[2024-01-24 12:45:10,261] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:45:10,265] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:45:10,265] [INFO] DQC Reference Directory: /var/lib/cwl/stg63391880-43ed-48fc-af2c-142c01a20902/dqc_reference
[2024-01-24 12:45:13,082] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:45:13,084] [INFO] Task started: Prodigal
[2024-01-24 12:45:13,084] [INFO] Running command: gunzip -c /var/lib/cwl/stg61e43d74-148d-442d-ae68-6fe8b0867562/GCF_014841215.1_ASM1484121v1_genomic.fna.gz | prodigal -d GCF_014841215.1_ASM1484121v1_genomic.fna/cds.fna -a GCF_014841215.1_ASM1484121v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:45:31,282] [INFO] Task succeeded: Prodigal
[2024-01-24 12:45:31,283] [INFO] Task started: HMMsearch
[2024-01-24 12:45:31,283] [INFO] Running command: hmmsearch --tblout GCF_014841215.1_ASM1484121v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg63391880-43ed-48fc-af2c-142c01a20902/dqc_reference/reference_markers.hmm GCF_014841215.1_ASM1484121v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:45:31,588] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:45:31,589] [INFO] Found 6/6 markers.
[2024-01-24 12:45:31,637] [INFO] Query marker FASTA was written to GCF_014841215.1_ASM1484121v1_genomic.fna/markers.fasta
[2024-01-24 12:45:31,638] [INFO] Task started: Blastn
[2024-01-24 12:45:31,638] [INFO] Running command: blastn -query GCF_014841215.1_ASM1484121v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg63391880-43ed-48fc-af2c-142c01a20902/dqc_reference/reference_markers.fasta -out GCF_014841215.1_ASM1484121v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:32,506] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:32,511] [INFO] Selected 28 target genomes.
[2024-01-24 12:45:32,511] [INFO] Target genome list was writen to GCF_014841215.1_ASM1484121v1_genomic.fna/target_genomes.txt
[2024-01-24 12:45:32,527] [INFO] Task started: fastANI
[2024-01-24 12:45:32,527] [INFO] Running command: fastANI --query /var/lib/cwl/stg61e43d74-148d-442d-ae68-6fe8b0867562/GCF_014841215.1_ASM1484121v1_genomic.fna.gz --refList GCF_014841215.1_ASM1484121v1_genomic.fna/target_genomes.txt --output GCF_014841215.1_ASM1484121v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:54,691] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:54,692] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg63391880-43ed-48fc-af2c-142c01a20902/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:54,692] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg63391880-43ed-48fc-af2c-142c01a20902/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:54,712] [INFO] Found 28 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:45:54,712] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:45:54,713] [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
Pseudomarimonas arenosa	strain=CAU 1598	GCA_014841215.1	2774145	2774145	type	True	100.0	1747	1754	95	conclusive
Arenimonas malthae	strain=CC-JY-1	GCA_000747075.1	354197	354197	type	True	77.5513	301	1754	95	below_threshold
Luteimonas weifangensis	strain=WF-2	GCA_003416885.1	2303539	2303539	type	True	77.4675	239	1754	95	below_threshold
Pseudoxanthomonas suwonensis	strain=DSM 17175	GCA_010093235.1	314722	314722	suspected-type	True	77.427	250	1754	95	below_threshold
Vulcaniibacterium tengchongense	strain=DSM 25623	GCA_003814555.1	1273429	1273429	type	True	77.4211	275	1754	95	below_threshold
Vulcaniibacterium tengchongense	strain=YIM 77520	GCA_008033455.1	1273429	1273429	type	True	77.3903	271	1754	95	below_threshold
Lysobacter luteus	strain=CECT 30171	GCA_907164845.1	2822368	2822368	type	True	77.3757	200	1754	95	below_threshold
Pseudoxanthomonas helianthi	strain=110414	GCA_017939625.1	1453541	1453541	type	True	77.3481	244	1754	95	below_threshold
Lysobacter maris	strain=KCTC 42381	GCA_006546735.2	1605891	1605891	type	True	77.2492	266	1754	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	77.2203	213	1754	95	below_threshold
Frateuria flava	strain=MAH-13	GCA_017837635.1	2821489	2821489	type	True	77.1805	190	1754	95	below_threshold
Stenotrophomonas maltophilia	strain=NBRC 14161	GCA_001591205.1	40324	40324	type	True	77.1665	244	1754	95	below_threshold
Luteimonas wenzhouensis	strain=YD-1	GCA_007859305.1	2599615	2599615	type	True	77.1642	245	1754	95	below_threshold
Fulvimonas soli	strain=DSM 14263	GCA_003148905.1	155197	155197	type	True	77.1625	231	1754	95	below_threshold
Lysobacter enzymogenes	strain=ATCC 29487	GCA_900106525.1	69	69	suspected-type	True	77.1065	332	1754	95	below_threshold
Rhodanobacter denitrificans	strain=2APBS1	GCA_000230695.3	666685	666685	type	True	77.0985	223	1754	95	below_threshold
Lysobacter capsici	strain=VKM B-2533	GCA_014779555.2	435897	435897	type	True	77.0894	316	1754	95	below_threshold
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	77.0891	217	1754	95	below_threshold
Stenotrophomonas pavanii	strain=DSM 25135	GCA_001431565.1	487698	487698	type	True	76.9561	252	1754	95	below_threshold
Xanthomonas euvesicatoria pv. alfalfae	strain=CFBP 3836	GCA_000488955.1	359387	456327	pathovar	True	76.9268	202	1754	95	below_threshold
Dyella choica	strain=4 M-K27	GCA_003977665.1	1927959	1927959	type	True	76.9263	151	1754	95	below_threshold
Xanthomonas phaseoli	strain=NCPPB 3035	GCA_000774035.2	1985254	1985254	pathovar	True	76.8981	204	1754	95	below_threshold
Xanthomonas phaseoli	strain=CFBP2534	GCA_017745345.1	1985254	1985254	pathovar	True	76.8955	200	1754	95	below_threshold
Xanthomonas phaseoli	strain=LMG 695	GCA_001402235.1	1985254	1985254	pathovar	True	76.8824	193	1754	95	below_threshold
Tahibacter aquaticus	strain=DSM 21667	GCA_004363655.1	520092	520092	type	True	76.8808	282	1754	95	below_threshold
Xanthomonas phaseoli	strain=LMG 695	GCA_001564415.1	1985254	1985254	pathovar	True	76.8689	213	1754	95	below_threshold
Xanthomonas citri	strain=CFBP 2913	GCA_002688625.1	346	346	pathovar	True	76.7471	209	1754	95	below_threshold
Rhodanobacter fulvus	strain=Jip2	GCA_000264315.1	219571	219571	type	True	76.4521	192	1754	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:54,716] [INFO] DFAST Taxonomy check result was written to GCF_014841215.1_ASM1484121v1_genomic.fna/tc_result.tsv
[2024-01-24 12:45:54,716] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:54,716] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:54,716] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg63391880-43ed-48fc-af2c-142c01a20902/dqc_reference/checkm_data
[2024-01-24 12:45:54,717] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:54,772] [INFO] Task started: CheckM
[2024-01-24 12:45:54,772] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014841215.1_ASM1484121v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014841215.1_ASM1484121v1_genomic.fna/checkm_input GCF_014841215.1_ASM1484121v1_genomic.fna/checkm_result
[2024-01-24 12:46:48,570] [INFO] Task succeeded: CheckM
[2024-01-24 12:46:48,572] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:46:48,594] [INFO] ===== Completeness check finished =====
[2024-01-24 12:46:48,594] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:46:48,595] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014841215.1_ASM1484121v1_genomic.fna/markers.fasta)
[2024-01-24 12:46:48,595] [INFO] Task started: Blastn
[2024-01-24 12:46:48,595] [INFO] Running command: blastn -query GCF_014841215.1_ASM1484121v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg63391880-43ed-48fc-af2c-142c01a20902/dqc_reference/reference_markers_gtdb.fasta -out GCF_014841215.1_ASM1484121v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:46:50,161] [INFO] Task succeeded: Blastn
[2024-01-24 12:46:50,165] [INFO] Selected 28 target genomes.
[2024-01-24 12:46:50,166] [INFO] Target genome list was writen to GCF_014841215.1_ASM1484121v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:46:50,212] [INFO] Task started: fastANI
[2024-01-24 12:46:50,213] [INFO] Running command: fastANI --query /var/lib/cwl/stg61e43d74-148d-442d-ae68-6fe8b0867562/GCF_014841215.1_ASM1484121v1_genomic.fna.gz --refList GCF_014841215.1_ASM1484121v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014841215.1_ASM1484121v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:47:12,070] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:12,104] [INFO] Found 28 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:47:12,104] [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_014841215.1	s__CAU-1598 sp014841215	100.0	1747	1754	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__CAU-1598	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014202935.1	s__Rehaibacterium terrae	77.8489	321	1754	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Rehaibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018847975.1	s__Lysobacter sp018847975	77.7679	332	1754	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000513995.1	s__Pseudoxanthomonas sp000513995	77.5386	256	1754	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000513955.1	s__Pseudoxanthomonas suwonensis_C	77.4589	268	1754	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	98.37	96.94	0.95	0.91	3	-
GCF_010093235.1	s__Pseudoxanthomonas suwonensis	77.4503	248	1754	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004346265.1	s__Thermomonas haemolytica	77.4219	237	1754	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	99.99	99.99	0.99	0.99	3	-
GCF_003814555.1	s__Lysobacter tengchongensis	77.4211	275	1754	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	99.99	99.99	0.99	0.99	2	-
GCF_001442515.1	s__Lysobacter enzymogenes_B	77.3603	306	1754	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	97.93	95.70	0.94	0.91	4	-
GCA_017305095.1	s__Thermomonas sp017305095	77.3206	240	1754	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000510725.1	s__Pseudoxanthomonas sp000510725	77.3064	266	1754	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	99.33	99.13	0.95	0.92	5	-
GCF_000336385.2	s__Lysobacter antibioticus_A	77.2736	290	1754	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004216795.1	s__Stenotrophomonas_A sp004216795	77.2493	242	1754	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_017837635.1	s__Frateuria_A sp017837635	77.1805	190	1754	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Frateuria_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003148905.1	s__Fulvimonas soli	77.1766	230	1754	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Fulvimonas	95.0	99.99	99.99	0.99	0.99	2	-
GCA_017302095.1	s__Thermomonas sp017302095	77.1743	154	1754	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001043115.1	s__Xanthomonas_A sp001043115	77.146	290	1754	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas_A	95.0	96.72	96.71	0.90	0.90	3	-
GCF_003086775.1	s__Stenotrophomonas sp003086775	77.1007	252	1754	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	98.05	97.07	0.94	0.87	8	-
GCA_014946745.1	s__Aquimonas sp014946745	77.0807	353	1754	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Aquimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003086695.1	s__Stenotrophomonas sp003086695	77.0547	251	1754	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	97.24	96.14	0.92	0.90	10	-
GCF_014779555.1	s__Lysobacter capsici	77.0313	310	1754	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	97.59	97.48	0.93	0.93	5	-
GCF_001617365.1	s__Rhodanobacter sp001617365	76.9986	220	1754	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	99.98	99.98	0.98	0.97	3	-
GCF_001304695.1	s__Xanthomonas axonopodis	76.9732	178	1754	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	98.43	97.90	0.94	0.92	5	-
GCF_000427505.1	s__Rhodanobacter sp000427505	76.9111	209	1754	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	99.93	99.93	0.96	0.96	2	-
GCA_013362045.1	s__Frateuria_A sp013362045	76.8994	173	1754	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Frateuria_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004363655.1	s__Tahibacter aquaticus	76.8732	283	1754	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Tahibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001431645.1	s__Stenotrophomonas_A panacihumi	76.8566	254	1754	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_001182895.1	s__Frateuria_B defendens	76.8559	231	1754	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Frateuria_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:47:12,106] [INFO] GTDB search result was written to GCF_014841215.1_ASM1484121v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:47:12,106] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:47:12,111] [INFO] DFAST_QC result json was written to GCF_014841215.1_ASM1484121v1_genomic.fna/dqc_result.json
[2024-01-24 12:47:12,112] [INFO] DFAST_QC completed!
[2024-01-24 12:47:12,112] [INFO] Total running time: 0h2m2s