[2024-01-24 14:39:29,624] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:39:29,629] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:39:29,630] [INFO] DQC Reference Directory: /var/lib/cwl/stg08d55a32-7fbd-4a9d-a57d-2988de52d680/dqc_reference
[2024-01-24 14:39:30,888] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:39:30,889] [INFO] Task started: Prodigal
[2024-01-24 14:39:30,889] [INFO] Running command: gunzip -c /var/lib/cwl/stga26e4f40-7cec-4055-8a46-48b322290a5b/GCF_019492055.1_ASM1949205v1_genomic.fna.gz | prodigal -d GCF_019492055.1_ASM1949205v1_genomic.fna/cds.fna -a GCF_019492055.1_ASM1949205v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:39:48,417] [INFO] Task succeeded: Prodigal
[2024-01-24 14:39:48,417] [INFO] Task started: HMMsearch
[2024-01-24 14:39:48,417] [INFO] Running command: hmmsearch --tblout GCF_019492055.1_ASM1949205v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg08d55a32-7fbd-4a9d-a57d-2988de52d680/dqc_reference/reference_markers.hmm GCF_019492055.1_ASM1949205v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:39:48,746] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:39:48,748] [INFO] Found 6/6 markers.
[2024-01-24 14:39:48,797] [INFO] Query marker FASTA was written to GCF_019492055.1_ASM1949205v1_genomic.fna/markers.fasta
[2024-01-24 14:39:48,797] [INFO] Task started: Blastn
[2024-01-24 14:39:48,798] [INFO] Running command: blastn -query GCF_019492055.1_ASM1949205v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg08d55a32-7fbd-4a9d-a57d-2988de52d680/dqc_reference/reference_markers.fasta -out GCF_019492055.1_ASM1949205v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:49,751] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:49,754] [INFO] Selected 32 target genomes.
[2024-01-24 14:39:49,755] [INFO] Target genome list was writen to GCF_019492055.1_ASM1949205v1_genomic.fna/target_genomes.txt
[2024-01-24 14:39:49,766] [INFO] Task started: fastANI
[2024-01-24 14:39:49,766] [INFO] Running command: fastANI --query /var/lib/cwl/stga26e4f40-7cec-4055-8a46-48b322290a5b/GCF_019492055.1_ASM1949205v1_genomic.fna.gz --refList GCF_019492055.1_ASM1949205v1_genomic.fna/target_genomes.txt --output GCF_019492055.1_ASM1949205v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:40:25,966] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:25,966] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg08d55a32-7fbd-4a9d-a57d-2988de52d680/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:40:25,967] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg08d55a32-7fbd-4a9d-a57d-2988de52d680/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:40:25,995] [INFO] Found 32 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:40:25,995] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:40:25,996] [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
Nitratireductor pacificus	strain=pht-3B	GCA_000300335.1	1231180	1231180	type	True	77.7805	286	1892	95	below_threshold
Hoeflea olei	strain=JC234	GCA_001703635.1	1480615	1480615	type	True	77.7767	323	1892	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	77.7593	323	1892	95	below_threshold
Rhizobium redzepovicii	strain=18T	GCA_019793435.1	2867518	2867518	type	True	77.6762	279	1892	95	below_threshold
Ciceribacter thiooxidans	strain=F43B	GCA_014126615.1	1969821	1969821	type	True	77.6697	240	1892	95	below_threshold
Ensifer sojae	strain=CCBAU 05684	GCA_002288525.1	716925	716925	type	True	77.5316	267	1892	95	below_threshold
Ensifer sojae	strain=CCBAU 05684	GCA_000261485.1	716925	716925	type	True	77.5198	260	1892	95	below_threshold
Nitratireductor soli	strain=ZZ-1	GCA_001050155.1	1670619	1670619	type	True	77.5017	283	1892	95	below_threshold
Nitratireductor arenosus	strain=CAU 1489	GCA_009742725.1	2682096	2682096	type	True	77.475	296	1892	95	below_threshold
Hoeflea halophila	strain=KCTC 23107	GCA_900220985.1	714899	714899	type	True	77.4528	245	1892	95	below_threshold
Hoeflea alexandrii	strain=DSM 16655	GCA_024105735.1	288436	288436	type	True	77.4411	291	1892	95	below_threshold
Mesorhizobium tamadayense	strain=DSM 28320	GCA_003863365.1	425306	425306	type	True	77.4236	302	1892	95	below_threshold
Mesorhizobium jarvisii	strain=LMG 28313	GCA_003601985.1	1777867	1777867	type	True	77.4152	309	1892	95	below_threshold
Mesorhizobium japonicum	strain=MAFF 303099	GCA_000009625.1	2066070	2066070	type	True	77.4112	296	1892	95	below_threshold
Aquibium carbonis	strain=B2.3	GCA_003970795.1	2495581	2495581	type	True	77.4067	300	1892	95	below_threshold
Zhengella mangrovi	strain=X9-2-2	GCA_002727065.1	1982044	1982044	type	True	77.3882	282	1892	95	below_threshold
Neorhizobium vignae	strain=CCBAU 05176	GCA_000732195.1	690585	690585	type	True	77.3854	257	1892	95	below_threshold
Rhizobium hainanense	strain=CCBAU 57015	GCA_900094555.1	52131	52131	type	True	77.3817	235	1892	95	below_threshold
Rhizobium aethiopicum	strain=HBR26	GCA_900094625.1	1138170	1138170	type	True	77.3551	260	1892	95	below_threshold
Oricola cellulosilytica	strain=JCM 19534	GCA_019966575.1	1429082	1429082	type	True	77.3298	194	1892	95	below_threshold
Rhizobium jaguaris	strain=CCGE525	GCA_003627755.1	1312183	1312183	type	True	77.2996	236	1892	95	below_threshold
Ensifer alkalisoli	strain=YIC4027	GCA_008932245.1	1752398	1752398	type	True	77.2897	265	1892	95	below_threshold
Sinorhizobium kostiense	strain=DSM 13372	GCA_017874595.1	76747	76747	type	True	77.2593	242	1892	95	below_threshold
Rhizobium tropici	strain=CIAT 899	GCA_000330885.1	398	398	type	True	77.2443	248	1892	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	77.1298	296	1892	95	below_threshold
Aurantimonas marina	strain=SW136	GCA_017183135.1	2780508	2780508	type	True	77.0616	203	1892	95	below_threshold
Xanthobacter aminoxidans	strain=ATCC BAA-299	GCA_023571765.1	186280	186280	type	True	76.556	134	1892	95	below_threshold
Bradyrhizobium aeschynomenes	strain=83002	GCA_013178945.1	2734909	2734909	type	True	76.544	157	1892	95	below_threshold
Rhizobium skierniewicense	strain=Ch11	GCA_023757665.1	984260	984260	type	True	76.5208	136	1892	95	below_threshold
Bradyrhizobium betae	strain=CECT 5829	GCA_024806875.1	244734	244734	type	True	76.4097	164	1892	95	below_threshold
Rhizobium skierniewicense	strain=DSM 26438	GCA_014196515.1	984260	984260	type	True	76.4081	135	1892	95	below_threshold
Bradyrhizobium pachyrhizi	strain=PAC 48	GCA_001189245.1	280333	280333	type	True	76.2699	188	1892	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:40:26,002] [INFO] DFAST Taxonomy check result was written to GCF_019492055.1_ASM1949205v1_genomic.fna/tc_result.tsv
[2024-01-24 14:40:26,003] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:40:26,003] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:40:26,003] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg08d55a32-7fbd-4a9d-a57d-2988de52d680/dqc_reference/checkm_data
[2024-01-24 14:40:26,004] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:40:26,058] [INFO] Task started: CheckM
[2024-01-24 14:40:26,058] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019492055.1_ASM1949205v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019492055.1_ASM1949205v1_genomic.fna/checkm_input GCF_019492055.1_ASM1949205v1_genomic.fna/checkm_result
[2024-01-24 14:41:19,694] [INFO] Task succeeded: CheckM
[2024-01-24 14:41:19,695] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:41:19,718] [INFO] ===== Completeness check finished =====
[2024-01-24 14:41:19,718] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:41:19,718] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019492055.1_ASM1949205v1_genomic.fna/markers.fasta)
[2024-01-24 14:41:19,719] [INFO] Task started: Blastn
[2024-01-24 14:41:19,719] [INFO] Running command: blastn -query GCF_019492055.1_ASM1949205v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg08d55a32-7fbd-4a9d-a57d-2988de52d680/dqc_reference/reference_markers_gtdb.fasta -out GCF_019492055.1_ASM1949205v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:41:21,430] [INFO] Task succeeded: Blastn
[2024-01-24 14:41:21,435] [INFO] Selected 27 target genomes.
[2024-01-24 14:41:21,436] [INFO] Target genome list was writen to GCF_019492055.1_ASM1949205v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:41:21,456] [INFO] Task started: fastANI
[2024-01-24 14:41:21,456] [INFO] Running command: fastANI --query /var/lib/cwl/stga26e4f40-7cec-4055-8a46-48b322290a5b/GCF_019492055.1_ASM1949205v1_genomic.fna.gz --refList GCF_019492055.1_ASM1949205v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019492055.1_ASM1949205v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:41:49,299] [INFO] Task succeeded: fastANI
[2024-01-24 14:41:49,320] [INFO] Found 27 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:41:49,321] [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
GCA_017794825.1	s__SPNT01 sp017794825	88.7352	1542	1892	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__SPNT01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004959855.1	s__SPNT01 sp004959855	78.4822	453	1892	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__SPNT01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000759435.1	s__Hoeflea sp000759435	77.7704	347	1892	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000300335.1	s__Nitratireductor pacificus	77.7693	287	1892	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014126615.1	s__Allorhizobium thiooxidans	77.6697	240	1892	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000378985.1	s__Sinorhizobium sp000378985	77.5916	299	1892	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001713395.1	s__Shinella sp001713395	77.5644	286	1892	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016756535.1	s__Mesorhizobium sp016756535	77.5592	307	1892	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902498795.1	s__Hoeflea sp902498795	77.5362	291	1892	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	97.67	97.67	0.92	0.92	2	-
GCF_900155885.1	s__RU20A sp900155885	77.5346	245	1892	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__RU20A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002288525.1	s__Sinorhizobium sojae	77.5316	267	1892	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_014197615.1	s__Rhizobium esperanzae_A	77.5085	282	1892	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900220985.1	s__Hoeflea halophila	77.4554	244	1892	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018829385.1	s__Hoeflea sp018829385	77.4242	213	1892	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017948245.1	s__Rhizobium sp017948245	77.4217	270	1892	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004791255.1	s__Mesorhizobium sp004791255	77.3709	292	1892	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.78	99.47	0.95	0.87	5	-
GCF_000746385.1	s__Rhizobium sp000746385	77.3022	264	1892	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	96.83	96.83	0.89	0.89	2	-
GCA_900465605.1	s__Allorhizobium sp900465605	77.2919	247	1892	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	96.96	95.85	0.92	0.91	5	-
GCF_001426685.1	s__Pararhizobium sp001426685	77.2664	255	1892	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pararhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017874595.1	s__Sinorhizobium kostiense	77.247	241	1892	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016756495.1	s__Mesorhizobium sp016756495	77.2399	324	1892	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733955.1	s__Hoeflea sp002733955	77.1333	275	1892	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014189455.1	s__Mesorhizobium huakuii_A	77.0633	306	1892	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003432385.1	s__Breoghania sp003432385	77.0396	216	1892	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Breoghania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001189245.1	s__Bradyrhizobium pachyrhizi	76.2891	186	1892	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	96.66	95.38	0.85	0.82	8	-
GCF_014138285.1	s__Phyllobacterium myrsinacearum_A	76.2572	159	1892	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Phyllobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003169835.1	s__Z2-YC6860 sp003169835	75.6368	60	1892	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Z2-YC6860	95.0	99.86	99.86	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:41:49,322] [INFO] GTDB search result was written to GCF_019492055.1_ASM1949205v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:41:49,323] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:41:49,329] [INFO] DFAST_QC result json was written to GCF_019492055.1_ASM1949205v1_genomic.fna/dqc_result.json
[2024-01-24 14:41:49,329] [INFO] DFAST_QC completed!
[2024-01-24 14:41:49,329] [INFO] Total running time: 0h2m20s