[2024-01-24 11:26:54,311] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:54,316] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:54,316] [INFO] DQC Reference Directory: /var/lib/cwl/stg05111fa6-5f61-43bf-88bd-822bbff099ea/dqc_reference
[2024-01-24 11:26:58,222] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:58,224] [INFO] Task started: Prodigal
[2024-01-24 11:26:58,225] [INFO] Running command: gunzip -c /var/lib/cwl/stga4f4512f-f2bb-4a3e-b019-3188478b7ac7/GCF_030161135.1_ASM3016113v1_genomic.fna.gz | prodigal -d GCF_030161135.1_ASM3016113v1_genomic.fna/cds.fna -a GCF_030161135.1_ASM3016113v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:27:19,099] [INFO] Task succeeded: Prodigal
[2024-01-24 11:27:19,099] [INFO] Task started: HMMsearch
[2024-01-24 11:27:19,099] [INFO] Running command: hmmsearch --tblout GCF_030161135.1_ASM3016113v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg05111fa6-5f61-43bf-88bd-822bbff099ea/dqc_reference/reference_markers.hmm GCF_030161135.1_ASM3016113v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:27:19,439] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:27:19,441] [INFO] Found 6/6 markers.
[2024-01-24 11:27:19,496] [INFO] Query marker FASTA was written to GCF_030161135.1_ASM3016113v1_genomic.fna/markers.fasta
[2024-01-24 11:27:19,497] [INFO] Task started: Blastn
[2024-01-24 11:27:19,497] [INFO] Running command: blastn -query GCF_030161135.1_ASM3016113v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg05111fa6-5f61-43bf-88bd-822bbff099ea/dqc_reference/reference_markers.fasta -out GCF_030161135.1_ASM3016113v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:20,610] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:20,614] [INFO] Selected 20 target genomes.
[2024-01-24 11:27:20,615] [INFO] Target genome list was writen to GCF_030161135.1_ASM3016113v1_genomic.fna/target_genomes.txt
[2024-01-24 11:27:20,635] [INFO] Task started: fastANI
[2024-01-24 11:27:20,636] [INFO] Running command: fastANI --query /var/lib/cwl/stga4f4512f-f2bb-4a3e-b019-3188478b7ac7/GCF_030161135.1_ASM3016113v1_genomic.fna.gz --refList GCF_030161135.1_ASM3016113v1_genomic.fna/target_genomes.txt --output GCF_030161135.1_ASM3016113v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:43,302] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:43,302] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg05111fa6-5f61-43bf-88bd-822bbff099ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:43,303] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg05111fa6-5f61-43bf-88bd-822bbff099ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:43,319] [INFO] Found 20 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:27:43,319] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:27:43,319] [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
Rhizobacter gummiphilus	strain=NBRC 109400	GCA_002762215.1	946333	946333	type	True	99.9982	2111	2112	95	conclusive
Rhizobacter gummiphilus	strain=NS21	GCA_002116905.1	946333	946333	type	True	99.9981	2111	2112	95	conclusive
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_003349825.1	215580	215580	type	True	80.5086	721	2112	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_015476235.1	215580	215580	type	True	80.4892	731	2112	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_002933415.1	215580	215580	type	True	80.4683	719	2112	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000190375.2	316997	316997	type	True	79.8866	680	2112	95	below_threshold
Sphaerotilus hippei	strain=DSM 566	GCA_003201595.1	744406	744406	type	True	79.8053	686	2112	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000420125.1	316997	316997	type	True	79.7258	714	2112	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_021049305.1	36863	36863	type	True	79.6519	621	2112	95	below_threshold
Sphaerotilus sulfidivorans	strain=D-501	GCA_013426975.1	639200	639200	type	True	79.6415	682	2112	95	below_threshold
Rubrivivax gelatinosus	strain=DSM 1709	GCA_016583525.1	28068	28068	suspected-type	True	79.548	754	2112	95	below_threshold
Sphaerotilus montanus	strain=HS	GCA_013426955.1	522889	522889	type	True	79.4715	652	2112	95	below_threshold
Aquabacterium soli	strain=SJQ9	GCA_003933735.1	2493092	2493092	type	True	79.4238	642	2112	95	below_threshold
Sphaerotilus montanus	strain=DSM 21226	GCA_013410775.1	522889	522889	type	True	79.3733	690	2112	95	below_threshold
Pelomonas saccharophila	strain=DSM 654	GCA_004342485.1	304	304	type	True	79.3167	721	2112	95	below_threshold
Variovorax guangxiensis	strain=DSM 27352	GCA_003952165.1	1775474	1775474	type	True	79.3151	797	2112	95	below_threshold
Mitsuaria chitinivorans	strain=HWN-4	GCA_002761755.1	2917965	2917965	type	True	79.2336	742	2112	95	below_threshold
Ideonella benzenivorans	strain=B7	GCA_020387415.1	2831643	2831643	type	True	79.225	619	2112	95	below_threshold
Variovorax paradoxus	strain=NBRC 15149	GCA_001591365.1	34073	34073	suspected-type	True	79.1356	765	2112	95	below_threshold
Pelomonas puraquae	strain=CCUG 52769	GCA_002205845.1	431059	431059	type	True	79.1258	706	2112	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:43,321] [INFO] DFAST Taxonomy check result was written to GCF_030161135.1_ASM3016113v1_genomic.fna/tc_result.tsv
[2024-01-24 11:27:43,322] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:43,322] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:43,322] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg05111fa6-5f61-43bf-88bd-822bbff099ea/dqc_reference/checkm_data
[2024-01-24 11:27:43,323] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:43,471] [INFO] Task started: CheckM
[2024-01-24 11:27:43,471] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030161135.1_ASM3016113v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030161135.1_ASM3016113v1_genomic.fna/checkm_input GCF_030161135.1_ASM3016113v1_genomic.fna/checkm_result
[2024-01-24 11:30:03,622] [INFO] Task succeeded: CheckM
[2024-01-24 11:30:03,623] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:30:03,647] [INFO] ===== Completeness check finished =====
[2024-01-24 11:30:03,647] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:30:03,648] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030161135.1_ASM3016113v1_genomic.fna/markers.fasta)
[2024-01-24 11:30:03,648] [INFO] Task started: Blastn
[2024-01-24 11:30:03,648] [INFO] Running command: blastn -query GCF_030161135.1_ASM3016113v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg05111fa6-5f61-43bf-88bd-822bbff099ea/dqc_reference/reference_markers_gtdb.fasta -out GCF_030161135.1_ASM3016113v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:30:05,835] [INFO] Task succeeded: Blastn
[2024-01-24 11:30:05,840] [INFO] Selected 17 target genomes.
[2024-01-24 11:30:05,840] [INFO] Target genome list was writen to GCF_030161135.1_ASM3016113v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:30:05,859] [INFO] Task started: fastANI
[2024-01-24 11:30:05,859] [INFO] Running command: fastANI --query /var/lib/cwl/stga4f4512f-f2bb-4a3e-b019-3188478b7ac7/GCF_030161135.1_ASM3016113v1_genomic.fna.gz --refList GCF_030161135.1_ASM3016113v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030161135.1_ASM3016113v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:30:27,583] [INFO] Task succeeded: fastANI
[2024-01-24 11:30:27,602] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:30:27,603] [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_002116905.1	s__Rhizobacter gummiphilus	99.9981	2111	2112	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhizobacter	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_001425785.1	s__Rhizobacter sp001425785	85.1145	1278	2112	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhizobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012932665.1	s__Rhizobacter sp012932665	81.7265	1052	2112	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhizobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000800095.1	s__Rhizobacter sp000800095	81.692	1051	2112	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhizobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142965.1	s__Rhizobacter sp900142965	81.6236	1033	2112	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhizobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425825.1	s__Rhizobacter sp001425825	81.571	1024	2112	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhizobacter	95.0	99.93	99.87	0.98	0.98	3	-
GCF_012275445.1	s__Rhizobacter sp012275445	81.5023	1050	2112	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhizobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016735515.1	s__Rhizobacter sp016735515	81.3835	966	2112	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhizobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016706565.1	s__Piscinibacter sp016706565	80.8298	800	2112	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Piscinibacter	95.0	98.34	98.34	0.95	0.95	2	-
GCA_017983795.1	s__Piscinibacter sp017983795	80.8036	774	2112	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Piscinibacter	95.0	97.66	96.21	0.89	0.79	4	-
GCF_017795745.1	s__Piscinibacter sp017795745	80.7507	816	2112	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Piscinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000799305.1	s__Rhizobacter sp000799305	80.549	929	2112	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhizobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425865.1	s__LMDS01 sp001425865	80.4485	789	2112	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__LMDS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903905475.1	s__PBB1 sp903905475	79.8014	421	2112	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__PBB1	95.0	99.20	99.17	0.87	0.87	3	-
GCA_002255905.1	s__PBB1 sp002255905	79.6656	517	2112	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__PBB1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017986065.1	s__PBB1 sp017986065	79.5747	444	2112	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__PBB1	95.0	99.66	99.66	0.90	0.90	2	-
GCA_016702655.1	s__CAIKUF01 sp016702655	79.4142	661	2112	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__CAIKUF01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:30:27,604] [INFO] GTDB search result was written to GCF_030161135.1_ASM3016113v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:30:27,605] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:30:27,609] [INFO] DFAST_QC result json was written to GCF_030161135.1_ASM3016113v1_genomic.fna/dqc_result.json
[2024-01-24 11:30:27,609] [INFO] DFAST_QC completed!
[2024-01-24 11:30:27,609] [INFO] Total running time: 0h3m33s