[2024-01-25 18:59:05,521] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:59:05,522] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:59:05,522] [INFO] DQC Reference Directory: /var/lib/cwl/stg53ac4c12-80fe-4636-892f-69053b6ea658/dqc_reference
[2024-01-25 18:59:06,727] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:59:06,727] [INFO] Task started: Prodigal
[2024-01-25 18:59:06,728] [INFO] Running command: gunzip -c /var/lib/cwl/stgaca5dbfb-c70b-477c-89f9-8f8cd089900e/GCF_030814475.1_ASM3081447v1_genomic.fna.gz | prodigal -d GCF_030814475.1_ASM3081447v1_genomic.fna/cds.fna -a GCF_030814475.1_ASM3081447v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:59:24,091] [INFO] Task succeeded: Prodigal
[2024-01-25 18:59:24,091] [INFO] Task started: HMMsearch
[2024-01-25 18:59:24,091] [INFO] Running command: hmmsearch --tblout GCF_030814475.1_ASM3081447v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg53ac4c12-80fe-4636-892f-69053b6ea658/dqc_reference/reference_markers.hmm GCF_030814475.1_ASM3081447v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:59:24,365] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:59:24,367] [INFO] Found 6/6 markers.
[2024-01-25 18:59:24,418] [INFO] Query marker FASTA was written to GCF_030814475.1_ASM3081447v1_genomic.fna/markers.fasta
[2024-01-25 18:59:24,418] [INFO] Task started: Blastn
[2024-01-25 18:59:24,418] [INFO] Running command: blastn -query GCF_030814475.1_ASM3081447v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg53ac4c12-80fe-4636-892f-69053b6ea658/dqc_reference/reference_markers.fasta -out GCF_030814475.1_ASM3081447v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:59:25,336] [INFO] Task succeeded: Blastn
[2024-01-25 18:59:25,339] [INFO] Selected 23 target genomes.
[2024-01-25 18:59:25,339] [INFO] Target genome list was writen to GCF_030814475.1_ASM3081447v1_genomic.fna/target_genomes.txt
[2024-01-25 18:59:25,355] [INFO] Task started: fastANI
[2024-01-25 18:59:25,355] [INFO] Running command: fastANI --query /var/lib/cwl/stgaca5dbfb-c70b-477c-89f9-8f8cd089900e/GCF_030814475.1_ASM3081447v1_genomic.fna.gz --refList GCF_030814475.1_ASM3081447v1_genomic.fna/target_genomes.txt --output GCF_030814475.1_ASM3081447v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:59:52,846] [INFO] Task succeeded: fastANI
[2024-01-25 18:59:52,847] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg53ac4c12-80fe-4636-892f-69053b6ea658/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:59:52,847] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg53ac4c12-80fe-4636-892f-69053b6ea658/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:59:52,860] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:59:52,860] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:59:52,860] [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 giardinii	strain=H152	GCA_000379605.1	56731	56731	type	True	81.2585	959	2155	95	below_threshold
Pararhizobium antarcticum	strain=NAQVI 59	GCA_001885585.1	1798805	1798805	type	True	80.5803	854	2155	95	below_threshold
Shinella kummerowiae	strain=CCBAU 25048	GCA_009827055.1	417745	417745	type	True	80.1361	800	2155	95	below_threshold
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	80.1349	727	2155	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	80.125	854	2155	95	below_threshold
Shinella curvata	strain=C3	GCA_022899935.1	1817964	1817964	type	True	80.1031	803	2155	95	below_threshold
Shinella zoogloeoides	strain=DSM 287	GCA_009826855.1	352475	352475	type	True	80.0906	711	2155	95	below_threshold
Ensifer sesbaniae	strain=CCBAU 65729	GCA_013283665.1	1214071	1214071	type	True	80.0493	844	2155	95	below_threshold
Shinella fusca	strain=DSM 21319	GCA_014203155.1	544480	544480	type	True	79.9234	760	2155	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	79.8113	709	2155	95	below_threshold
Sinorhizobium fredii	strain=USDA205	GCA_009601405.1	380	380	type	True	79.6255	757	2155	95	below_threshold
Sinorhizobium fredii	strain=NBRC 14780	GCA_006539605.1	380	380	type	True	79.5692	727	2155	95	below_threshold
Sinorhizobium fredii	strain=USDA 205	GCA_001461695.1	380	380	type	True	79.5605	741	2155	95	below_threshold
Ensifer psoraleae	strain=CCBAU 65732	GCA_013283645.1	520838	520838	type	True	79.5115	745	2155	95	below_threshold
Rhizobium redzepovicii	strain=18T	GCA_019793435.1	2867518	2867518	type	True	79.4923	690	2155	95	below_threshold
Rhizobium croatiense	strain=13T	GCA_019793465.1	2867516	2867516	type	True	79.4575	676	2155	95	below_threshold
Rhizobium etli	strain=CFN 42	GCA_000092045.1	29449	29449	suspected-type	True	79.4445	661	2155	95	below_threshold
Rhizobium wuzhouense	strain=W44	GCA_003205195.1	1986026	1986026	type	True	79.3161	569	2155	95	below_threshold
Rhizobium chutanense	strain=C5	GCA_002531935.1	2035448	2035448	type	True	79.3107	699	2155	95	below_threshold
Rhizobium lentis	strain=BLR27	GCA_019684715.1	1138194	1138194	type	True	79.1857	669	2155	95	below_threshold
Ciceribacter thiooxidans	strain=F43B	GCA_014126615.1	1969821	1969821	type	True	78.9921	522	2155	95	below_threshold
Ensifer sojae	strain=CCBAU 05684	GCA_000261485.1	716925	716925	type	True	78.9465	656	2155	95	below_threshold
Rhizobium dioscoreae	strain=S-93	GCA_009176305.1	2653122	2653122	type	True	78.9024	635	2155	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:59:52,861] [INFO] DFAST Taxonomy check result was written to GCF_030814475.1_ASM3081447v1_genomic.fna/tc_result.tsv
[2024-01-25 18:59:52,862] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:59:52,862] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:59:52,862] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg53ac4c12-80fe-4636-892f-69053b6ea658/dqc_reference/checkm_data
[2024-01-25 18:59:52,863] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:59:52,926] [INFO] Task started: CheckM
[2024-01-25 18:59:52,926] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030814475.1_ASM3081447v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030814475.1_ASM3081447v1_genomic.fna/checkm_input GCF_030814475.1_ASM3081447v1_genomic.fna/checkm_result
[2024-01-25 19:00:42,739] [INFO] Task succeeded: CheckM
[2024-01-25 19:00:42,740] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:00:42,759] [INFO] ===== Completeness check finished =====
[2024-01-25 19:00:42,760] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:00:42,761] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030814475.1_ASM3081447v1_genomic.fna/markers.fasta)
[2024-01-25 19:00:42,761] [INFO] Task started: Blastn
[2024-01-25 19:00:42,761] [INFO] Running command: blastn -query GCF_030814475.1_ASM3081447v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg53ac4c12-80fe-4636-892f-69053b6ea658/dqc_reference/reference_markers_gtdb.fasta -out GCF_030814475.1_ASM3081447v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:00:44,607] [INFO] Task succeeded: Blastn
[2024-01-25 19:00:44,610] [INFO] Selected 16 target genomes.
[2024-01-25 19:00:44,610] [INFO] Target genome list was writen to GCF_030814475.1_ASM3081447v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:00:44,636] [INFO] Task started: fastANI
[2024-01-25 19:00:44,636] [INFO] Running command: fastANI --query /var/lib/cwl/stgaca5dbfb-c70b-477c-89f9-8f8cd089900e/GCF_030814475.1_ASM3081447v1_genomic.fna.gz --refList GCF_030814475.1_ASM3081447v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030814475.1_ASM3081447v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:01:04,564] [INFO] Task succeeded: fastANI
[2024-01-25 19:01:04,579] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:01:04,579] [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_001931685.1	s__Pararhizobium arenae	84.0772	1069	2155	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pararhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001424985.1	s__Pararhizobium sp001424985	84.0185	1146	2155	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pararhizobium	95.0	99.99	99.99	1.00	1.00	2	-
GCA_900473795.1	s__Pararhizobium sp900473795	81.4441	952	2155	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pararhizobium	95.0	99.56	99.35	0.89	0.88	3	-
GCF_017873135.1	s__Pararhizobium herbae	81.3744	1005	2155	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pararhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000379605.1	s__Pararhizobium giardinii	81.2485	960	2155	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pararhizobium	95.0	98.65	96.17	0.91	0.82	6	-
GCA_900468065.1	s__Pararhizobium sp900468065	81.208	1005	2155	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pararhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900472175.1	s__Pararhizobium sp900472175	81.1065	968	2155	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pararhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900474095.1	s__Pararhizobium sp900474095	80.9383	861	2155	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pararhizobium	95.0	99.97	99.97	0.97	0.97	2	-
GCF_001426565.1	s__Pararhizobium sp001426565	80.8809	854	2155	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pararhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001426665.1	s__Pararhizobium sp001426665	80.8438	996	2155	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pararhizobium	95.0	99.66	98.98	0.96	0.87	4	-
GCA_900469625.1	s__Ensifer sp900469625	80.0237	862	2155	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Ensifer	95.0	98.94	98.62	0.97	0.96	3	-
GCA_900467185.1	s__Pararhizobium sp900467185	80.017	744	2155	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pararhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002002725.1	s__Ensifer sp002002725	79.9743	867	2155	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Ensifer	95.0	98.52	98.52	0.94	0.94	2	-
GCF_013371465.1	s__Ensifer sp013371465	79.955	840	2155	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Ensifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001424045.1	s__Pararhizobium sp001424045	79.8793	768	2155	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pararhizobium	95.0	97.68	97.68	0.89	0.89	2	-
GCF_014195095.1	s__Rhizobium sp014195095	79.4518	697	2155	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:01:04,580] [INFO] GTDB search result was written to GCF_030814475.1_ASM3081447v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:01:04,581] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:01:04,584] [INFO] DFAST_QC result json was written to GCF_030814475.1_ASM3081447v1_genomic.fna/dqc_result.json
[2024-01-25 19:01:04,584] [INFO] DFAST_QC completed!
[2024-01-25 19:01:04,584] [INFO] Total running time: 0h1m59s