[2024-01-24 14:19:01,051] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:01,054] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:01,054] [INFO] DQC Reference Directory: /var/lib/cwl/stg5d9488e6-abcb-4000-9a9a-eb9399036060/dqc_reference
[2024-01-24 14:19:02,409] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:02,410] [INFO] Task started: Prodigal
[2024-01-24 14:19:02,410] [INFO] Running command: gunzip -c /var/lib/cwl/stgb9263a61-c3e1-4302-bddc-bb43ac4b60ff/GCF_022662575.1_ASM2266257v1_genomic.fna.gz | prodigal -d GCF_022662575.1_ASM2266257v1_genomic.fna/cds.fna -a GCF_022662575.1_ASM2266257v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:13,870] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:13,870] [INFO] Task started: HMMsearch
[2024-01-24 14:19:13,870] [INFO] Running command: hmmsearch --tblout GCF_022662575.1_ASM2266257v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5d9488e6-abcb-4000-9a9a-eb9399036060/dqc_reference/reference_markers.hmm GCF_022662575.1_ASM2266257v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:14,137] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:14,138] [INFO] Found 6/6 markers.
[2024-01-24 14:19:14,175] [INFO] Query marker FASTA was written to GCF_022662575.1_ASM2266257v1_genomic.fna/markers.fasta
[2024-01-24 14:19:14,176] [INFO] Task started: Blastn
[2024-01-24 14:19:14,176] [INFO] Running command: blastn -query GCF_022662575.1_ASM2266257v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5d9488e6-abcb-4000-9a9a-eb9399036060/dqc_reference/reference_markers.fasta -out GCF_022662575.1_ASM2266257v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:15,374] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:15,379] [INFO] Selected 19 target genomes.
[2024-01-24 14:19:15,380] [INFO] Target genome list was writen to GCF_022662575.1_ASM2266257v1_genomic.fna/target_genomes.txt
[2024-01-24 14:19:15,390] [INFO] Task started: fastANI
[2024-01-24 14:19:15,390] [INFO] Running command: fastANI --query /var/lib/cwl/stgb9263a61-c3e1-4302-bddc-bb43ac4b60ff/GCF_022662575.1_ASM2266257v1_genomic.fna.gz --refList GCF_022662575.1_ASM2266257v1_genomic.fna/target_genomes.txt --output GCF_022662575.1_ASM2266257v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:19:34,275] [INFO] Task succeeded: fastANI
[2024-01-24 14:19:34,276] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5d9488e6-abcb-4000-9a9a-eb9399036060/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:19:34,276] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5d9488e6-abcb-4000-9a9a-eb9399036060/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:19:34,295] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:19:34,295] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:19:34,295] [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
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	100.0	1253	1255	95	conclusive
Luteimonas panaciterrae	strain=Gsoil 068	GCA_020511115.1	363885	363885	type	True	85.712	984	1255	95	below_threshold
Luteimonas mephitis	strain=DSM 12574	GCA_000422305.1	83615	83615	type	True	83.3386	732	1255	95	below_threshold
Luteimonas marina	strain=FR1330	GCA_007859325.1	488485	488485	type	True	82.9289	745	1255	95	below_threshold
Vulcaniibacterium tengchongense	strain=DSM 25623	GCA_003814555.1	1273429	1273429	type	True	82.9174	752	1255	95	below_threshold
Luteimonas arsenica	strain=26-35	GCA_004352825.1	1586242	1586242	type	True	82.6796	650	1255	95	below_threshold
Luteimonas padinae	strain=KCTC 52403	GCA_014652935.1	1714359	1714359	type	True	82.6555	632	1255	95	below_threshold
Vulcaniibacterium gelatinicum	strain=R-5-52-3	GCA_008033445.1	2598725	2598725	type	True	82.5169	597	1255	95	below_threshold
Luteimonas colneyensis	strain=Sa2BVA3	GCA_014836665.1	2762230	2762230	type	True	82.3428	655	1255	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	82.3316	543	1255	95	below_threshold
Luteimonas terricola	strain=CGMCC 1.8985	GCA_014645675.1	645597	645597	type	True	82.2033	607	1255	95	below_threshold
Luteimonas terricola	strain=BZ92r	GCA_004352845.1	645597	645597	type	True	82.1828	603	1255	95	below_threshold
Luteimonas viscosa	strain=XBU10	GCA_008244685.1	1132694	1132694	type	True	81.9497	726	1255	95	below_threshold
Luteimonas saliphila	strain=SJ-9	GCA_016774335.1	2804919	2804919	type	True	81.9368	723	1255	95	below_threshold
Pseudoxanthomonas taiwanensis	strain=DSM 22914	GCA_010093135.1	176598	176598	type	True	81.9346	603	1255	95	below_threshold
Luteimonas gilva	strain=H23	GCA_005239095.1	2572684	2572684	type	True	81.7478	725	1255	95	below_threshold
Vulcaniibacterium thermophilum	strain=KCTC 32020	GCA_014656335.1	1169913	1169913	type	True	81.745	636	1255	95	below_threshold
Luteimonas aestuarii	strain=B9	GCA_004357985.1	453837	453837	type	True	81.6898	641	1255	95	below_threshold
Xanthomonas indica	strain=PPL560	GCA_022669045.1	2912242	2912242	type	True	81.4949	744	1255	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:19:34,298] [INFO] DFAST Taxonomy check result was written to GCF_022662575.1_ASM2266257v1_genomic.fna/tc_result.tsv
[2024-01-24 14:19:34,299] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:19:34,299] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:19:34,299] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5d9488e6-abcb-4000-9a9a-eb9399036060/dqc_reference/checkm_data
[2024-01-24 14:19:34,300] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:19:34,339] [INFO] Task started: CheckM
[2024-01-24 14:19:34,339] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022662575.1_ASM2266257v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022662575.1_ASM2266257v1_genomic.fna/checkm_input GCF_022662575.1_ASM2266257v1_genomic.fna/checkm_result
[2024-01-24 14:20:13,135] [INFO] Task succeeded: CheckM
[2024-01-24 14:20:13,137] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:20:13,155] [INFO] ===== Completeness check finished =====
[2024-01-24 14:20:13,155] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:20:13,156] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022662575.1_ASM2266257v1_genomic.fna/markers.fasta)
[2024-01-24 14:20:13,156] [INFO] Task started: Blastn
[2024-01-24 14:20:13,156] [INFO] Running command: blastn -query GCF_022662575.1_ASM2266257v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5d9488e6-abcb-4000-9a9a-eb9399036060/dqc_reference/reference_markers_gtdb.fasta -out GCF_022662575.1_ASM2266257v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:15,438] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:15,443] [INFO] Selected 24 target genomes.
[2024-01-24 14:20:15,444] [INFO] Target genome list was writen to GCF_022662575.1_ASM2266257v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:20:15,493] [INFO] Task started: fastANI
[2024-01-24 14:20:15,494] [INFO] Running command: fastANI --query /var/lib/cwl/stgb9263a61-c3e1-4302-bddc-bb43ac4b60ff/GCF_022662575.1_ASM2266257v1_genomic.fna.gz --refList GCF_022662575.1_ASM2266257v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022662575.1_ASM2266257v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:20:35,014] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:35,040] [INFO] Found 24 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:20:35,040] [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_000422305.1	s__Luteimonas mephitis	83.3289	733	1255	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003814555.1	s__Lysobacter tengchongensis	82.9482	749	1255	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	99.99	99.99	0.99	0.99	2	-
GCF_007859325.1	s__Luteimonas marina	82.9436	743	1255	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004352825.1	s__Luteimonas arsenica	82.6934	649	1255	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	82.6555	632	1255	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008033445.1	s__Vulcaniibacterium_B gelatinicum	82.527	596	1255	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_014836665.1	s__Luteimonas sp014836665	82.4362	647	1255	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008312895.1	s__Luteimonas sp008312895	82.4272	721	1255	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004352845.1	s__Luteimonas terricola	82.1756	605	1255	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	99.99	99.99	0.99	0.99	2	-
GCF_007859305.1	s__Luteimonas wenzhouensis	82.1608	660	1255	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	99.47	99.47	0.98	0.98	2	-
GCF_016615955.1	s__Luteimonas sp016615955	82.0747	619	1255	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	99.39	98.78	0.97	0.95	3	-
GCF_000513995.1	s__Pseudoxanthomonas sp000513995	82.0041	654	1255	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013425525.1	s__Luteimonas sp013425525	81.9824	716	1255	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006337105.1	s__Thermomonas sp006337105	81.9745	635	1255	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010093135.1	s__Pseudoxanthomonas taiwanensis	81.9718	600	1255	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	99.04	99.04	0.90	0.90	2	-
GCF_008244685.1	s__Luteimonas sp008244685	81.9636	725	1255	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	81.9619	721	1255	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007923255.1	s__Lysobacter thermophilus	81.7742	622	1255	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	99.99	99.99	0.98	0.98	2	-
GCF_004357985.1	s__Luteimonas aestuarii	81.6947	641	1255	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013362405.1	s__JABFWF01 sp013362405	81.6938	469	1255	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__JABFWF01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009769165.1	s__Xanthomonas_A hyacinthi	81.6024	716	1255	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_017163755.1	s__Xanthomonas_A sp017163755	81.5542	771	1255	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017302075.1	s__Thermomonas sp017302075	81.3889	512	1255	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002240395.1	s__Luteimonas citri_A	80.6846	642	1255	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 14:20:35,042] [INFO] GTDB search result was written to GCF_022662575.1_ASM2266257v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:20:35,043] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:20:35,047] [INFO] DFAST_QC result json was written to GCF_022662575.1_ASM2266257v1_genomic.fna/dqc_result.json
[2024-01-24 14:20:35,047] [INFO] DFAST_QC completed!
[2024-01-24 14:20:35,047] [INFO] Total running time: 0h1m34s