[2024-01-24 13:55:18,753] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:18,755] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:18,755] [INFO] DQC Reference Directory: /var/lib/cwl/stgb2670973-176f-487c-a851-5abbda9f3c80/dqc_reference
[2024-01-24 13:55:20,129] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:20,130] [INFO] Task started: Prodigal
[2024-01-24 13:55:20,130] [INFO] Running command: gunzip -c /var/lib/cwl/stg147d66d1-1088-4f10-8cbd-cfbd21d2a896/GCF_009792795.1_ASM979279v1_genomic.fna.gz | prodigal -d GCF_009792795.1_ASM979279v1_genomic.fna/cds.fna -a GCF_009792795.1_ASM979279v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:55:29,875] [INFO] Task succeeded: Prodigal
[2024-01-24 13:55:29,875] [INFO] Task started: HMMsearch
[2024-01-24 13:55:29,875] [INFO] Running command: hmmsearch --tblout GCF_009792795.1_ASM979279v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb2670973-176f-487c-a851-5abbda9f3c80/dqc_reference/reference_markers.hmm GCF_009792795.1_ASM979279v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:55:30,188] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:55:30,189] [INFO] Found 6/6 markers.
[2024-01-24 13:55:30,225] [INFO] Query marker FASTA was written to GCF_009792795.1_ASM979279v1_genomic.fna/markers.fasta
[2024-01-24 13:55:30,225] [INFO] Task started: Blastn
[2024-01-24 13:55:30,225] [INFO] Running command: blastn -query GCF_009792795.1_ASM979279v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb2670973-176f-487c-a851-5abbda9f3c80/dqc_reference/reference_markers.fasta -out GCF_009792795.1_ASM979279v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:55:31,182] [INFO] Task succeeded: Blastn
[2024-01-24 13:55:31,185] [INFO] Selected 21 target genomes.
[2024-01-24 13:55:31,185] [INFO] Target genome list was writen to GCF_009792795.1_ASM979279v1_genomic.fna/target_genomes.txt
[2024-01-24 13:55:31,194] [INFO] Task started: fastANI
[2024-01-24 13:55:31,194] [INFO] Running command: fastANI --query /var/lib/cwl/stg147d66d1-1088-4f10-8cbd-cfbd21d2a896/GCF_009792795.1_ASM979279v1_genomic.fna.gz --refList GCF_009792795.1_ASM979279v1_genomic.fna/target_genomes.txt --output GCF_009792795.1_ASM979279v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:55:45,434] [INFO] Task succeeded: fastANI
[2024-01-24 13:55:45,434] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb2670973-176f-487c-a851-5abbda9f3c80/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:55:45,435] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb2670973-176f-487c-a851-5abbda9f3c80/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:55:45,451] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:55:45,451] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:55:45,452] [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 profundi	strain=CHu50b-3-2	GCA_009792795.1	2594501	2594501	type	True	100.0	898	898	95	conclusive
Luteimonas weifangensis	strain=WF-2	GCA_003416885.1	2303539	2303539	type	True	81.3951	548	898	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	80.6385	478	898	95	below_threshold
Luteimonas cucumeris	strain=CGMCC 1.10821	GCA_007830035.1	985012	985012	type	True	80.4278	491	898	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	80.3513	510	898	95	below_threshold
Lysobacter arenosi	strain=R7	GCA_016613475.2	2795387	2795387	type	True	80.3173	488	898	95	below_threshold
Vulcaniibacterium gelatinicum	strain=R-5-52-3	GCA_008033445.1	2598725	2598725	type	True	80.2883	477	898	95	below_threshold
Lysobacter arseniciresistens	strain=ZS79	GCA_000768335.1	1385522	1385522	type	True	80.2826	486	898	95	below_threshold
Luteimonas marina	strain=FR1330	GCA_007859325.1	488485	488485	type	True	80.2533	493	898	95	below_threshold
Thermomonas aquatica	strain=SY21	GCA_006337105.1	2202149	2202149	type	True	80.2366	486	898	95	below_threshold
Luteimonas terricola	strain=BZ92r	GCA_004352845.1	645597	645597	type	True	80.1104	438	898	95	below_threshold
Luteimonas padinae	strain=KCTC 52403	GCA_014652935.1	1714359	1714359	type	True	80.0484	442	898	95	below_threshold
Luteimonas gilva	strain=H23	GCA_005239095.1	2572684	2572684	type	True	80.0298	464	898	95	below_threshold
Luteimonas terricola	strain=CGMCC 1.8985	GCA_014645675.1	645597	645597	type	True	79.9743	448	898	95	below_threshold
Lysobacter gilvus	strain=HX-5-24	GCA_009740395.1	2682097	2682097	type	True	79.9635	448	898	95	below_threshold
Lysobacter luteus	strain=CECT 30171	GCA_907164845.1	2822368	2822368	type	True	79.9163	443	898	95	below_threshold
Lysobacter dokdonensis	strain=DS-58	GCA_000770795.1	414050	414050	type	True	79.8945	461	898	95	below_threshold
Luteimonas huabeiensis	strain=HB2	GCA_000559025.1	1244513	1244513	type	True	79.8464	443	898	95	below_threshold
Lysobacter spongiae	strain=119BY6-57	GCA_014145325.1	2025720	2025720	type	True	79.7824	441	898	95	below_threshold
Lysobacter psychrotolerans	strain=ZS60	GCA_003719825.1	1327343	1327343	type	True	79.7466	447	898	95	below_threshold
Luteimonas terrae	strain=THG-MD21	GCA_004358165.1	1530191	1530191	type	True	79.4504	429	898	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:55:45,454] [INFO] DFAST Taxonomy check result was written to GCF_009792795.1_ASM979279v1_genomic.fna/tc_result.tsv
[2024-01-24 13:55:45,455] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:55:45,455] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:55:45,455] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb2670973-176f-487c-a851-5abbda9f3c80/dqc_reference/checkm_data
[2024-01-24 13:55:45,456] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:55:45,490] [INFO] Task started: CheckM
[2024-01-24 13:55:45,490] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009792795.1_ASM979279v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009792795.1_ASM979279v1_genomic.fna/checkm_input GCF_009792795.1_ASM979279v1_genomic.fna/checkm_result
[2024-01-24 13:56:38,645] [INFO] Task succeeded: CheckM
[2024-01-24 13:56:38,646] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:56:38,661] [INFO] ===== Completeness check finished =====
[2024-01-24 13:56:38,661] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:56:38,662] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009792795.1_ASM979279v1_genomic.fna/markers.fasta)
[2024-01-24 13:56:38,662] [INFO] Task started: Blastn
[2024-01-24 13:56:38,662] [INFO] Running command: blastn -query GCF_009792795.1_ASM979279v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb2670973-176f-487c-a851-5abbda9f3c80/dqc_reference/reference_markers_gtdb.fasta -out GCF_009792795.1_ASM979279v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:40,358] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:40,362] [INFO] Selected 19 target genomes.
[2024-01-24 13:56:40,363] [INFO] Target genome list was writen to GCF_009792795.1_ASM979279v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:56:40,405] [INFO] Task started: fastANI
[2024-01-24 13:56:40,405] [INFO] Running command: fastANI --query /var/lib/cwl/stg147d66d1-1088-4f10-8cbd-cfbd21d2a896/GCF_009792795.1_ASM979279v1_genomic.fna.gz --refList GCF_009792795.1_ASM979279v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009792795.1_ASM979279v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:56:52,727] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:52,745] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:56:52,746] [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_009792795.1	s__Luteimonas_B profundi	100.0	898	898	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas_B	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_011320095.1	s__Luteimonas_B telluris	82.3722	598	898	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_003416885.1	s__Luteimonas_B sp003416885	81.4046	547	898	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013362405.1	s__JABFWF01 sp013362405	80.8726	434	898	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__JABFWF01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422305.1	s__Luteimonas mephitis	80.7538	501	898	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006476065.1	s__Luteimonas_B lumbrici	80.631	479	898	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_007830035.1	s__Luteimonas_C cucumeris	80.4342	490	898	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_016613475.2	s__Lysobacter arenosi	80.3766	483	898	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000768335.1	s__Lysobacter arseniciresistens	80.2892	485	898	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018406645.1	s__Lysobacter_A helvus	80.2736	499	898	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_006337105.1	s__Thermomonas sp006337105	80.2368	486	898	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859325.1	s__Luteimonas marina	80.2357	495	898	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014764385.1	s__Luteimonas sp014212025	80.1477	459	898	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	99.36	98.72	0.98	0.96	3	-
GCF_004352845.1	s__Luteimonas terricola	80.0977	439	898	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	99.99	99.99	0.99	0.99	2	-
GCF_016615815.1	s__Luteimonas sp016615815	80.0273	470	898	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	99.14	98.29	0.98	0.95	3	-
GCA_014380115.1	s__JACMKK01 sp014380115	80.0231	391	898	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__JACMKK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902825775.1	s__Luteimonas_C sp902825775	79.7661	449	898	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_001014645.1	s__Luteimonas sp001014645	79.7586	443	898	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003719825.1	s__Lysobacter psychrotolerans	79.7583	446	898	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:56:52,747] [INFO] GTDB search result was written to GCF_009792795.1_ASM979279v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:56:52,748] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:56:52,752] [INFO] DFAST_QC result json was written to GCF_009792795.1_ASM979279v1_genomic.fna/dqc_result.json
[2024-01-24 13:56:52,753] [INFO] DFAST_QC completed!
[2024-01-24 13:56:52,753] [INFO] Total running time: 0h1m34s