[2024-01-24 15:02:07,444] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:07,446] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:07,446] [INFO] DQC Reference Directory: /var/lib/cwl/stgdaa80ceb-fc81-4974-bcb7-50ea4d619dea/dqc_reference
[2024-01-24 15:02:09,603] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:09,604] [INFO] Task started: Prodigal
[2024-01-24 15:02:09,605] [INFO] Running command: gunzip -c /var/lib/cwl/stg80f74a1c-ab21-4be4-ae42-5a8e222094b7/GCF_017163705.1_ASM1716370v1_genomic.fna.gz | prodigal -d GCF_017163705.1_ASM1716370v1_genomic.fna/cds.fna -a GCF_017163705.1_ASM1716370v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:25,837] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:25,838] [INFO] Task started: HMMsearch
[2024-01-24 15:02:25,838] [INFO] Running command: hmmsearch --tblout GCF_017163705.1_ASM1716370v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdaa80ceb-fc81-4974-bcb7-50ea4d619dea/dqc_reference/reference_markers.hmm GCF_017163705.1_ASM1716370v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:02:26,077] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:02:26,079] [INFO] Found 6/6 markers.
[2024-01-24 15:02:26,130] [INFO] Query marker FASTA was written to GCF_017163705.1_ASM1716370v1_genomic.fna/markers.fasta
[2024-01-24 15:02:26,130] [INFO] Task started: Blastn
[2024-01-24 15:02:26,130] [INFO] Running command: blastn -query GCF_017163705.1_ASM1716370v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdaa80ceb-fc81-4974-bcb7-50ea4d619dea/dqc_reference/reference_markers.fasta -out GCF_017163705.1_ASM1716370v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:27,189] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:27,192] [INFO] Selected 11 target genomes.
[2024-01-24 15:02:27,192] [INFO] Target genome list was writen to GCF_017163705.1_ASM1716370v1_genomic.fna/target_genomes.txt
[2024-01-24 15:02:27,197] [INFO] Task started: fastANI
[2024-01-24 15:02:27,197] [INFO] Running command: fastANI --query /var/lib/cwl/stg80f74a1c-ab21-4be4-ae42-5a8e222094b7/GCF_017163705.1_ASM1716370v1_genomic.fna.gz --refList GCF_017163705.1_ASM1716370v1_genomic.fna/target_genomes.txt --output GCF_017163705.1_ASM1716370v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:02:42,882] [INFO] Task succeeded: fastANI
[2024-01-24 15:02:42,883] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdaa80ceb-fc81-4974-bcb7-50ea4d619dea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:02:42,883] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdaa80ceb-fc81-4974-bcb7-50ea4d619dea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:02:42,893] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:02:42,893] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:02:42,894] [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 hyacinthi	strain=CFBP1156	GCA_002939895.1	56455	56455	type	True	93.3455	1251	1761	95	below_threshold
Xanthomonas hyacinthi	strain=CFBP 1156	GCA_009769165.1	56455	56455	type	True	93.3075	1264	1761	95	below_threshold
Xanthomonas translucens	strain=ATCC 19319	GCA_020880735.1	343	343	type	True	92.8013	1056	1761	95	below_threshold
Xanthomonas translucens	strain=DSM 18974	GCA_000331775.1	343	343	type	True	92.75	1019	1761	95	below_threshold
Xanthomonas theicola	strain=CFBP 4691	GCA_002940605.1	56464	56464	type	True	90.871	1058	1761	95	below_threshold
Xanthomonas indica	strain=PPL560	GCA_022669045.1	2912242	2912242	type	True	88.9422	1323	1761	95	below_threshold
Xanthomonas sacchari	strain=CFBP4641	GCA_002940085.1	56458	56458	suspected-type	True	88.8501	1344	1761	95	below_threshold
Stenotrophomonas bentonitica	strain=DSM 103927	GCA_013185915.1	1450134	1450134	type	True	82.9291	851	1761	95	below_threshold
Xanthomonas hydrangeae	strain=LMG 31884	GCA_905142475.1	2775159	2775159	type	True	82.4025	1049	1761	95	below_threshold
Xanthomonas euvesicatoria	strain=ATCC 11633	GCA_020880415.1	456327	456327	type	True	82.1088	1020	1761	95	below_threshold
Xanthomonas citri	strain=ICMP5732	GCA_021474205.1	346	346	pathovar	True	81.987	1034	1761	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:02:42,895] [INFO] DFAST Taxonomy check result was written to GCF_017163705.1_ASM1716370v1_genomic.fna/tc_result.tsv
[2024-01-24 15:02:42,896] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:02:42,896] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:02:42,896] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdaa80ceb-fc81-4974-bcb7-50ea4d619dea/dqc_reference/checkm_data
[2024-01-24 15:02:42,897] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:02:42,949] [INFO] Task started: CheckM
[2024-01-24 15:02:42,949] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017163705.1_ASM1716370v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017163705.1_ASM1716370v1_genomic.fna/checkm_input GCF_017163705.1_ASM1716370v1_genomic.fna/checkm_result
[2024-01-24 15:03:41,785] [INFO] Task succeeded: CheckM
[2024-01-24 15:03:41,786] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:03:41,806] [INFO] ===== Completeness check finished =====
[2024-01-24 15:03:41,806] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:03:41,806] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017163705.1_ASM1716370v1_genomic.fna/markers.fasta)
[2024-01-24 15:03:41,807] [INFO] Task started: Blastn
[2024-01-24 15:03:41,807] [INFO] Running command: blastn -query GCF_017163705.1_ASM1716370v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdaa80ceb-fc81-4974-bcb7-50ea4d619dea/dqc_reference/reference_markers_gtdb.fasta -out GCF_017163705.1_ASM1716370v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:43,927] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:43,930] [INFO] Selected 7 target genomes.
[2024-01-24 15:03:43,930] [INFO] Target genome list was writen to GCF_017163705.1_ASM1716370v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:03:43,935] [INFO] Task started: fastANI
[2024-01-24 15:03:43,935] [INFO] Running command: fastANI --query /var/lib/cwl/stg80f74a1c-ab21-4be4-ae42-5a8e222094b7/GCF_017163705.1_ASM1716370v1_genomic.fna.gz --refList GCF_017163705.1_ASM1716370v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017163705.1_ASM1716370v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:03:56,623] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:56,630] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:03:56,630] [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_014236855.1	s__Xanthomonas_A sp014236855	95.048	1536	1761	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas_A	95.0	95.82	95.01	0.91	0.88	7	conclusive
GCF_014197395.1	s__Xanthomonas_A translucens_B	93.8284	1536	1761	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007829315.1	s__Xanthomonas_A translucens_A	93.653	1546	1761	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009769165.1	s__Xanthomonas_A hyacinthi	93.3375	1261	1761	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000331775.1	s__Xanthomonas_A translucens	92.75	1019	1761	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas_A	95.0	97.09	95.18	0.88	0.77	59	-
GCF_014236795.1	s__Xanthomonas_A theicola	90.5696	1136	1761	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas_A	95.0	99.99	99.99	1.00	1.00	2	-
GCF_014199795.1	s__Xanthomonas_A sp014199795	88.8575	1330	1761	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas_A	95.0	98.20	98.15	0.95	0.95	4	-
--------------------------------------------------------------------------------
[2024-01-24 15:03:56,635] [INFO] GTDB search result was written to GCF_017163705.1_ASM1716370v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:03:56,636] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:03:56,641] [INFO] DFAST_QC result json was written to GCF_017163705.1_ASM1716370v1_genomic.fna/dqc_result.json
[2024-01-24 15:03:56,642] [INFO] DFAST_QC completed!
[2024-01-24 15:03:56,642] [INFO] Total running time: 0h1m49s