[2024-01-24 14:11:46,246] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:11:46,247] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:11:46,248] [INFO] DQC Reference Directory: /var/lib/cwl/stgd6840719-6995-486e-99cc-4b861bba161d/dqc_reference
[2024-01-24 14:11:47,453] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:11:47,454] [INFO] Task started: Prodigal
[2024-01-24 14:11:47,454] [INFO] Running command: gunzip -c /var/lib/cwl/stgcc1e586c-b5bc-466f-95e3-5fd2eedf6d9c/GCF_030551875.1_ASM3055187v1_genomic.fna.gz | prodigal -d GCF_030551875.1_ASM3055187v1_genomic.fna/cds.fna -a GCF_030551875.1_ASM3055187v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:12:03,099] [INFO] Task succeeded: Prodigal
[2024-01-24 14:12:03,099] [INFO] Task started: HMMsearch
[2024-01-24 14:12:03,099] [INFO] Running command: hmmsearch --tblout GCF_030551875.1_ASM3055187v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd6840719-6995-486e-99cc-4b861bba161d/dqc_reference/reference_markers.hmm GCF_030551875.1_ASM3055187v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:12:03,412] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:12:03,413] [INFO] Found 6/6 markers.
[2024-01-24 14:12:03,474] [INFO] Query marker FASTA was written to GCF_030551875.1_ASM3055187v1_genomic.fna/markers.fasta
[2024-01-24 14:12:03,474] [INFO] Task started: Blastn
[2024-01-24 14:12:03,475] [INFO] Running command: blastn -query GCF_030551875.1_ASM3055187v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd6840719-6995-486e-99cc-4b861bba161d/dqc_reference/reference_markers.fasta -out GCF_030551875.1_ASM3055187v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:12:04,521] [INFO] Task succeeded: Blastn
[2024-01-24 14:12:04,524] [INFO] Selected 31 target genomes.
[2024-01-24 14:12:04,525] [INFO] Target genome list was writen to GCF_030551875.1_ASM3055187v1_genomic.fna/target_genomes.txt
[2024-01-24 14:12:04,541] [INFO] Task started: fastANI
[2024-01-24 14:12:04,541] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc1e586c-b5bc-466f-95e3-5fd2eedf6d9c/GCF_030551875.1_ASM3055187v1_genomic.fna.gz --refList GCF_030551875.1_ASM3055187v1_genomic.fna/target_genomes.txt --output GCF_030551875.1_ASM3055187v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:12:36,773] [INFO] Task succeeded: fastANI
[2024-01-24 14:12:36,773] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd6840719-6995-486e-99cc-4b861bba161d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:12:36,774] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd6840719-6995-486e-99cc-4b861bba161d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:12:36,796] [INFO] Found 31 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:12:36,796] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:12:36,797] [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
Ciceribacter selenitireducens	strain=ATCC BAA-1503	GCA_000518785.1	448181	448181	type	True	78.9779	555	1710	95	below_threshold
Rhizobium rosettiformans	strain=DSM 26376	GCA_014202175.1	1368430	1368430	type	True	78.802	477	1710	95	below_threshold
Shinella zoogloeoides	strain=DSM 287	GCA_009826855.1	352475	352475	type	True	78.7597	507	1710	95	below_threshold
Rhizobium rosettiformans	strain=W3	GCA_004912135.1	1368430	1368430	type	True	78.7271	484	1710	95	below_threshold
Shinella fusca	strain=DSM 21319	GCA_014203155.1	544480	544480	type	True	78.6878	503	1710	95	below_threshold
Shinella granuli	strain=DSM 18401	GCA_004341885.1	323621	323621	type	True	78.6862	594	1710	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	78.6601	573	1710	95	below_threshold
Shinella sumterensis	strain=MEC087	GCA_004514425.2	1967501	1967501	type	True	78.6496	531	1710	95	below_threshold
Rhizobium giardinii	strain=H152	GCA_000379605.1	56731	56731	type	True	78.6283	519	1710	95	below_threshold
Rhizobium indicum	strain=JKLM 12A2	GCA_005862305.2	2583231	2583231	type	True	78.6007	496	1710	95	below_threshold
Rhizobium ruizarguesonis	strain=UPM1133	GCA_012349115.1	2081791	2081791	type	True	78.5764	505	1710	95	below_threshold
Rhizobium wuzhouense	strain=W44	GCA_003205195.1	1986026	1986026	type	True	78.5754	500	1710	95	below_threshold
Rhizobium pseudoryzae	strain=DSM 19479	GCA_011046245.1	379684	379684	type	True	78.5524	497	1710	95	below_threshold
Shinella oryzae	strain=Z-25	GCA_023038235.1	2871820	2871820	type	True	78.5465	528	1710	95	below_threshold
Rhizobium halophytocola	strain=DSM 21600	GCA_017873095.1	735519	735519	type	True	78.5311	466	1710	95	below_threshold
Ciceribacter thiooxidans	strain=F43B	GCA_014126615.1	1969821	1969821	type	True	78.5081	445	1710	95	below_threshold
Ensifer sesbaniae	strain=CCBAU 65729	GCA_013283665.1	1214071	1214071	type	True	78.4984	519	1710	95	below_threshold
Agrobacterium leguminum	strain=MOPV5	GCA_015704895.1	2792015	2792015	type	True	78.4795	415	1710	95	below_threshold
Rhizobium laguerreae	strain=FB206	GCA_002008165.1	1076926	1076926	type	True	78.4539	508	1710	95	below_threshold
Ciceribacter lividus	strain=DSM 25528	GCA_003337715.1	1197950	1197950	type	True	78.4493	469	1710	95	below_threshold
Rhizobium laguerreae	strain=CECT 8280	GCA_014192445.1	1076926	1076926	type	True	78.4382	505	1710	95	below_threshold
Neorhizobium vignae	strain=CCBAU 05176	GCA_000732195.1	690585	690585	type	True	78.4348	463	1710	95	below_threshold
Sinorhizobium fredii	strain=NBRC 14780	GCA_006539605.1	380	380	type	True	78.4253	471	1710	95	below_threshold
Sinorhizobium fredii	strain=USDA 205	GCA_001461695.1	380	380	type	True	78.375	482	1710	95	below_threshold
Agrobacterium rhizogenes	strain=NBRC 13257	GCA_000696095.1	359	359	type	True	78.3339	487	1710	95	below_threshold
Rhizobium lentis	strain=BLR27	GCA_017352135.1	1138194	1138194	type	True	78.2708	486	1710	95	below_threshold
Rhizobium lentis	strain=BLR27	GCA_019684715.1	1138194	1138194	type	True	78.2345	486	1710	95	below_threshold
Neorhizobium alkalisoli	strain=DSM 21826	GCA_002968635.1	528178	528178	type	True	78.2287	420	1710	95	below_threshold
Rhizobium viscosum	strain=DSM 7307	GCA_014873945.1	1673	1673	type	True	78.1903	483	1710	95	below_threshold
Shinella daejeonensis	strain=JCM 16236	GCA_024281235.1	659017	659017	type	True	78.0942	425	1710	95	below_threshold
Hoeflea alexandrii	strain=DSM 16655	GCA_024105735.1	288436	288436	type	True	77.5682	352	1710	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:12:36,798] [INFO] DFAST Taxonomy check result was written to GCF_030551875.1_ASM3055187v1_genomic.fna/tc_result.tsv
[2024-01-24 14:12:36,799] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:12:36,799] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:12:36,800] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd6840719-6995-486e-99cc-4b861bba161d/dqc_reference/checkm_data
[2024-01-24 14:12:36,801] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:12:36,849] [INFO] Task started: CheckM
[2024-01-24 14:12:36,849] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030551875.1_ASM3055187v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030551875.1_ASM3055187v1_genomic.fna/checkm_input GCF_030551875.1_ASM3055187v1_genomic.fna/checkm_result
[2024-01-24 14:13:25,632] [INFO] Task succeeded: CheckM
[2024-01-24 14:13:25,634] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:13:25,656] [INFO] ===== Completeness check finished =====
[2024-01-24 14:13:25,657] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:13:25,657] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030551875.1_ASM3055187v1_genomic.fna/markers.fasta)
[2024-01-24 14:13:25,658] [INFO] Task started: Blastn
[2024-01-24 14:13:25,658] [INFO] Running command: blastn -query GCF_030551875.1_ASM3055187v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd6840719-6995-486e-99cc-4b861bba161d/dqc_reference/reference_markers_gtdb.fasta -out GCF_030551875.1_ASM3055187v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:27,501] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:27,506] [INFO] Selected 22 target genomes.
[2024-01-24 14:13:27,506] [INFO] Target genome list was writen to GCF_030551875.1_ASM3055187v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:13:27,562] [INFO] Task started: fastANI
[2024-01-24 14:13:27,562] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc1e586c-b5bc-466f-95e3-5fd2eedf6d9c/GCF_030551875.1_ASM3055187v1_genomic.fna.gz --refList GCF_030551875.1_ASM3055187v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030551875.1_ASM3055187v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:13:50,275] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:50,296] [INFO] Found 22 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:13:50,296] [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_005222915.1	s__FKL33 sp005222915	79.8848	778	1710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__FKL33	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014158035.1	s__FKL33 sp014158035	79.6682	739	1710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__FKL33	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016722925.1	s__FKL33 sp016722925	79.1562	623	1710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__FKL33	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002796995.1	s__Allorhizobium sp002796995	79.0863	566	1710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	96.22	96.20	0.94	0.93	7	-
GCF_000518785.1	s__Allorhizobium selenitireducens	78.9858	554	1710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900492205.1	s__Allorhizobium naphthalenivorans_A	78.9386	545	1710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	95.27	95.27	0.88	0.88	2	-
GCA_900467685.1	s__Ensifer_A sp900467685	78.8652	483	1710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Ensifer_A	95.0	100.00	99.99	1.00	1.00	3	-
GCF_900215285.1	s__Ensifer_A adhaerens_A	78.8343	478	1710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Ensifer_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001424985.1	s__Pararhizobium sp001424985	78.7653	519	1710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pararhizobium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000172795.2	s__Rhizobium sp000172795	78.7039	515	1710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003574625.1	s__Shinella zoogloeoides_A	78.6396	524	1710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014195095.1	s__Rhizobium sp014195095	78.6234	510	1710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177415.1	s__Neorhizobium oryzae_A	78.6192	505	1710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017877135.1	s__Rhizobium_A galegae_A	78.6112	460	1710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001426565.1	s__Pararhizobium sp001426565	78.543	525	1710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pararhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017873095.1	s__Allorhizobium halophytocola	78.5398	465	1710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014193025.1	s__Rhizobium sp014193025	78.5023	523	1710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000271845.1	s__Rhizobium leguminosarum_G	78.4795	516	1710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000722615.1	s__Pseudorhizobium pelagicum	78.3887	393	1710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudorhizobium	95.0	97.63	97.12	0.87	0.82	8	-
GCF_002968635.1	s__Neorhizobium alkalisoli	78.2252	421	1710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873945.1	s__Rhizobium viscosum	78.1896	483	1710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900466475.1	s__Rhizobium sp900466475	78.1692	478	1710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.15	97.80	0.95	0.94	17	-
--------------------------------------------------------------------------------
[2024-01-24 14:13:50,298] [INFO] GTDB search result was written to GCF_030551875.1_ASM3055187v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:13:50,298] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:13:50,303] [INFO] DFAST_QC result json was written to GCF_030551875.1_ASM3055187v1_genomic.fna/dqc_result.json
[2024-01-24 14:13:50,303] [INFO] DFAST_QC completed!
[2024-01-24 14:13:50,304] [INFO] Total running time: 0h2m4s