[2024-01-24 13:36:57,320] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:36:57,321] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:36:57,322] [INFO] DQC Reference Directory: /var/lib/cwl/stge48212f1-606c-44e6-b548-3d971b413c03/dqc_reference
[2024-01-24 13:36:58,600] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:36:58,601] [INFO] Task started: Prodigal
[2024-01-24 13:36:58,602] [INFO] Running command: gunzip -c /var/lib/cwl/stgd503a5a7-63ef-4dc9-bd04-62eb68fe5429/GCF_014635165.1_ASM1463516v1_genomic.fna.gz | prodigal -d GCF_014635165.1_ASM1463516v1_genomic.fna/cds.fna -a GCF_014635165.1_ASM1463516v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:13,024] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:13,025] [INFO] Task started: HMMsearch
[2024-01-24 13:37:13,025] [INFO] Running command: hmmsearch --tblout GCF_014635165.1_ASM1463516v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge48212f1-606c-44e6-b548-3d971b413c03/dqc_reference/reference_markers.hmm GCF_014635165.1_ASM1463516v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:13,378] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:13,379] [INFO] Found 6/6 markers.
[2024-01-24 13:37:13,415] [INFO] Query marker FASTA was written to GCF_014635165.1_ASM1463516v1_genomic.fna/markers.fasta
[2024-01-24 13:37:13,416] [INFO] Task started: Blastn
[2024-01-24 13:37:13,416] [INFO] Running command: blastn -query GCF_014635165.1_ASM1463516v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge48212f1-606c-44e6-b548-3d971b413c03/dqc_reference/reference_markers.fasta -out GCF_014635165.1_ASM1463516v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:14,433] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:14,436] [INFO] Selected 24 target genomes.
[2024-01-24 13:37:14,437] [INFO] Target genome list was writen to GCF_014635165.1_ASM1463516v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:14,448] [INFO] Task started: fastANI
[2024-01-24 13:37:14,448] [INFO] Running command: fastANI --query /var/lib/cwl/stgd503a5a7-63ef-4dc9-bd04-62eb68fe5429/GCF_014635165.1_ASM1463516v1_genomic.fna.gz --refList GCF_014635165.1_ASM1463516v1_genomic.fna/target_genomes.txt --output GCF_014635165.1_ASM1463516v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:35,251] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:35,251] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge48212f1-606c-44e6-b548-3d971b413c03/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:35,252] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge48212f1-606c-44e6-b548-3d971b413c03/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:35,270] [INFO] Found 24 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:37:35,271] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:35,271] [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
Pseudoxanthomonas indica	strain=CCM 7430	GCA_014635165.1	428993	428993	type	True	100.0	1312	1313	95	conclusive
Pseudoxanthomonas indica	strain=P15	GCA_900167565.1	428993	428993	type	True	99.9969	1311	1313	95	conclusive
Pseudoxanthomonas beigongshangi	strain=REN9	GCA_016820515.1	2782537	2782537	type	True	83.902	920	1313	95	below_threshold
Pseudoxanthomonas wuyuanensis	strain=DSM 100640	GCA_010093325.1	1073196	1073196	type	True	82.2311	762	1313	95	below_threshold
Pseudoxanthomonas mexicana	strain=DSM 17121	GCA_010093385.1	128785	128785	type	True	82.1472	733	1313	95	below_threshold
Pseudoxanthomonas japonensis	strain=DSM 17109	GCA_010093445.1	69284	69284	type	True	82.1252	775	1313	95	below_threshold
Pseudoxanthomonas wuyuanensis	strain=CGMCC 1.10978	GCA_900215535.1	1073196	1073196	type	True	82.0665	792	1313	95	below_threshold
Pseudoxanthomonas helianthi	strain=110414	GCA_017939625.1	1453541	1453541	type	True	81.0767	662	1313	95	below_threshold
Xanthomonas indica	strain=PPL560	GCA_022669045.1	2912242	2912242	type	True	81.0762	693	1313	95	below_threshold
Pseudoxanthomonas dokdonensis	strain=DSM 21858	GCA_001431405.1	344882	344882	type	True	81.0375	706	1313	95	below_threshold
Pseudoxanthomonas winnipegensis	strain=NML 130738	GCA_004283755.1	2480810	2480810	type	True	81.0185	649	1313	95	below_threshold
Xanthomonas translucens	strain=ATCC 19319	GCA_020880735.1	343	343	type	True	80.9951	578	1313	95	below_threshold
Xanthomonas sacchari	strain=CFBP4641	GCA_002940085.1	56458	56458	suspected-type	True	80.965	695	1313	95	below_threshold
Stenotrophomonas bentonitica	strain=DSM 103927	GCA_013185915.1	1450134	1450134	type	True	80.8618	626	1313	95	below_threshold
Pseudoxanthomonas composti	strain=GSS15	GCA_004122095.1	2137479	2137479	type	True	80.7093	659	1313	95	below_threshold
Pseudoxanthomonas taiwanensis	strain=DSM 22914	GCA_010093135.1	176598	176598	type	True	80.6575	557	1313	95	below_threshold
Vulcaniibacterium tengchongense	strain=YIM 77520	GCA_008033455.1	1273429	1273429	type	True	80.1906	583	1313	95	below_threshold
Vulcaniibacterium tengchongense	strain=DSM 25623	GCA_003814555.1	1273429	1273429	type	True	80.1881	601	1313	95	below_threshold
Luteimonas cucumeris	strain=CGMCC 1.10821	GCA_007830035.1	985012	985012	type	True	80.1516	583	1313	95	below_threshold
Luteimonas arsenica	strain=26-35	GCA_004352825.1	1586242	1586242	type	True	80.0584	493	1313	95	below_threshold
Xanthomonas hydrangeae	strain=LMG 31884	GCA_905142475.1	2775159	2775159	type	True	80.0458	602	1313	95	below_threshold
Luteimonas padinae	strain=KCTC 52403	GCA_014652935.1	1714359	1714359	type	True	79.7317	505	1313	95	below_threshold
Arenimonas terrae	strain=R29	GCA_006265115.1	2546226	2546226	type	True	79.2756	482	1313	95	below_threshold
Arenimonas metalli	strain=CF5-1	GCA_000747155.1	948077	948077	type	True	79.2517	446	1313	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:35,273] [INFO] DFAST Taxonomy check result was written to GCF_014635165.1_ASM1463516v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:35,273] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:35,273] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:35,274] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge48212f1-606c-44e6-b548-3d971b413c03/dqc_reference/checkm_data
[2024-01-24 13:37:35,275] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:35,321] [INFO] Task started: CheckM
[2024-01-24 13:37:35,321] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014635165.1_ASM1463516v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014635165.1_ASM1463516v1_genomic.fna/checkm_input GCF_014635165.1_ASM1463516v1_genomic.fna/checkm_result
[2024-01-24 13:38:30,955] [INFO] Task succeeded: CheckM
[2024-01-24 13:38:30,956] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:38:30,976] [INFO] ===== Completeness check finished =====
[2024-01-24 13:38:30,976] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:38:30,977] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014635165.1_ASM1463516v1_genomic.fna/markers.fasta)
[2024-01-24 13:38:30,977] [INFO] Task started: Blastn
[2024-01-24 13:38:30,977] [INFO] Running command: blastn -query GCF_014635165.1_ASM1463516v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge48212f1-606c-44e6-b548-3d971b413c03/dqc_reference/reference_markers_gtdb.fasta -out GCF_014635165.1_ASM1463516v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:32,569] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:32,574] [INFO] Selected 20 target genomes.
[2024-01-24 13:38:32,574] [INFO] Target genome list was writen to GCF_014635165.1_ASM1463516v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:32,596] [INFO] Task started: fastANI
[2024-01-24 13:38:32,596] [INFO] Running command: fastANI --query /var/lib/cwl/stgd503a5a7-63ef-4dc9-bd04-62eb68fe5429/GCF_014635165.1_ASM1463516v1_genomic.fna.gz --refList GCF_014635165.1_ASM1463516v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014635165.1_ASM1463516v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:49,696] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:49,718] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:38:49,719] [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_900167565.1	s__Pseudoxanthomonas_A indica	99.9969	1311	1313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCA_019218945.1	s__Pseudoxanthomonas_A sp019218945	83.9015	924	1313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	99.15	98.62	0.97	0.96	4	-
GCF_006542425.1	s__Pseudoxanthomonas_A sp006542425	83.5955	933	1313	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_001427635.1	s__Pseudoxanthomonas_A sp001427635	82.2782	769	1313	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_010093445.1	s__Pseudoxanthomonas_A japonensis	82.1529	771	1313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	96.78	96.68	0.83	0.68	4	-
GCF_010093385.1	s__Pseudoxanthomonas_A mexicana	82.1369	734	1313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	96.97	96.88	0.87	0.86	4	-
GCF_900215535.1	s__Pseudoxanthomonas_A wuyuanensis	82.0727	791	1313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	99.99	99.99	0.99	0.99	2	-
GCF_001427585.1	s__Pseudoxanthomonas_A sp001427585	82.0328	787	1313	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_900104255.1	s__Pseudoxanthomonas_A sp900104255	81.9989	793	1313	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_014851805.1	s__Pseudoxanthomonas_A sp014851805	81.7958	794	1313	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_006716465.1	s__Pseudoxanthomonas_A sp006716465	81.6328	776	1313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003505795.1	s__UBA8801 sp003505795	81.2301	424	1313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__UBA8801	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001431405.1	s__Pseudoxanthomonas_A dokdonensis	81.0463	705	1313	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_002940085.1	s__Xanthomonas_A sacchari	80.9614	696	1313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas_A	95.0	97.45	95.41	0.95	0.91	6	-
GCF_900109775.1	s__Pseudoxanthomonas_A sp900109775	80.869	640	1313	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_002893095.1	s__Stenotrophomonas sp002893095	80.822	611	1313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	97.47	97.41	0.90	0.90	3	-
GCF_900107375.1	s__Lysobacter sp900107375	80.3957	631	1313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003814555.1	s__Lysobacter tengchongensis	80.2171	598	1313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	99.99	99.99	0.99	0.99	2	-
GCF_004352825.1	s__Luteimonas arsenica	80.0364	495	1313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652935.1	s__Luteimonas padinae	79.7319	505	1313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:38:49,720] [INFO] GTDB search result was written to GCF_014635165.1_ASM1463516v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:49,721] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:49,729] [INFO] DFAST_QC result json was written to GCF_014635165.1_ASM1463516v1_genomic.fna/dqc_result.json
[2024-01-24 13:38:49,730] [INFO] DFAST_QC completed!
[2024-01-24 13:38:49,730] [INFO] Total running time: 0h1m52s