[2024-01-24 14:47:21,270] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:47:21,292] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:47:21,293] [INFO] DQC Reference Directory: /var/lib/cwl/stg62f7dc17-f881-40cd-afb4-176f84780e70/dqc_reference
[2024-01-24 14:47:25,110] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:47:25,111] [INFO] Task started: Prodigal
[2024-01-24 14:47:25,112] [INFO] Running command: gunzip -c /var/lib/cwl/stgf1e2a54c-913c-4068-86e2-12e3365a97c3/GCF_013177435.1_ASM1317743v1_genomic.fna.gz | prodigal -d GCF_013177435.1_ASM1317743v1_genomic.fna/cds.fna -a GCF_013177435.1_ASM1317743v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:35,203] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:35,203] [INFO] Task started: HMMsearch
[2024-01-24 14:47:35,203] [INFO] Running command: hmmsearch --tblout GCF_013177435.1_ASM1317743v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg62f7dc17-f881-40cd-afb4-176f84780e70/dqc_reference/reference_markers.hmm GCF_013177435.1_ASM1317743v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:35,525] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:35,527] [INFO] Found 6/6 markers.
[2024-01-24 14:47:35,556] [INFO] Query marker FASTA was written to GCF_013177435.1_ASM1317743v1_genomic.fna/markers.fasta
[2024-01-24 14:47:35,557] [INFO] Task started: Blastn
[2024-01-24 14:47:35,557] [INFO] Running command: blastn -query GCF_013177435.1_ASM1317743v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg62f7dc17-f881-40cd-afb4-176f84780e70/dqc_reference/reference_markers.fasta -out GCF_013177435.1_ASM1317743v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:36,436] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:36,439] [INFO] Selected 11 target genomes.
[2024-01-24 14:47:36,440] [INFO] Target genome list was writen to GCF_013177435.1_ASM1317743v1_genomic.fna/target_genomes.txt
[2024-01-24 14:47:37,062] [INFO] Task started: fastANI
[2024-01-24 14:47:37,063] [INFO] Running command: fastANI --query /var/lib/cwl/stgf1e2a54c-913c-4068-86e2-12e3365a97c3/GCF_013177435.1_ASM1317743v1_genomic.fna.gz --refList GCF_013177435.1_ASM1317743v1_genomic.fna/target_genomes.txt --output GCF_013177435.1_ASM1317743v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:47:45,814] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:45,815] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg62f7dc17-f881-40cd-afb4-176f84780e70/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:47:45,815] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg62f7dc17-f881-40cd-afb4-176f84780e70/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:47:45,827] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:47:45,827] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:47:45,827] [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 taiwanensis	strain=PLS229	GCA_013177435.1	1444770	1444770	type	True	100.0	936	941	95	conclusive
Xylella taiwanensis	strain=PLS229	GCA_000576405.1	1444770	1444770	type	True	99.9598	863	941	95	conclusive
Xylella fastidiosa subsp. multiplex	strain=ATCC 35871	GCA_000428665.1	644357	2371	type	True	83.0159	632	941	95	below_threshold
Xylella fastidiosa	strain=DSM 10026	GCA_900129695.1	2371	2371	type	True	82.8545	646	941	95	below_threshold
Xylella fastidiosa	strain=ATCC 35879	GCA_000767565.1	2371	2371	type	True	82.6531	670	941	95	below_threshold
Xylella fastidiosa	strain=ATCC 35879	GCA_011801475.1	2371	2371	type	True	82.6527	667	941	95	below_threshold
Xanthomonas hydrangeae	strain=LMG 31884	GCA_905142475.1	2775159	2775159	type	True	76.7323	121	941	95	below_threshold
Xanthomonas indica	strain=PPL560	GCA_022669045.1	2912242	2912242	type	True	76.6437	128	941	95	below_threshold
Xanthomonas translucens	strain=ATCC 19319	GCA_020880735.1	343	343	type	True	76.5761	109	941	95	below_threshold
Xanthomonas hortorum	strain=CFBP2533	GCA_012922215.1	56454	56454	pathovar	True	76.4036	125	941	95	below_threshold
Xanthomonas hortorum	strain=CFBP 2533	GCA_021353095.1	56454	56454	pathovar	True	76.353	126	941	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:47:45,829] [INFO] DFAST Taxonomy check result was written to GCF_013177435.1_ASM1317743v1_genomic.fna/tc_result.tsv
[2024-01-24 14:47:45,829] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:47:45,830] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:47:45,830] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg62f7dc17-f881-40cd-afb4-176f84780e70/dqc_reference/checkm_data
[2024-01-24 14:47:45,831] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:47:45,862] [INFO] Task started: CheckM
[2024-01-24 14:47:45,862] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013177435.1_ASM1317743v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013177435.1_ASM1317743v1_genomic.fna/checkm_input GCF_013177435.1_ASM1317743v1_genomic.fna/checkm_result
[2024-01-24 14:48:20,133] [INFO] Task succeeded: CheckM
[2024-01-24 14:48:20,134] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.24%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:48:20,151] [INFO] ===== Completeness check finished =====
[2024-01-24 14:48:20,152] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:48:20,152] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013177435.1_ASM1317743v1_genomic.fna/markers.fasta)
[2024-01-24 14:48:20,153] [INFO] Task started: Blastn
[2024-01-24 14:48:20,153] [INFO] Running command: blastn -query GCF_013177435.1_ASM1317743v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg62f7dc17-f881-40cd-afb4-176f84780e70/dqc_reference/reference_markers_gtdb.fasta -out GCF_013177435.1_ASM1317743v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:48:21,214] [INFO] Task succeeded: Blastn
[2024-01-24 14:48:21,218] [INFO] Selected 21 target genomes.
[2024-01-24 14:48:21,219] [INFO] Target genome list was writen to GCF_013177435.1_ASM1317743v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:48:21,241] [INFO] Task started: fastANI
[2024-01-24 14:48:21,242] [INFO] Running command: fastANI --query /var/lib/cwl/stgf1e2a54c-913c-4068-86e2-12e3365a97c3/GCF_013177435.1_ASM1317743v1_genomic.fna.gz --refList GCF_013177435.1_ASM1317743v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013177435.1_ASM1317743v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:48:35,662] [INFO] Task succeeded: fastANI
[2024-01-24 14:48:35,684] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:48:35,685] [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_013177435.1	s__Xylella taiwanensis	100.0	937	941	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xylella	95.0	100.00	99.99	1.00	0.99	4	conclusive
GCF_011801475.1	s__Xylella fastidiosa	82.6602	670	941	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xylella	95.0	98.40	96.23	0.96	0.89	130	-
GCF_000972865.1	s__Pseudoxanthomonas suwonensis_B	76.8939	80	941	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001431425.1	s__Stenotrophomonas nitritireducens	76.8921	84	941	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	98.94	98.42	0.92	0.89	3	-
GCF_014852005.1	s__Pseudoxanthomonas_A sp014852005	76.8628	71	941	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_905142465.1	s__Xanthomonas sp905142465	76.7945	124	941	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.1927	99.49	99.23	0.97	0.96	4	-
GCA_014654535.1	s__Pseudomonas_S boreopolis	76.7932	129	941	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudomonas_S	95.0	98.68	98.68	0.91	0.91	2	-
GCF_001431645.1	s__Stenotrophomonas_A panacihumi	76.7186	99	941	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas_A	95.0	99.98	99.98	0.99	0.99	2	-
GCF_014199795.1	s__Xanthomonas_A sp014199795	76.5931	119	941	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas_A	95.0	98.20	98.15	0.95	0.95	4	-
GCF_001660815.1	s__Xanthomonas nasturtii	76.5861	103	941	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	98.97	98.97	0.95	0.95	2	-
GCA_002471015.1	s__Stenotrophomonas sp002471015	76.5615	76	941	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	96.17	95.12	0.84	0.81	4	-
GCF_001304695.1	s__Xanthomonas axonopodis	76.5513	109	941	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	98.43	97.90	0.94	0.92	5	-
GCF_002940065.1	s__Xanthomonas populi	76.5493	99	941	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002940205.1	s__Xanthomonas arboricola_C	76.5465	115	941	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	99.99	99.99	0.99	0.99	2	-
GCF_002939985.1	s__Xanthomonas hortorum_A	76.5411	114	941	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	96.0883	98.80	97.51	0.93	0.89	28	-
GCF_001423495.1	s__Xanthomonas sp001423495	76.5404	106	941	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001013475.1	s__Xanthomonas arboricola	76.5349	117	941	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	96.94	96.17	0.91	0.85	117	-
GCF_008801575.1	s__Xanthomonas cissicola	76.4844	104	941	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	97.71	95.83	0.91	0.86	247	-
GCF_002836635.1	s__Stenotrophomonas sp002836635	76.4732	80	941	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	97.91	95.43	0.91	0.85	8	-
GCF_003064105.1	s__Xanthomonas hortorum	76.4567	107	941	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	96.0883	96.84	96.16	0.86	0.83	8	-
GCF_002940665.1	s__Xanthomonas arboricola_B	76.2941	118	941	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	97.97	97.84	0.92	0.92	4	-
--------------------------------------------------------------------------------
[2024-01-24 14:48:35,686] [INFO] GTDB search result was written to GCF_013177435.1_ASM1317743v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:48:35,687] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:48:35,691] [INFO] DFAST_QC result json was written to GCF_013177435.1_ASM1317743v1_genomic.fna/dqc_result.json
[2024-01-24 14:48:35,691] [INFO] DFAST_QC completed!
[2024-01-24 14:48:35,692] [INFO] Total running time: 0h1m14s