[2024-01-24 11:22:49,503] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:22:49,505] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:22:49,505] [INFO] DQC Reference Directory: /var/lib/cwl/stg347f913b-ed4b-48af-91ee-a5909df2a0ac/dqc_reference
[2024-01-24 11:22:50,711] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:22:50,712] [INFO] Task started: Prodigal
[2024-01-24 11:22:50,712] [INFO] Running command: gunzip -c /var/lib/cwl/stg85fe94bc-0794-4eca-b147-aa29592d53fb/GCF_003293695.1_ASM329369v1_genomic.fna.gz | prodigal -d GCF_003293695.1_ASM329369v1_genomic.fna/cds.fna -a GCF_003293695.1_ASM329369v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:22:59,285] [INFO] Task succeeded: Prodigal
[2024-01-24 11:22:59,285] [INFO] Task started: HMMsearch
[2024-01-24 11:22:59,286] [INFO] Running command: hmmsearch --tblout GCF_003293695.1_ASM329369v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg347f913b-ed4b-48af-91ee-a5909df2a0ac/dqc_reference/reference_markers.hmm GCF_003293695.1_ASM329369v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:22:59,535] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:22:59,537] [INFO] Found 6/6 markers.
[2024-01-24 11:22:59,562] [INFO] Query marker FASTA was written to GCF_003293695.1_ASM329369v1_genomic.fna/markers.fasta
[2024-01-24 11:22:59,563] [INFO] Task started: Blastn
[2024-01-24 11:22:59,563] [INFO] Running command: blastn -query GCF_003293695.1_ASM329369v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg347f913b-ed4b-48af-91ee-a5909df2a0ac/dqc_reference/reference_markers.fasta -out GCF_003293695.1_ASM329369v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:23:00,554] [INFO] Task succeeded: Blastn
[2024-01-24 11:23:00,557] [INFO] Selected 21 target genomes.
[2024-01-24 11:23:00,558] [INFO] Target genome list was writen to GCF_003293695.1_ASM329369v1_genomic.fna/target_genomes.txt
[2024-01-24 11:23:00,565] [INFO] Task started: fastANI
[2024-01-24 11:23:00,565] [INFO] Running command: fastANI --query /var/lib/cwl/stg85fe94bc-0794-4eca-b147-aa29592d53fb/GCF_003293695.1_ASM329369v1_genomic.fna.gz --refList GCF_003293695.1_ASM329369v1_genomic.fna/target_genomes.txt --output GCF_003293695.1_ASM329369v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:23:14,348] [INFO] Task succeeded: fastANI
[2024-01-24 11:23:14,349] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg347f913b-ed4b-48af-91ee-a5909df2a0ac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:23:14,349] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg347f913b-ed4b-48af-91ee-a5909df2a0ac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:23:14,369] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:23:14,369] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:23:14,369] [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 oculi	strain=83-4	GCA_003293695.1	2698682	2698682	type	True	100.0	864	864	95	conclusive
Lysobacter pythonis	strain=4284/11	GCA_003697345.1	2483112	2483112	type	True	82.6408	568	864	95	below_threshold
Lysobacter tolerans	strain=UM1	GCA_900155935.1	1604334	1604334	type	True	82.4446	559	864	95	below_threshold
Thermomonas aquatica	strain=SY21	GCA_006337105.1	2202149	2202149	type	True	82.2038	548	864	95	below_threshold
Thermomonas haemolytica	strain=DSM 13605	GCA_004346265.1	141949	141949	type	True	81.5108	486	864	95	below_threshold
Thermomonas haemolytica	strain=LMG 19653	GCA_006352395.1	141949	141949	type	True	81.4571	469	864	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	81.3057	526	864	95	below_threshold
Thermomonas carbonis	strain=KCTC 42013	GCA_014396975.1	1463158	1463158	type	True	81.2286	518	864	95	below_threshold
Luteimonas arsenica	strain=26-35	GCA_004352825.1	1586242	1586242	type	True	81.1834	508	864	95	below_threshold
Thermomonas carbonis	strain=KCTC 42013	GCA_014652775.1	1463158	1463158	type	True	81.1765	514	864	95	below_threshold
Luteimonas padinae	strain=KCTC 52403	GCA_014652935.1	1714359	1714359	type	True	81.1487	513	864	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	81.0821	458	864	95	below_threshold
Lysobacter panacisoli	strain=JCM 19212	GCA_009765165.1	1255263	1255263	type	True	81.0411	500	864	95	below_threshold
Lysobacter silvisoli	strain=zong2l5	GCA_003382365.1	2293254	2293254	type	True	80.9815	552	864	95	below_threshold
Pseudoxanthomonas helianthi	strain=110414	GCA_017939625.1	1453541	1453541	type	True	80.9779	505	864	95	below_threshold
Luteimonas cucumeris	strain=CGMCC 1.10821	GCA_007830035.1	985012	985012	type	True	80.833	504	864	95	below_threshold
Lysobacter silvestris	strain=AM20-91	GCA_002895945.1	1645665	1645665	type	True	80.806	464	864	95	below_threshold
Luteimonas aestuarii	strain=B9	GCA_004357985.1	453837	453837	type	True	80.7732	484	864	95	below_threshold
Luteimonas viscosa	strain=XBU10	GCA_008244685.1	1132694	1132694	type	True	80.7683	514	864	95	below_threshold
Luteimonas yindakuii	strain=S-1072	GCA_004803715.2	2565782	2565782	type	True	80.7581	474	864	95	below_threshold
Xanthomonas indica	strain=PPL560	GCA_022669045.1	2912242	2912242	type	True	80.5188	510	864	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:23:14,371] [INFO] DFAST Taxonomy check result was written to GCF_003293695.1_ASM329369v1_genomic.fna/tc_result.tsv
[2024-01-24 11:23:14,371] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:23:14,371] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:23:14,372] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg347f913b-ed4b-48af-91ee-a5909df2a0ac/dqc_reference/checkm_data
[2024-01-24 11:23:14,373] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:23:14,400] [INFO] Task started: CheckM
[2024-01-24 11:23:14,400] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003293695.1_ASM329369v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003293695.1_ASM329369v1_genomic.fna/checkm_input GCF_003293695.1_ASM329369v1_genomic.fna/checkm_result
[2024-01-24 11:23:53,665] [INFO] Task succeeded: CheckM
[2024-01-24 11:23:53,667] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:23:53,686] [INFO] ===== Completeness check finished =====
[2024-01-24 11:23:53,686] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:23:53,687] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003293695.1_ASM329369v1_genomic.fna/markers.fasta)
[2024-01-24 11:23:53,687] [INFO] Task started: Blastn
[2024-01-24 11:23:53,688] [INFO] Running command: blastn -query GCF_003293695.1_ASM329369v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg347f913b-ed4b-48af-91ee-a5909df2a0ac/dqc_reference/reference_markers_gtdb.fasta -out GCF_003293695.1_ASM329369v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:23:55,583] [INFO] Task succeeded: Blastn
[2024-01-24 11:23:55,588] [INFO] Selected 20 target genomes.
[2024-01-24 11:23:55,588] [INFO] Target genome list was writen to GCF_003293695.1_ASM329369v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:23:55,608] [INFO] Task started: fastANI
[2024-01-24 11:23:55,609] [INFO] Running command: fastANI --query /var/lib/cwl/stg85fe94bc-0794-4eca-b147-aa29592d53fb/GCF_003293695.1_ASM329369v1_genomic.fna.gz --refList GCF_003293695.1_ASM329369v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003293695.1_ASM329369v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:24:08,679] [INFO] Task succeeded: fastANI
[2024-01-24 11:24:08,700] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:24:08,700] [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_003293695.1	s__Lysobacter_B oculi	100.0	864	864	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter_B	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_014879375.1	s__Lysobacter_B sp014879375	83.7874	485	864	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003697345.1	s__Lysobacter_B pythonis	82.6374	569	864	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900155935.1	s__Lysobacter_B tolerans	82.4446	559	864	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006337105.1	s__Thermomonas sp006337105	82.1834	549	864	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423885.1	s__Thermomonas fusca	81.5808	514	864	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	96.57	96.57	0.92	0.92	2	-
GCF_004346265.1	s__Thermomonas haemolytica	81.5056	486	864	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	99.99	99.99	0.99	0.99	3	-
GCA_017302095.1	s__Thermomonas sp017302095	81.4245	355	864	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004352825.1	s__Luteimonas arsenica	81.1836	508	864	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	81.157	512	864	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018242425.1	s__Lysobacter_B sp018242425	81.1559	480	864	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter_B	95.0	98.53	98.53	0.95	0.95	2	-
GCA_017305095.1	s__Thermomonas sp017305095	81.1231	493	864	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009765165.1	s__Lysobacter panacisoli	81.0354	501	864	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007830035.1	s__Luteimonas_C cucumeris	80.8181	505	864	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_004357985.1	s__Luteimonas aestuarii	80.7995	482	864	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008244685.1	s__Luteimonas sp008244685	80.7822	513	864	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001442515.1	s__Lysobacter enzymogenes_B	80.7216	554	864	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	97.93	95.70	0.94	0.91	4	-
GCF_017163755.1	s__Xanthomonas_A sp017163755	80.6946	521	864	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_013362405.1	s__JABFWF01 sp013362405	80.5678	380	864	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__JABFWF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018242405.1	s__Lysobacter_B sp018242405	80.4333	399	864	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:24:08,702] [INFO] GTDB search result was written to GCF_003293695.1_ASM329369v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:24:08,702] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:24:08,706] [INFO] DFAST_QC result json was written to GCF_003293695.1_ASM329369v1_genomic.fna/dqc_result.json
[2024-01-24 11:24:08,706] [INFO] DFAST_QC completed!
[2024-01-24 11:24:08,706] [INFO] Total running time: 0h1m19s