[2024-01-24 14:12:33,966] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:12:33,968] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:12:33,969] [INFO] DQC Reference Directory: /var/lib/cwl/stg9b194024-e508-4184-99cb-03e245141119/dqc_reference
[2024-01-24 14:12:35,240] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:12:35,244] [INFO] Task started: Prodigal
[2024-01-24 14:12:35,244] [INFO] Running command: gunzip -c /var/lib/cwl/stg517ad41b-89fd-47b6-9920-c5feb3af09f3/GCF_000770795.1_ASM77079v1_genomic.fna.gz | prodigal -d GCF_000770795.1_ASM77079v1_genomic.fna/cds.fna -a GCF_000770795.1_ASM77079v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:12:46,197] [INFO] Task succeeded: Prodigal
[2024-01-24 14:12:46,197] [INFO] Task started: HMMsearch
[2024-01-24 14:12:46,197] [INFO] Running command: hmmsearch --tblout GCF_000770795.1_ASM77079v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9b194024-e508-4184-99cb-03e245141119/dqc_reference/reference_markers.hmm GCF_000770795.1_ASM77079v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:12:46,481] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:12:46,483] [INFO] Found 6/6 markers.
[2024-01-24 14:12:46,514] [INFO] Query marker FASTA was written to GCF_000770795.1_ASM77079v1_genomic.fna/markers.fasta
[2024-01-24 14:12:46,514] [INFO] Task started: Blastn
[2024-01-24 14:12:46,515] [INFO] Running command: blastn -query GCF_000770795.1_ASM77079v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9b194024-e508-4184-99cb-03e245141119/dqc_reference/reference_markers.fasta -out GCF_000770795.1_ASM77079v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:12:47,508] [INFO] Task succeeded: Blastn
[2024-01-24 14:12:47,512] [INFO] Selected 22 target genomes.
[2024-01-24 14:12:47,513] [INFO] Target genome list was writen to GCF_000770795.1_ASM77079v1_genomic.fna/target_genomes.txt
[2024-01-24 14:12:47,531] [INFO] Task started: fastANI
[2024-01-24 14:12:47,532] [INFO] Running command: fastANI --query /var/lib/cwl/stg517ad41b-89fd-47b6-9920-c5feb3af09f3/GCF_000770795.1_ASM77079v1_genomic.fna.gz --refList GCF_000770795.1_ASM77079v1_genomic.fna/target_genomes.txt --output GCF_000770795.1_ASM77079v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:13:03,524] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:03,524] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9b194024-e508-4184-99cb-03e245141119/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:13:03,525] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9b194024-e508-4184-99cb-03e245141119/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:13:03,545] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:13:03,545] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:13:03,545] [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
Lysobacter dokdonensis	strain=DS-58	GCA_000770795.1	414050	414050	type	True	100.0	1075	1077	95	conclusive
Lysobacter gilvus	strain=HX-5-24	GCA_009740395.1	2682097	2682097	type	True	87.8958	861	1077	95	below_threshold
Lysobacter soli	strain=KCTC 22011	GCA_003382285.1	453783	453783	type	True	81.1992	599	1077	95	below_threshold
Vulcaniibacterium gelatinicum	strain=R-5-52-3	GCA_008033445.1	2598725	2598725	type	True	80.9588	523	1077	95	below_threshold
Thermomonas aquatica	strain=SY21	GCA_006337105.1	2202149	2202149	type	True	80.9005	520	1077	95	below_threshold
Luteimonas marina	strain=FR1330	GCA_007859325.1	488485	488485	type	True	80.5997	532	1077	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	80.5892	470	1077	95	below_threshold
Vulcaniibacterium tengchongense	strain=YIM 77520	GCA_008033455.1	1273429	1273429	type	True	80.5881	528	1077	95	below_threshold
Vulcaniibacterium tengchongense	strain=DSM 25623	GCA_003814555.1	1273429	1273429	type	True	80.585	542	1077	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	80.5585	533	1077	95	below_threshold
Lysobacter segetis	strain=17J68-2	GCA_004359965.1	2492394	2492394	type	True	80.5187	485	1077	95	below_threshold
Lysobacter silvisoli	strain=zong2l5	GCA_003382365.1	2293254	2293254	type	True	80.4228	576	1077	95	below_threshold
Luteimonas cucumeris	strain=CGMCC 1.10821	GCA_007830035.1	985012	985012	type	True	80.2779	532	1077	95	below_threshold
Lysobacter daejeonensis	strain=GH1-9	GCA_000768355.1	346181	346181	type	True	80.1463	469	1077	95	below_threshold
Pseudoxanthomonas sangjuensis	strain=DSM 28345	GCA_010211755.1	1503750	1503750	type	True	80.1446	498	1077	95	below_threshold
Lysobacter capsici	strain=VKM B-2533	GCA_014779555.2	435897	435897	type	True	80.0728	573	1077	95	below_threshold
Luteimonas saliphila	strain=SJ-9	GCA_016774335.1	2804919	2804919	type	True	80.0696	488	1077	95	below_threshold
Pseudoxanthomonas japonensis	strain=DSM 17109	GCA_010093445.1	69284	69284	type	True	80.0192	500	1077	95	below_threshold
Luteimonas viscosa	strain=XBU10	GCA_008244685.1	1132694	1132694	type	True	79.91	500	1077	95	below_threshold
Thermomonas carbonis	strain=KCTC 42013	GCA_014396975.1	1463158	1463158	type	True	79.7333	481	1077	95	below_threshold
Stenotrophomonas acidaminiphila	strain=DSM 13117	GCA_024221815.1	128780	128780	type	True	79.595	432	1077	95	below_threshold
Luteimonas salinisoli	strain=SJ-92	GCA_013425525.1	2752307	2752307	type	True	79.3859	491	1077	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:13:03,547] [INFO] DFAST Taxonomy check result was written to GCF_000770795.1_ASM77079v1_genomic.fna/tc_result.tsv
[2024-01-24 14:13:03,548] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:13:03,548] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:13:03,548] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9b194024-e508-4184-99cb-03e245141119/dqc_reference/checkm_data
[2024-01-24 14:13:03,549] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:13:03,591] [INFO] Task started: CheckM
[2024-01-24 14:13:03,591] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000770795.1_ASM77079v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000770795.1_ASM77079v1_genomic.fna/checkm_input GCF_000770795.1_ASM77079v1_genomic.fna/checkm_result
[2024-01-24 14:14:02,478] [INFO] Task succeeded: CheckM
[2024-01-24 14:14:02,479] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:14:02,499] [INFO] ===== Completeness check finished =====
[2024-01-24 14:14:02,499] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:14:02,500] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000770795.1_ASM77079v1_genomic.fna/markers.fasta)
[2024-01-24 14:14:02,500] [INFO] Task started: Blastn
[2024-01-24 14:14:02,500] [INFO] Running command: blastn -query GCF_000770795.1_ASM77079v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9b194024-e508-4184-99cb-03e245141119/dqc_reference/reference_markers_gtdb.fasta -out GCF_000770795.1_ASM77079v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:04,046] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:04,049] [INFO] Selected 19 target genomes.
[2024-01-24 14:14:04,050] [INFO] Target genome list was writen to GCF_000770795.1_ASM77079v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:14:04,089] [INFO] Task started: fastANI
[2024-01-24 14:14:04,089] [INFO] Running command: fastANI --query /var/lib/cwl/stg517ad41b-89fd-47b6-9920-c5feb3af09f3/GCF_000770795.1_ASM77079v1_genomic.fna.gz --refList GCF_000770795.1_ASM77079v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000770795.1_ASM77079v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:14:17,878] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:17,900] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:14:17,900] [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_000770795.1	s__Lysobacter_A dokdonensis	100.0	1076	1077	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009740395.1	s__Lysobacter_A gilvus	87.8621	861	1077	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018406645.1	s__Lysobacter_A helvus	84.8516	777	1077	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter_A	95.0	100.00	100.00	1.00	1.00	2	-
GCA_013362405.1	s__JABFWF01 sp013362405	81.0101	435	1077	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__JABFWF01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008033445.1	s__Vulcaniibacterium_B gelatinicum	80.9463	524	1077	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_006337105.1	s__Thermomonas sp006337105	80.8407	525	1077	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011320095.1	s__Luteimonas_B telluris	80.6486	486	1077	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004359965.1	s__Lysobacter segetis	80.4942	486	1077	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005502915.1	s__SCMT01 sp005502915	80.4888	510	1077	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__SCMT01	95.0	99.99	99.99	0.99	0.99	2	-
GCF_001442515.1	s__Lysobacter enzymogenes_B	80.403	590	1077	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	97.93	95.70	0.94	0.91	4	-
GCF_007830035.1	s__Luteimonas_C cucumeris	80.2857	531	1077	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003367355.1	s__Lysobacter sp003367355	80.2161	503	1077	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010211755.1	s__Pseudoxanthomonas_A sangjuensis	80.1665	496	1077	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_016774335.1	s__Luteimonas sp016774335	80.1155	484	1077	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011302915.1	s__Thermomonas sp011302915	79.9947	460	1077	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001427635.1	s__Pseudoxanthomonas_A sp001427635	79.9139	498	1077	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_008244685.1	s__Luteimonas sp008244685	79.8846	503	1077	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014396975.1	s__Thermomonas carbonis	79.7624	482	1077	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001043115.1	s__Xanthomonas_A sp001043115	79.4352	454	1077	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas_A	95.0	96.72	96.71	0.90	0.90	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:14:17,902] [INFO] GTDB search result was written to GCF_000770795.1_ASM77079v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:14:17,902] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:14:17,906] [INFO] DFAST_QC result json was written to GCF_000770795.1_ASM77079v1_genomic.fna/dqc_result.json
[2024-01-24 14:14:17,907] [INFO] DFAST_QC completed!
[2024-01-24 14:14:17,907] [INFO] Total running time: 0h1m44s