[2024-01-24 14:39:59,222] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:39:59,225] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:39:59,225] [INFO] DQC Reference Directory: /var/lib/cwl/stge94467ec-2247-4756-b428-be525ba3b142/dqc_reference
[2024-01-24 14:40:00,696] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:40:00,697] [INFO] Task started: Prodigal
[2024-01-24 14:40:00,697] [INFO] Running command: gunzip -c /var/lib/cwl/stgd756ce6b-b992-4bcd-ad07-937c542fe6ce/GCF_004331955.1_ASM433195v1_genomic.fna.gz | prodigal -d GCF_004331955.1_ASM433195v1_genomic.fna/cds.fna -a GCF_004331955.1_ASM433195v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:40:11,570] [INFO] Task succeeded: Prodigal
[2024-01-24 14:40:11,571] [INFO] Task started: HMMsearch
[2024-01-24 14:40:11,571] [INFO] Running command: hmmsearch --tblout GCF_004331955.1_ASM433195v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge94467ec-2247-4756-b428-be525ba3b142/dqc_reference/reference_markers.hmm GCF_004331955.1_ASM433195v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:40:11,840] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:40:11,842] [INFO] Found 6/6 markers.
[2024-01-24 14:40:11,876] [INFO] Query marker FASTA was written to GCF_004331955.1_ASM433195v1_genomic.fna/markers.fasta
[2024-01-24 14:40:11,876] [INFO] Task started: Blastn
[2024-01-24 14:40:11,876] [INFO] Running command: blastn -query GCF_004331955.1_ASM433195v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge94467ec-2247-4756-b428-be525ba3b142/dqc_reference/reference_markers.fasta -out GCF_004331955.1_ASM433195v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:40:13,030] [INFO] Task succeeded: Blastn
[2024-01-24 14:40:13,034] [INFO] Selected 31 target genomes.
[2024-01-24 14:40:13,035] [INFO] Target genome list was writen to GCF_004331955.1_ASM433195v1_genomic.fna/target_genomes.txt
[2024-01-24 14:40:13,054] [INFO] Task started: fastANI
[2024-01-24 14:40:13,054] [INFO] Running command: fastANI --query /var/lib/cwl/stgd756ce6b-b992-4bcd-ad07-937c542fe6ce/GCF_004331955.1_ASM433195v1_genomic.fna.gz --refList GCF_004331955.1_ASM433195v1_genomic.fna/target_genomes.txt --output GCF_004331955.1_ASM433195v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:40:47,291] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:47,292] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge94467ec-2247-4756-b428-be525ba3b142/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:40:47,292] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge94467ec-2247-4756-b428-be525ba3b142/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:40:47,317] [INFO] Found 31 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:40:47,317] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:40:47,317] [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
Oricola indica	strain=JL-62	GCA_019966595.1	2872591	2872591	type	True	78.7618	453	1179	95	below_threshold
Hoeflea olei	strain=JC234	GCA_001703635.1	1480615	1480615	type	True	78.7407	445	1179	95	below_threshold
Nitratireductor pacificus	strain=pht-3B	GCA_000300335.1	1231180	1231180	type	True	78.6112	430	1179	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	78.5921	436	1179	95	below_threshold
Nitratireductor alexandrii	strain=Z3-1	GCA_004000215.1	2448161	2448161	type	True	78.5633	479	1179	95	below_threshold
Aquibium microcysteis	strain=NIBR3	GCA_014495845.1	675281	675281	type	True	78.4123	473	1179	95	below_threshold
Aquibium oceanicum	strain=B7	GCA_001889605.1	1670800	1670800	type	True	78.3714	385	1179	95	below_threshold
Zhengella mangrovi	strain=X9-2-2	GCA_002727065.1	1982044	1982044	type	True	78.366	374	1179	95	below_threshold
Mesorhizobium intechi	strain=BD68	GCA_002879535.2	537601	537601	type	True	78.2501	372	1179	95	below_threshold
Mesorhizobium tamadayense	strain=DSM 28320	GCA_003863365.1	425306	425306	type	True	78.2492	426	1179	95	below_threshold
Aminobacter aganoensis	strain=DSM 7051	GCA_014206975.1	83264	83264	type	True	78.2412	404	1179	95	below_threshold
Nitratireductor soli	strain=ZZ-1	GCA_001050155.1	1670619	1670619	type	True	78.2186	415	1179	95	below_threshold
Aquibium carbonis	strain=B2.3	GCA_003970795.1	2495581	2495581	type	True	78.1949	420	1179	95	below_threshold
Mesorhizobium erdmanii	strain=USDA 3471	GCA_000472705.1	1777866	1777866	type	True	78.1886	386	1179	95	below_threshold
Mesorhizobium caraganae	strain=LMG 24397	GCA_016836705.1	483206	483206	type	True	78.1702	400	1179	95	below_threshold
Rhizobium azooxidifex	strain=DSM 100211	GCA_014196765.1	1636188	1636188	type	True	78.1505	374	1179	95	below_threshold
Shinella granuli	strain=DSM 18401	GCA_004341885.1	323621	323621	type	True	78.1226	403	1179	95	below_threshold
Mesorhizobium camelthorni	strain=CCNWXJ 40-4	GCA_011045125.1	475069	475069	type	True	78.1209	383	1179	95	below_threshold
Mesorhizobium sanjuanii	strain=BSA136	GCA_002529485.1	2037900	2037900	type	True	78.0578	374	1179	95	below_threshold
Aurantimonas endophytica	strain=KCTC 52296	GCA_024105745.1	1522175	1522175	type	True	78.034	368	1179	95	below_threshold
Mesorhizobium metallidurans	strain=STM 2683	GCA_000350085.1	489722	489722	type	True	78.0237	402	1179	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	77.964	424	1179	95	below_threshold
Shinella sumterensis	strain=MEC087	GCA_004514425.2	1967501	1967501	type	True	77.9421	334	1179	95	below_threshold
Hoeflea marina	strain=DSM 16791	GCA_003182275.1	274592	274592	type	True	77.9362	417	1179	95	below_threshold
Aquamicrobium lusatiense	strain=DSM 11099	GCA_014201615.1	89772	89772	type	True	77.9091	283	1179	95	below_threshold
Mesorhizobium wenxiniae	strain=WYCCWR 10195	GCA_002284535.1	2014805	2014805	type	True	77.82	391	1179	95	below_threshold
Shinella daejeonensis	strain=JCM 16236	GCA_024281235.1	659017	659017	type	True	77.7527	296	1179	95	below_threshold
Hoeflea halophila	strain=KCTC 23107	GCA_900220985.1	714899	714899	type	True	77.7273	286	1179	95	below_threshold
Nitratireductor indicus	strain=C115	GCA_000300515.1	721133	721133	type	True	77.445	232	1179	95	below_threshold
Rhizobium redzepovicii	strain=18T	GCA_019793435.1	2867518	2867518	type	True	77.4264	315	1179	95	below_threshold
Phyllobacterium salinisoli	strain=LLAN61	GCA_003335045.1	1899321	1899321	type	True	77.3937	273	1179	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:40:47,319] [INFO] DFAST Taxonomy check result was written to GCF_004331955.1_ASM433195v1_genomic.fna/tc_result.tsv
[2024-01-24 14:40:47,319] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:40:47,319] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:40:47,320] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge94467ec-2247-4756-b428-be525ba3b142/dqc_reference/checkm_data
[2024-01-24 14:40:47,320] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:40:47,357] [INFO] Task started: CheckM
[2024-01-24 14:40:47,357] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004331955.1_ASM433195v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004331955.1_ASM433195v1_genomic.fna/checkm_input GCF_004331955.1_ASM433195v1_genomic.fna/checkm_result
[2024-01-24 14:41:30,205] [INFO] Task succeeded: CheckM
[2024-01-24 14:41:30,207] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:41:30,228] [INFO] ===== Completeness check finished =====
[2024-01-24 14:41:30,229] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:41:30,229] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004331955.1_ASM433195v1_genomic.fna/markers.fasta)
[2024-01-24 14:41:30,230] [INFO] Task started: Blastn
[2024-01-24 14:41:30,230] [INFO] Running command: blastn -query GCF_004331955.1_ASM433195v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge94467ec-2247-4756-b428-be525ba3b142/dqc_reference/reference_markers_gtdb.fasta -out GCF_004331955.1_ASM433195v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:41:32,405] [INFO] Task succeeded: Blastn
[2024-01-24 14:41:32,409] [INFO] Selected 15 target genomes.
[2024-01-24 14:41:32,410] [INFO] Target genome list was writen to GCF_004331955.1_ASM433195v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:41:32,419] [INFO] Task started: fastANI
[2024-01-24 14:41:32,419] [INFO] Running command: fastANI --query /var/lib/cwl/stgd756ce6b-b992-4bcd-ad07-937c542fe6ce/GCF_004331955.1_ASM433195v1_genomic.fna.gz --refList GCF_004331955.1_ASM433195v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004331955.1_ASM433195v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:41:45,558] [INFO] Task succeeded: fastANI
[2024-01-24 14:41:45,575] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:41:45,576] [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_004331955.1	s__Roseitalea porphyridii	100.0	1179	1179	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Roseitalea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003149475.2	s__Roseitalea stylonematis	83.3606	832	1179	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Roseitalea	95.0	98.99	98.97	0.96	0.95	13	-
GCA_017642895.1	s__Roseitalea sp017642895	82.3831	804	1179	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Roseitalea	95.0	99.99	99.99	1.00	1.00	3	-
GCF_014904745.1	s__Oricola sp014904745	79.3043	533	1179	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Oricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000759435.1	s__Hoeflea sp000759435	78.8722	466	1179	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002698425.1	s__Oricola sp002698425	78.8174	517	1179	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Oricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000300335.1	s__Nitratireductor pacificus	78.6311	428	1179	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014860725.1	s__Aquamicrobium_A sp014860725	78.5476	257	1179	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aquamicrobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007922615.2	s__Nitratireductor_D sp007922615	78.4317	429	1179	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900469965.1	s__Mycoplana sp900469965	78.393	396	1179	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mycoplana	95.0	98.03	97.96	0.94	0.92	10	-
GCF_001889605.1	s__Mesorhizobium_E oceanicum	78.3827	385	1179	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905339215.1	s__DUSC01 sp008933895	78.2174	402	1179	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__DUSC01	95.0	99.82	99.82	0.93	0.93	2	-
GCF_014873545.1	s__OAS926 sp014873545	78.1717	418	1179	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__OAS926	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018829385.1	s__Hoeflea sp018829385	78.1551	251	1179	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012911015.1	s__Aliihoeflea sp012911015	78.1395	379	1179	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aliihoeflea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:41:45,577] [INFO] GTDB search result was written to GCF_004331955.1_ASM433195v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:41:45,578] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:41:45,583] [INFO] DFAST_QC result json was written to GCF_004331955.1_ASM433195v1_genomic.fna/dqc_result.json
[2024-01-24 14:41:45,583] [INFO] DFAST_QC completed!
[2024-01-24 14:41:45,583] [INFO] Total running time: 0h1m46s