[2024-01-24 13:31:44,599] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:44,601] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:44,601] [INFO] DQC Reference Directory: /var/lib/cwl/stg24e677e8-24b2-406d-b3ad-45a933204c26/dqc_reference
[2024-01-24 13:31:45,832] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:45,832] [INFO] Task started: Prodigal
[2024-01-24 13:31:45,833] [INFO] Running command: gunzip -c /var/lib/cwl/stga925f698-4663-4bd2-ab8e-c8bd0bf9cfb3/GCF_028891345.1_ASM2889134v1_genomic.fna.gz | prodigal -d GCF_028891345.1_ASM2889134v1_genomic.fna/cds.fna -a GCF_028891345.1_ASM2889134v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:31:54,058] [INFO] Task succeeded: Prodigal
[2024-01-24 13:31:54,058] [INFO] Task started: HMMsearch
[2024-01-24 13:31:54,058] [INFO] Running command: hmmsearch --tblout GCF_028891345.1_ASM2889134v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg24e677e8-24b2-406d-b3ad-45a933204c26/dqc_reference/reference_markers.hmm GCF_028891345.1_ASM2889134v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:31:54,329] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:31:54,331] [INFO] Found 6/6 markers.
[2024-01-24 13:31:54,371] [INFO] Query marker FASTA was written to GCF_028891345.1_ASM2889134v1_genomic.fna/markers.fasta
[2024-01-24 13:31:54,371] [INFO] Task started: Blastn
[2024-01-24 13:31:54,371] [INFO] Running command: blastn -query GCF_028891345.1_ASM2889134v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg24e677e8-24b2-406d-b3ad-45a933204c26/dqc_reference/reference_markers.fasta -out GCF_028891345.1_ASM2889134v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:55,056] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:55,061] [INFO] Selected 10 target genomes.
[2024-01-24 13:31:55,062] [INFO] Target genome list was writen to GCF_028891345.1_ASM2889134v1_genomic.fna/target_genomes.txt
[2024-01-24 13:31:55,066] [INFO] Task started: fastANI
[2024-01-24 13:31:55,067] [INFO] Running command: fastANI --query /var/lib/cwl/stga925f698-4663-4bd2-ab8e-c8bd0bf9cfb3/GCF_028891345.1_ASM2889134v1_genomic.fna.gz --refList GCF_028891345.1_ASM2889134v1_genomic.fna/target_genomes.txt --output GCF_028891345.1_ASM2889134v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:00,952] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:00,952] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg24e677e8-24b2-406d-b3ad-45a933204c26/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:00,953] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg24e677e8-24b2-406d-b3ad-45a933204c26/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:00,963] [INFO] Found 6 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 13:32:00,963] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:00,963] [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
Xylella fastidiosa	strain=ATCC 35879	GCA_011801475.1	2371	2371	type	True	99.982	858	865	95	conclusive
Xylella fastidiosa	strain=ATCC 35879	GCA_000767565.1	2371	2371	type	True	99.9589	818	865	95	conclusive
Xylella fastidiosa	strain=DSM 10026	GCA_900129695.1	2371	2371	type	True	99.904	774	865	95	conclusive
Xylella fastidiosa subsp. multiplex	strain=ATCC 35871	GCA_000428665.1	644357	2371	type	True	97.9616	753	865	95	conclusive
Xylella taiwanensis	strain=PLS229	GCA_013177435.1	1444770	1444770	type	True	82.7602	671	865	95	below_threshold
Xanthomonas translucens	strain=ATCC 19319	GCA_020880735.1	343	343	type	True	76.5826	54	865	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:00,965] [INFO] DFAST Taxonomy check result was written to GCF_028891345.1_ASM2889134v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:00,966] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:00,966] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:00,966] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg24e677e8-24b2-406d-b3ad-45a933204c26/dqc_reference/checkm_data
[2024-01-24 13:32:00,968] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:01,003] [INFO] Task started: CheckM
[2024-01-24 13:32:01,004] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_028891345.1_ASM2889134v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_028891345.1_ASM2889134v1_genomic.fna/checkm_input GCF_028891345.1_ASM2889134v1_genomic.fna/checkm_result
[2024-01-24 13:32:32,019] [INFO] Task succeeded: CheckM
[2024-01-24 13:32:32,021] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:32:32,041] [INFO] ===== Completeness check finished =====
[2024-01-24 13:32:32,041] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:32:32,042] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_028891345.1_ASM2889134v1_genomic.fna/markers.fasta)
[2024-01-24 13:32:32,042] [INFO] Task started: Blastn
[2024-01-24 13:32:32,042] [INFO] Running command: blastn -query GCF_028891345.1_ASM2889134v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg24e677e8-24b2-406d-b3ad-45a933204c26/dqc_reference/reference_markers_gtdb.fasta -out GCF_028891345.1_ASM2889134v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:33,088] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:33,093] [INFO] Selected 23 target genomes.
[2024-01-24 13:32:33,094] [INFO] Target genome list was writen to GCF_028891345.1_ASM2889134v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:32:33,129] [INFO] Task started: fastANI
[2024-01-24 13:32:33,129] [INFO] Running command: fastANI --query /var/lib/cwl/stga925f698-4663-4bd2-ab8e-c8bd0bf9cfb3/GCF_028891345.1_ASM2889134v1_genomic.fna.gz --refList GCF_028891345.1_ASM2889134v1_genomic.fna/target_genomes_gtdb.txt --output GCF_028891345.1_ASM2889134v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:32:47,128] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:47,140] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:32:47,141] [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_011801475.1	s__Xylella fastidiosa	99.9819	856	865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xylella	95.0	98.40	96.23	0.96	0.89	130	conclusive
GCF_013177435.1	s__Xylella taiwanensis	82.7564	669	865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xylella	95.0	100.00	99.99	1.00	0.99	4	-
GCF_001423585.1	s__Xanthomonas sp001423585	76.9858	67	865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	98.11	97.14	0.95	0.93	10	-
GCF_004348115.1	s__Stenotrophomonas sp004348115	76.8536	53	865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	98.00	98.00	0.94	0.94	2	-
GCF_900183975.1	s__Xanthomonas fragariae	76.838	61	865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	99.74	99.53	0.99	0.96	62	-
GCF_013387485.1	s__Stenotrophomonas maltophilia_AA	76.7906	58	865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	97.19	96.54	0.90	0.89	3	-
GCF_002939865.1	s__Xanthomonas dyei	76.7866	51	865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001431465.1	s__Stenotrophomonas terrae	76.7064	53	865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004216795.1	s__Stenotrophomonas_A sp004216795	76.6937	54	865	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_000007145.1	s__Xanthomonas campestris	76.6628	58	865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	98.22	96.56	0.94	0.87	68	-
GCF_000331775.1	s__Xanthomonas_A translucens	76.5816	54	865	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_001908725.1	s__Xanthomonas vesicatoria	76.5439	57	865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	99.30	98.65	0.97	0.94	15	-
GCF_002940205.1	s__Xanthomonas arboricola_C	76.4639	64	865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:32:47,143] [INFO] GTDB search result was written to GCF_028891345.1_ASM2889134v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:32:47,144] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:32:47,148] [INFO] DFAST_QC result json was written to GCF_028891345.1_ASM2889134v1_genomic.fna/dqc_result.json
[2024-01-24 13:32:47,148] [INFO] DFAST_QC completed!
[2024-01-24 13:32:47,148] [INFO] Total running time: 0h1m3s