers.fasta -db /var/lib/cwl/stg8e3b08f6-4dee-4373-9b30-ed6e1533d0b4/dqc_reference/reference_markers.fasta -out GCF_000454545.1_20120625_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:27,977] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:27,981] [INFO] Selected 16 target genomes.
[2024-01-24 12:54:27,981] [INFO] Target genome list was writen to GCF_000454545.1_20120625_genomic.fna/target_genomes.txt
[2024-01-24 12:54:27,995] [INFO] Task started: fastANI
[2024-01-24 12:54:27,995] [INFO] Running command: fastANI --query /var/lib/cwl/stgb9083a9f-01fc-448c-8d97-62fb742dcdd1/GCF_000454545.1_20120625_genomic.fna.gz --refList GCF_000454545.1_20120625_genomic.fna/target_genomes.txt --output GCF_000454545.1_20120625_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:54:54,065] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:54,066] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8e3b08f6-4dee-4373-9b30-ed6e1533d0b4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:54:54,066] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8e3b08f6-4dee-4373-9b30-ed6e1533d0b4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:54:54,080] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:54:54,080] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:54:54,080] [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 cassavae	strain=CFBP 4642	GCA_000454545.1	56450	56450	type	True	100.0	1753	1754	95	conclusive
Xanthomonas cassavae	strain=NCPPB 101	GCA_020783895.1	56450	56450	type	True	99.897	1602	1754	95	conclusive
Xanthomonas floridensis	strain=WHRI 8848	GCA_001642575.1	1843580	1843580	type	True	93.3008	1398	1754	95	below_threshold
Xanthomonas cucurbitae	strain=CFBP2542	GCA_002939885.1	56453	56453	type	True	89.7183	1207	1754	95	below_threshold
Xanthomonas melonis	strain=NCPPB 3434	GCA_020783655.1	56456	56456	type	True	88.215	1322	1754	95	below_threshold
Xanthomonas pisi	strain=DSM 18956	GCA_001010415.1	56457	56457	type	True	87.8531	1028	1754	95	below_threshold
Xanthomonas vesicatoria	strain=ATCC 35937	GCA_000192025.2	56460	56460	type	True	87.7127	1304	1754	95	below_threshold
Xanthomonas vesicatoria	strain=LMG911	GCA_001908725.1	56460	56460	type	True	87.709	1370	1754	95	below_threshold
Xanthomonas euvesicatoria	strain=ATCC 11633	GCA_020880415.1	456327	456327	type	True	87.2772	1299	1754	95	below_threshold
Xanthomonas citri	strain=ICMP5732	GCA_021474205.1	346	346	pathovar	True	87.1699	1361	1754	95	below_threshold
Xanthomonas hydrangeae	strain=LMG 31884	GCA_905142475.1	2775159	2775159	type	True	87.0313	1338	1754	95	below_threshold
Xanthomonas hortorum	strain=CFBP2533	GCA_012922215.1	56454	56454	pathovar	True	86.91	1315	1754	95	below_threshold
Xanthomonas hortorum	strain=CFBP 2533	GCA_021353095.1	56454	56454	pathovar	True	86.8583	1327	1754	95	below_threshold
Xanthomonas oryzae	strain=WHRI 5234	GCA_003064145.1	347	347	pathovar	True	86.5237	1153	1754	95	below_threshold
Xanthomonas campestris	strain=NCPPB 347	GCA_020731405.1	339	339	pathovar	True	86.2759	1278	1754	95	below_threshold
Xanthomonas oryzae	strain=ICMP3125	GCA_004136375.1	347	347	type	True	86.1319	1153	1754	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:54:54,083] [INFO] DFAST Taxonomy check result was written to GCF_000454545.1_20120625_genomic.fna/tc_result.tsv
[2024-01-24 12:54:54,084] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:54:54,084] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:54:54,084] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8e3b08f6-4dee-4373-9b30-ed6e1533d0b4/dqc_reference/checkm_data
[2024-01-24 12:54:54,086] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:54:54,141] [INFO] Task started: CheckM
[2024-01-24 12:54:54,142] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000454545.1_20120625_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000454545.1_20120625_genomic.fna/checkm_input GCF_000454545.1_20120625_genomic.fna/checkm_result
[2024-01-24 12:56:03,042] [INFO] Task succeeded: CheckM
[2024-01-24 12:56:03,043] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:56:03,068] [INFO] ===== Completeness check finished =====
[2024-01-24 12:56:03,069] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:56:03,069] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000454545.1_20120625_genomic.fna/markers.fasta)
[2024-01-24 12:56:03,069] [INFO] Task started: Blastn
[2024-01-24 12:56:03,069] [INFO] Running command: blastn -query GCF_000454545.1_20120625_genomic.fna/markers.fasta -db /var/lib/cwl/stg8e3b08f6-4dee-4373-9b30-ed6e1533d0b4/dqc_reference/reference_markers_gtdb.fasta -out GCF_000454545.1_20120625_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:56:04,780] [INFO] Task succeeded: Blastn
[2024-01-24 12:56:04,784] [INFO] Selected 10 target genomes.
[2024-01-24 12:56:04,785] [INFO] Target genome list was writen to GCF_000454545.1_20120625_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:56:04,810] [INFO] Task started: fastANI
[2024-01-24 12:56:04,811] [INFO] Running command: fastANI --query /var/lib/cwl/stgb9083a9f-01fc-448c-8d97-62fb742dcdd1/GCF_000454545.1_20120625_genomic.fna.gz --refList GCF_000454545.1_20120625_genomic.fna/target_genomes_gtdb.txt --output GCF_000454545.1_20120625_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:56:22,229] [INFO] Task succeeded: fastANI
[2024-01-24 12:56:22,243] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:56:22,243] [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_000454545.1	s__Xanthomonas cassavae	100.0	1754	1754	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_001642575.1	s__Xanthomonas floridensis	93.3122	1397	1754	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	93.2048	1406	1754	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	91.859	1387	1754	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	89.731	1206	1754	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	99.30	99.30	0.96	0.96	2	-
GCF_002940015.1	s__Xanthomonas melonis	88.2355	1329	1754	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	87.8559	1028	1754	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001908725.1	s__Xanthomonas vesicatoria	87.6865	1373	1754	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	99.30	98.65	0.97	0.94	15	-
GCF_003999565.1	s__Xanthomonas phaseoli	87.112	1353	1754	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	86.1338	1155	1754	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	99.14	96.34	0.95	0.82	364	-
--------------------------------------------------------------------------------
[2024-01-24 12:56:22,245] [INFO] GTDB search result was written to GCF_000454545.1_20120625_genomic.fna/result_gtdb.tsv
[2024-01-24 12:56:22,245] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:56:22,249] [INFO] DFAST_QC result json was written to GCF_000454545.1_20120625_genomic.fna/dqc_result.json
[2024-01-24 12:56:22,249] [INFO] DFAST_QC completed!
[2024-01-24 12:56:22,249] [INFO] Total running time: 0h2m17s