[2024-01-25 17:48:50,865] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:48:50,867] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:48:50,867] [INFO] DQC Reference Directory: /var/lib/cwl/stg17c176b8-76e0-40d3-ab2a-e9b18aa25d06/dqc_reference
[2024-01-25 17:48:51,971] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:48:51,972] [INFO] Task started: Prodigal
[2024-01-25 17:48:51,972] [INFO] Running command: gunzip -c /var/lib/cwl/stgced510b5-9ca0-4f21-b448-a864d10aab9c/GCF_030551335.1_Xvh_NCPPB_2417_v3_genomic.fna.gz | prodigal -d GCF_030551335.1_Xvh_NCPPB_2417_v3_genomic.fna/cds.fna -a GCF_030551335.1_Xvh_NCPPB_2417_v3_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:49:07,389] [INFO] Task succeeded: Prodigal
[2024-01-25 17:49:07,389] [INFO] Task started: HMMsearch
[2024-01-25 17:49:07,389] [INFO] Running command: hmmsearch --tblout GCF_030551335.1_Xvh_NCPPB_2417_v3_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg17c176b8-76e0-40d3-ab2a-e9b18aa25d06/dqc_reference/reference_markers.hmm GCF_030551335.1_Xvh_NCPPB_2417_v3_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:49:07,652] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:49:07,655] [INFO] Found 6/6 markers.
[2024-01-25 17:49:07,691] [INFO] Query marker FASTA was written to GCF_030551335.1_Xvh_NCPPB_2417_v3_genomic.fna/markers.fasta
[2024-01-25 17:49:07,691] [INFO] Task started: Blastn
[2024-01-25 17:49:07,691] [INFO] Running command: blastn -query GCF_030551335.1_Xvh_NCPPB_2417_v3_genomic.fna/markers.fasta -db /var/lib/cwl/stg17c176b8-76e0-40d3-ab2a-e9b18aa25d06/dqc_reference/reference_markers.fasta -out GCF_030551335.1_Xvh_NCPPB_2417_v3_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:49:08,504] [INFO] Task succeeded: Blastn
[2024-01-25 17:49:08,507] [INFO] Selected 10 target genomes.
[2024-01-25 17:49:08,507] [INFO] Target genome list was writen to GCF_030551335.1_Xvh_NCPPB_2417_v3_genomic.fna/target_genomes.txt
[2024-01-25 17:49:08,513] [INFO] Task started: fastANI
[2024-01-25 17:49:08,513] [INFO] Running command: fastANI --query /var/lib/cwl/stgced510b5-9ca0-4f21-b448-a864d10aab9c/GCF_030551335.1_Xvh_NCPPB_2417_v3_genomic.fna.gz --refList GCF_030551335.1_Xvh_NCPPB_2417_v3_genomic.fna/target_genomes.txt --output GCF_030551335.1_Xvh_NCPPB_2417_v3_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:49:22,197] [INFO] Task succeeded: fastANI
[2024-01-25 17:49:22,198] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg17c176b8-76e0-40d3-ab2a-e9b18aa25d06/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:49:22,198] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg17c176b8-76e0-40d3-ab2a-e9b18aa25d06/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:49:22,205] [INFO] Found 10 fastANI hits (5 hits with ANI > threshold)
[2024-01-25 17:49:22,205] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:49:22,205] [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 vasicola	strain=NCPPB 2417	GCA_000772705.2	56459	56459	type	True	99.997	1584	1589	95	conclusive
Xanthomonas vasicola	strain=CFBP2543	GCA_002939925.1	56459	56459	type	True	99.9924	1549	1589	95	conclusive
Xanthomonas vasicola	strain=SAM119	GCA_003015715.1	56459	56459	pathovar	True	98.6652	1495	1589	95	conclusive
Xanthomonas vasicola	strain=SAM119	GCA_002191955.1	56459	56459	pathovar	True	98.6354	1471	1589	95	conclusive
Xanthomonas vasicola	strain=NCPPB 2649	GCA_000770355.2	56459	56459	pathovar	True	98.565	1499	1589	95	conclusive
Xanthomonas euvesicatoria	strain=ATCC 11633	GCA_020880415.1	456327	456327	type	True	90.2593	1357	1589	95	below_threshold
Xanthomonas citri	strain=ICMP5732	GCA_021474205.1	346	346	pathovar	True	90.2224	1396	1589	95	below_threshold
Xanthomonas hydrangeae	strain=LMG 31884	GCA_905142475.1	2775159	2775159	type	True	86.7664	1307	1589	95	below_threshold
Xanthomonas hortorum	strain=CFBP 2533	GCA_021353095.1	56454	56454	pathovar	True	86.7525	1278	1589	95	below_threshold
Xanthomonas hortorum	strain=CFBP2533	GCA_012922215.1	56454	56454	pathovar	True	86.7255	1288	1589	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:49:22,226] [INFO] DFAST Taxonomy check result was written to GCF_030551335.1_Xvh_NCPPB_2417_v3_genomic.fna/tc_result.tsv
[2024-01-25 17:49:22,226] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:49:22,226] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:49:22,226] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg17c176b8-76e0-40d3-ab2a-e9b18aa25d06/dqc_reference/checkm_data
[2024-01-25 17:49:22,227] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:49:22,274] [INFO] Task started: CheckM
[2024-01-25 17:49:22,274] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030551335.1_Xvh_NCPPB_2417_v3_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030551335.1_Xvh_NCPPB_2417_v3_genomic.fna/checkm_input GCF_030551335.1_Xvh_NCPPB_2417_v3_genomic.fna/checkm_result
[2024-01-25 17:50:09,003] [INFO] Task succeeded: CheckM
[2024-01-25 17:50:09,004] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:50:09,053] [INFO] ===== Completeness check finished =====
[2024-01-25 17:50:09,053] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:50:09,054] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030551335.1_Xvh_NCPPB_2417_v3_genomic.fna/markers.fasta)
[2024-01-25 17:50:09,054] [INFO] Task started: Blastn
[2024-01-25 17:50:09,054] [INFO] Running command: blastn -query GCF_030551335.1_Xvh_NCPPB_2417_v3_genomic.fna/markers.fasta -db /var/lib/cwl/stg17c176b8-76e0-40d3-ab2a-e9b18aa25d06/dqc_reference/reference_markers_gtdb.fasta -out GCF_030551335.1_Xvh_NCPPB_2417_v3_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:50:10,653] [INFO] Task succeeded: Blastn
[2024-01-25 17:50:10,656] [INFO] Selected 9 target genomes.
[2024-01-25 17:50:10,656] [INFO] Target genome list was writen to GCF_030551335.1_Xvh_NCPPB_2417_v3_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:50:10,671] [INFO] Task started: fastANI
[2024-01-25 17:50:10,671] [INFO] Running command: fastANI --query /var/lib/cwl/stgced510b5-9ca0-4f21-b448-a864d10aab9c/GCF_030551335.1_Xvh_NCPPB_2417_v3_genomic.fna.gz --refList GCF_030551335.1_Xvh_NCPPB_2417_v3_genomic.fna/target_genomes_gtdb.txt --output GCF_030551335.1_Xvh_NCPPB_2417_v3_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:50:23,159] [INFO] Task succeeded: fastANI
[2024-01-25 17:50:23,166] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:50:23,166] [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_000772705.2	s__Xanthomonas vasicola	99.997	1584	1589	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	98.75	98.20	0.95	0.92	113	conclusive
GCF_002846205.1	s__Xanthomonas prunicola	91.2493	1361	1589	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	99.99	99.99	1.00	0.99	3	-
GCF_004136375.1	s__Xanthomonas oryzae	90.8872	1261	1589	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	99.14	96.34	0.95	0.82	364	-
GCF_013112235.1	s__Xanthomonas perforans	90.352	1399	1589	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	90.2863	1351	1589	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	89.8147	1368	1589	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	89.743	1205	1589	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	89.5261	1299	1589	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	88.9182	1286	1589	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	98.97	98.97	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2024-01-25 17:50:23,168] [INFO] GTDB search result was written to GCF_030551335.1_Xvh_NCPPB_2417_v3_genomic.fna/result_gtdb.tsv
[2024-01-25 17:50:23,168] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:50:23,171] [INFO] DFAST_QC result json was written to GCF_030551335.1_Xvh_NCPPB_2417_v3_genomic.fna/dqc_result.json
[2024-01-25 17:50:23,171] [INFO] DFAST_QC completed!
[2024-01-25 17:50:23,171] [INFO] Total running time: 0h1m32s