[2024-01-24 14:31:14,612] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:31:14,614] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:31:14,614] [INFO] DQC Reference Directory: /var/lib/cwl/stgd399e561-81d2-4c8c-a922-345a4006889f/dqc_reference
[2024-01-24 14:31:15,895] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:31:15,895] [INFO] Task started: Prodigal
[2024-01-24 14:31:15,896] [INFO] Running command: gunzip -c /var/lib/cwl/stgdaf5dc44-39fa-424a-8088-d77f9f78d298/GCF_005860795.2_ASM586079v2_genomic.fna.gz | prodigal -d GCF_005860795.2_ASM586079v2_genomic.fna/cds.fna -a GCF_005860795.2_ASM586079v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:31:29,835] [INFO] Task succeeded: Prodigal
[2024-01-24 14:31:29,836] [INFO] Task started: HMMsearch
[2024-01-24 14:31:29,836] [INFO] Running command: hmmsearch --tblout GCF_005860795.2_ASM586079v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd399e561-81d2-4c8c-a922-345a4006889f/dqc_reference/reference_markers.hmm GCF_005860795.2_ASM586079v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:31:30,233] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:31:30,235] [INFO] Found 6/6 markers.
[2024-01-24 14:31:30,281] [INFO] Query marker FASTA was written to GCF_005860795.2_ASM586079v2_genomic.fna/markers.fasta
[2024-01-24 14:31:30,281] [INFO] Task started: Blastn
[2024-01-24 14:31:30,282] [INFO] Running command: blastn -query GCF_005860795.2_ASM586079v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgd399e561-81d2-4c8c-a922-345a4006889f/dqc_reference/reference_markers.fasta -out GCF_005860795.2_ASM586079v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:31,440] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:31,444] [INFO] Selected 19 target genomes.
[2024-01-24 14:31:31,445] [INFO] Target genome list was writen to GCF_005860795.2_ASM586079v2_genomic.fna/target_genomes.txt
[2024-01-24 14:31:31,454] [INFO] Task started: fastANI
[2024-01-24 14:31:31,455] [INFO] Running command: fastANI --query /var/lib/cwl/stgdaf5dc44-39fa-424a-8088-d77f9f78d298/GCF_005860795.2_ASM586079v2_genomic.fna.gz --refList GCF_005860795.2_ASM586079v2_genomic.fna/target_genomes.txt --output GCF_005860795.2_ASM586079v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:50,145] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:50,145] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd399e561-81d2-4c8c-a922-345a4006889f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:50,146] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd399e561-81d2-4c8c-a922-345a4006889f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:50,167] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:31:50,167] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:31:50,167] [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
Rhizobium rosettiformans	strain=W3	GCA_004912135.1	1368430	1368430	type	True	81.8546	756	1446	95	below_threshold
Rhizobium rosettiformans	strain=DSM 26376	GCA_014202175.1	1368430	1368430	type	True	81.852	763	1446	95	below_threshold
Rhizobium glycinendophyticum	strain=CL12	GCA_006443685.1	2589807	2589807	type	True	81.3472	718	1446	95	below_threshold
Rhizobium wuzhouense	strain=W44	GCA_003205195.1	1986026	1986026	type	True	81.2449	709	1446	95	below_threshold
Rhizobium rhizophilum	strain=7209-2	GCA_004912145.1	1850373	1850373	type	True	81.243	760	1446	95	below_threshold
Ciceribacter selenitireducens	strain=ATCC BAA-1503	GCA_000518785.1	448181	448181	type	True	79.918	625	1446	95	below_threshold
Rhizobium pseudoryzae	strain=DSM 19479	GCA_011046245.1	379684	379684	type	True	79.5379	529	1446	95	below_threshold
Ciceribacter lividus	strain=DSM 25528	GCA_003337715.1	1197950	1197950	type	True	79.3453	502	1446	95	below_threshold
Ciceribacter thiooxidans	strain=F43B	GCA_014126615.1	1969821	1969821	type	True	79.3021	523	1446	95	below_threshold
Ciceribacter ferrooxidans	strain=F8825	GCA_004137355.1	2509717	2509717	type	True	79.1577	527	1446	95	below_threshold
Rhizobium populisoli	strain=XQZ8	GCA_019430945.1	2859785	2859785	type	True	78.9976	455	1446	95	below_threshold
Shinella curvata	strain=C3	GCA_022899935.1	1817964	1817964	type	True	78.934	448	1446	95	below_threshold
Pseudorhizobium endolithicum	strain=JC140	GCA_902153245.3	1191678	1191678	type	True	78.8434	401	1446	95	below_threshold
Rhizobium viscosum	strain=DSM 7307	GCA_014873945.1	1673	1673	type	True	78.8123	432	1446	95	below_threshold
Agrobacterium leguminum	strain=MOPV5	GCA_015704895.1	2792015	2792015	type	True	78.79	429	1446	95	below_threshold
Shinella fusca	strain=DSM 21319	GCA_014203155.1	544480	544480	type	True	78.7814	441	1446	95	below_threshold
Rhizobium jaguaris	strain=CCGE525	GCA_003627755.1	1312183	1312183	type	True	78.6291	401	1446	95	below_threshold
Rhizobium petrolearium	strain=DSM 26482	GCA_017873175.1	515361	515361	type	True	78.5373	424	1446	95	below_threshold
Rhizobium skierniewicense	strain=Ch11	GCA_023757665.1	984260	984260	type	True	78.1663	304	1446	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:50,169] [INFO] DFAST Taxonomy check result was written to GCF_005860795.2_ASM586079v2_genomic.fna/tc_result.tsv
[2024-01-24 14:31:50,170] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:50,170] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:50,170] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd399e561-81d2-4c8c-a922-345a4006889f/dqc_reference/checkm_data
[2024-01-24 14:31:50,171] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:50,213] [INFO] Task started: CheckM
[2024-01-24 14:31:50,213] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005860795.2_ASM586079v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005860795.2_ASM586079v2_genomic.fna/checkm_input GCF_005860795.2_ASM586079v2_genomic.fna/checkm_result
[2024-01-24 14:32:35,416] [INFO] Task succeeded: CheckM
[2024-01-24 14:32:35,417] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:32:35,440] [INFO] ===== Completeness check finished =====
[2024-01-24 14:32:35,441] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:32:35,441] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005860795.2_ASM586079v2_genomic.fna/markers.fasta)
[2024-01-24 14:32:35,442] [INFO] Task started: Blastn
[2024-01-24 14:32:35,442] [INFO] Running command: blastn -query GCF_005860795.2_ASM586079v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgd399e561-81d2-4c8c-a922-345a4006889f/dqc_reference/reference_markers_gtdb.fasta -out GCF_005860795.2_ASM586079v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:32:37,280] [INFO] Task succeeded: Blastn
[2024-01-24 14:32:37,284] [INFO] Selected 21 target genomes.
[2024-01-24 14:32:37,284] [INFO] Target genome list was writen to GCF_005860795.2_ASM586079v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:32:37,300] [INFO] Task started: fastANI
[2024-01-24 14:32:37,301] [INFO] Running command: fastANI --query /var/lib/cwl/stgdaf5dc44-39fa-424a-8088-d77f9f78d298/GCF_005860795.2_ASM586079v2_genomic.fna.gz --refList GCF_005860795.2_ASM586079v2_genomic.fna/target_genomes_gtdb.txt --output GCF_005860795.2_ASM586079v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:32:57,212] [INFO] Task succeeded: fastANI
[2024-01-24 14:32:57,232] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:32:57,233] [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_005860795.2	s__Allorhizobium desertarenae	100.0	1446	1446	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014237835.1	s__Allorhizobium sp014237835	82.4314	768	1446	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004912135.1	s__Allorhizobium rosettiformans	81.8545	756	1446	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	96.40	95.42	0.87	0.84	7	-
GCF_016806065.1	s__Allorhizobium sp001724035	81.7905	763	1446	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	96.77	96.77	0.91	0.91	2	-
GCF_001713475.1	s__Allorhizobium sp001713475	81.7819	794	1446	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	98.17	97.98	0.95	0.89	6	-
GCA_900473805.1	s__Allorhizobium sp900473805	81.6583	698	1446	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	99.45	97.28	0.98	0.92	6	-
GCF_002855515.1	s__Allorhizobium sp002855515	81.563	757	1446	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000300855.1	s__Allorhizobium albertimagni	81.507	745	1446	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156055.1	s__Allorhizobium sp900156055	81.4615	755	1446	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004912165.1	s__Allorhizobium ipomoeae	81.035	662	1446	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001429245.1	s__Allorhizobium sp001429245	80.9842	707	1446	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_902706095.1	s__Allorhizobium sp902706095	80.1482	712	1446	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002796995.1	s__Allorhizobium sp002796995	80.0265	607	1446	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	96.22	96.20	0.94	0.93	7	-
GCF_900492205.1	s__Allorhizobium naphthalenivorans_A	79.9161	621	1446	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	95.27	95.27	0.88	0.88	2	-
GCF_000518785.1	s__Allorhizobium selenitireducens	79.8953	627	1446	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012927355.1	s__Allorhizobium sp012927355	79.5686	612	1446	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003337715.1	s__Allorhizobium lividum	79.3306	504	1446	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900465605.1	s__Allorhizobium sp900465605	79.1599	510	1446	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	96.96	95.85	0.92	0.91	5	-
GCA_900466005.1	s__Allorhizobium sp900466005	79.118	527	1446	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	99.03	99.00	0.93	0.93	3	-
GCF_014873945.1	s__Rhizobium viscosum	78.8821	434	1446	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005222845.1	s__Rhizobium_A sp005222845	78.8314	498	1446	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:32:57,234] [INFO] GTDB search result was written to GCF_005860795.2_ASM586079v2_genomic.fna/result_gtdb.tsv
[2024-01-24 14:32:57,235] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:32:57,239] [INFO] DFAST_QC result json was written to GCF_005860795.2_ASM586079v2_genomic.fna/dqc_result.json
[2024-01-24 14:32:57,239] [INFO] DFAST_QC completed!
[2024-01-24 14:32:57,240] [INFO] Total running time: 0h1m43s