[2024-01-24 14:56:22,693] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:56:22,695] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:56:22,695] [INFO] DQC Reference Directory: /var/lib/cwl/stg1aadc28d-b139-4b6f-9be6-0bcd02460e07/dqc_reference
[2024-01-24 14:56:26,555] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:56:26,556] [INFO] Task started: Prodigal
[2024-01-24 14:56:26,557] [INFO] Running command: gunzip -c /var/lib/cwl/stg5fcc32e0-2bc8-44b7-b7a8-7aed2fccef05/GCF_007923255.1_ASM792325v1_genomic.fna.gz | prodigal -d GCF_007923255.1_ASM792325v1_genomic.fna/cds.fna -a GCF_007923255.1_ASM792325v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:56:35,644] [INFO] Task succeeded: Prodigal
[2024-01-24 14:56:35,644] [INFO] Task started: HMMsearch
[2024-01-24 14:56:35,644] [INFO] Running command: hmmsearch --tblout GCF_007923255.1_ASM792325v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1aadc28d-b139-4b6f-9be6-0bcd02460e07/dqc_reference/reference_markers.hmm GCF_007923255.1_ASM792325v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:56:35,972] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:56:35,974] [INFO] Found 6/6 markers.
[2024-01-24 14:56:36,016] [INFO] Query marker FASTA was written to GCF_007923255.1_ASM792325v1_genomic.fna/markers.fasta
[2024-01-24 14:56:36,017] [INFO] Task started: Blastn
[2024-01-24 14:56:36,017] [INFO] Running command: blastn -query GCF_007923255.1_ASM792325v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1aadc28d-b139-4b6f-9be6-0bcd02460e07/dqc_reference/reference_markers.fasta -out GCF_007923255.1_ASM792325v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:37,369] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:37,372] [INFO] Selected 14 target genomes.
[2024-01-24 14:56:37,373] [INFO] Target genome list was writen to GCF_007923255.1_ASM792325v1_genomic.fna/target_genomes.txt
[2024-01-24 14:56:37,381] [INFO] Task started: fastANI
[2024-01-24 14:56:37,381] [INFO] Running command: fastANI --query /var/lib/cwl/stg5fcc32e0-2bc8-44b7-b7a8-7aed2fccef05/GCF_007923255.1_ASM792325v1_genomic.fna.gz --refList GCF_007923255.1_ASM792325v1_genomic.fna/target_genomes.txt --output GCF_007923255.1_ASM792325v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:56:51,163] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:51,163] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1aadc28d-b139-4b6f-9be6-0bcd02460e07/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:56:51,164] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1aadc28d-b139-4b6f-9be6-0bcd02460e07/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:56:51,176] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:56:51,176] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:56:51,176] [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
Vulcaniibacterium thermophilum	strain=KCTC 32020	GCA_007923255.1	1169913	1169913	type	True	100.0	980	989	95	conclusive
Vulcaniibacterium thermophilum	strain=KCTC 32020	GCA_014656335.1	1169913	1169913	type	True	99.9852	969	989	95	conclusive
Vulcaniibacterium tengchongense	strain=YIM 77520	GCA_008033455.1	1273429	1273429	type	True	83.892	645	989	95	below_threshold
Vulcaniibacterium tengchongense	strain=DSM 25623	GCA_003814555.1	1273429	1273429	type	True	83.7451	695	989	95	below_threshold
Vulcaniibacterium gelatinicum	strain=R-5-52-3	GCA_008033445.1	2598725	2598725	type	True	83.7253	617	989	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	82.1091	533	989	95	below_threshold
Lysobacter silvisoli	strain=zong2l5	GCA_003382365.1	2293254	2293254	type	True	82.0717	669	989	95	below_threshold
Luteimonas marina	strain=FR1330	GCA_007859325.1	488485	488485	type	True	81.9083	648	989	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	81.8394	635	989	95	below_threshold
Pseudoxanthomonas sangjuensis	strain=DSM 28345	GCA_010211755.1	1503750	1503750	type	True	81.7688	565	989	95	below_threshold
Lysobacter chinensis	strain=TLK-CK17	GCA_021725675.1	2912247	2912247	type	True	81.6432	648	989	95	below_threshold
Lysobacter soli	strain=KCTC 22011	GCA_003382285.1	453783	453783	type	True	81.6085	658	989	95	below_threshold
Lysobacter luteus	strain=CECT 30171	GCA_907164845.1	2822368	2822368	type	True	81.4325	580	989	95	below_threshold
Luteimonas saliphila	strain=SJ-9	GCA_016774335.1	2804919	2804919	type	True	81.003	653	989	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:56:51,178] [INFO] DFAST Taxonomy check result was written to GCF_007923255.1_ASM792325v1_genomic.fna/tc_result.tsv
[2024-01-24 14:56:51,178] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:56:51,179] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:56:51,179] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1aadc28d-b139-4b6f-9be6-0bcd02460e07/dqc_reference/checkm_data
[2024-01-24 14:56:51,180] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:56:51,213] [INFO] Task started: CheckM
[2024-01-24 14:56:51,213] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007923255.1_ASM792325v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007923255.1_ASM792325v1_genomic.fna/checkm_input GCF_007923255.1_ASM792325v1_genomic.fna/checkm_result
[2024-01-24 14:57:28,635] [INFO] Task succeeded: CheckM
[2024-01-24 14:57:28,637] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:57:28,657] [INFO] ===== Completeness check finished =====
[2024-01-24 14:57:28,657] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:57:28,658] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007923255.1_ASM792325v1_genomic.fna/markers.fasta)
[2024-01-24 14:57:28,658] [INFO] Task started: Blastn
[2024-01-24 14:57:28,658] [INFO] Running command: blastn -query GCF_007923255.1_ASM792325v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1aadc28d-b139-4b6f-9be6-0bcd02460e07/dqc_reference/reference_markers_gtdb.fasta -out GCF_007923255.1_ASM792325v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:57:30,914] [INFO] Task succeeded: Blastn
[2024-01-24 14:57:30,918] [INFO] Selected 18 target genomes.
[2024-01-24 14:57:30,918] [INFO] Target genome list was writen to GCF_007923255.1_ASM792325v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:57:30,936] [INFO] Task started: fastANI
[2024-01-24 14:57:30,936] [INFO] Running command: fastANI --query /var/lib/cwl/stg5fcc32e0-2bc8-44b7-b7a8-7aed2fccef05/GCF_007923255.1_ASM792325v1_genomic.fna.gz --refList GCF_007923255.1_ASM792325v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007923255.1_ASM792325v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:57:47,852] [INFO] Task succeeded: fastANI
[2024-01-24 14:57:47,883] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:57:47,884] [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_007923255.1	s__Lysobacter thermophilus	100.0	979	989	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	99.99	99.99	0.98	0.98	2	conclusive
GCF_003814555.1	s__Lysobacter tengchongensis	83.727	697	989	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	99.99	99.99	0.99	0.99	2	-
GCF_008033445.1	s__Vulcaniibacterium_B gelatinicum	83.7097	618	989	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Vulcaniibacterium_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003586305.1	s__Lysobacter tabacisoli	82.7212	668	989	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017308985.1	s__Lysobacter sp017308985	81.9657	671	989	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001429785.1	s__Lysobacter sp001429785	81.963	662	989	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	98.47	98.45	0.97	0.97	3	-
GCF_007859325.1	s__Luteimonas marina	81.9324	647	989	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013361435.1	s__Lysobacter sp013361435	81.9246	596	989	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013362405.1	s__JABFWF01 sp013362405	81.8763	480	989	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__JABFWF01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010211755.1	s__Pseudoxanthomonas_A sangjuensis	81.8086	561	989	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_003382285.1	s__Lysobacter soli	81.6045	657	989	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	96.84	96.81	0.94	0.93	3	-
GCF_000513995.1	s__Pseudoxanthomonas sp000513995	81.4732	596	989	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010093135.1	s__Pseudoxanthomonas taiwanensis	81.4255	561	989	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	99.04	99.04	0.90	0.90	2	-
GCF_000472505.1	s__Luteimonas sp000472505	81.4142	611	989	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	99.95	99.95	0.99	0.99	2	-
GCF_008244685.1	s__Luteimonas sp008244685	81.0188	640	989	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016774335.1	s__Luteimonas sp016774335	80.9595	659	989	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001043115.1	s__Xanthomonas_A sp001043115	80.6248	616	989	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_014199795.1	s__Xanthomonas_A sp014199795	80.5905	622	989	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 14:57:47,887] [INFO] GTDB search result was written to GCF_007923255.1_ASM792325v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:57:47,896] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:57:47,903] [INFO] DFAST_QC result json was written to GCF_007923255.1_ASM792325v1_genomic.fna/dqc_result.json
[2024-01-24 14:57:47,904] [INFO] DFAST_QC completed!
[2024-01-24 14:57:47,904] [INFO] Total running time: 0h1m25s