[2023-03-19 00:01:03,324] [INFO] DFAST_QC pipeline started.
[2023-03-19 00:01:03,324] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 00:01:03,324] [INFO] DQC Reference Directory: /var/lib/cwl/stg14ec554e-2108-41f1-91ce-05f6921ed36c/dqc_reference
[2023-03-19 00:01:04,456] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 00:01:04,457] [INFO] Task started: Prodigal
[2023-03-19 00:01:04,457] [INFO] Running command: cat /var/lib/cwl/stgeb73a8bd-910c-4b74-84de-3d66701b2b12/OceanDNA-b32148.fa | prodigal -d OceanDNA-b32148/cds.fna -a OceanDNA-b32148/protein.faa -g 11 -q > /dev/null
[2023-03-19 00:01:14,372] [INFO] Task succeeded: Prodigal
[2023-03-19 00:01:14,372] [INFO] Task started: HMMsearch
[2023-03-19 00:01:14,372] [INFO] Running command: hmmsearch --tblout OceanDNA-b32148/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg14ec554e-2108-41f1-91ce-05f6921ed36c/dqc_reference/reference_markers.hmm OceanDNA-b32148/protein.faa > /dev/null
[2023-03-19 00:01:14,584] [INFO] Task succeeded: HMMsearch
[2023-03-19 00:01:14,585] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgeb73a8bd-910c-4b74-84de-3d66701b2b12/OceanDNA-b32148.fa]
[2023-03-19 00:01:14,599] [INFO] Query marker FASTA was written to OceanDNA-b32148/markers.fasta
[2023-03-19 00:01:14,600] [INFO] Task started: Blastn
[2023-03-19 00:01:14,600] [INFO] Running command: blastn -query OceanDNA-b32148/markers.fasta -db /var/lib/cwl/stg14ec554e-2108-41f1-91ce-05f6921ed36c/dqc_reference/reference_markers.fasta -out OceanDNA-b32148/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:01:15,322] [INFO] Task succeeded: Blastn
[2023-03-19 00:01:15,323] [INFO] Selected 13 target genomes.
[2023-03-19 00:01:15,323] [INFO] Target genome list was writen to OceanDNA-b32148/target_genomes.txt
[2023-03-19 00:01:15,329] [INFO] Task started: fastANI
[2023-03-19 00:01:15,329] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb73a8bd-910c-4b74-84de-3d66701b2b12/OceanDNA-b32148.fa --refList OceanDNA-b32148/target_genomes.txt --output OceanDNA-b32148/fastani_result.tsv --threads 1
[2023-03-19 00:01:25,207] [INFO] Task succeeded: fastANI
[2023-03-19 00:01:25,208] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg14ec554e-2108-41f1-91ce-05f6921ed36c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 00:01:25,208] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg14ec554e-2108-41f1-91ce-05f6921ed36c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 00:01:25,216] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 00:01:25,216] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 00:01:25,216] [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
Sphingopyxis bauzanensis	strain=DSM 22271	GCA_002205675.1	651663	651663	type	True	90.1935	452	501	95	below_threshold
Sphingopyxis bauzanensis	strain=CGMCC 1.8959	GCA_014645635.1	651663	651663	type	True	90.1546	457	501	95	below_threshold
Sphingopyxis microcysteis	strain=Z10-6	GCA_012274265.1	2484145	2484145	type	True	87.6683	459	501	95	below_threshold
Sphingopyxis solisilvae	strain=R366	GCA_015475875.1	1886788	1886788	type	True	86.9245	436	501	95	below_threshold
Sphingopyxis italica	strain=DSM 25229	GCA_011926545.1	1129133	1129133	type	True	85.2791	445	501	95	below_threshold
Sphingopyxis fribergensis	strain=Kp5.2	GCA_000803645.1	1515612	1515612	type	True	85.2276	442	501	95	below_threshold
Sphingopyxis witflariensis	strain=DSM 14551	GCA_002205635.1	173675	173675	type	True	83.9952	418	501	95	below_threshold
Sphingopyxis lindanitolerans	strain=WS5A3p	GCA_002993885.1	2054227	2054227	type	True	83.8463	412	501	95	below_threshold
Novosphingobium percolationis	strain=c1	GCA_020179425.1	2871811	2871811	type	True	77.8449	152	501	95	below_threshold
Novosphingobium huizhouense	strain=c7	GCA_020179475.1	2866625	2866625	type	True	77.7044	180	501	95	below_threshold
Sphingobium sufflavum	strain=HL-25	GCA_021403115.1	1129547	1129547	type	True	77.5404	148	501	95	below_threshold
Novosphingobium aquimarinum	strain=M24A2M	GCA_009746585.1	2682494	2682494	type	True	77.3298	152	501	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	77.2004	109	501	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 00:01:25,216] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32148/tc_result.tsv
[2023-03-19 00:01:25,216] [INFO] ===== Taxonomy check completed =====
[2023-03-19 00:01:25,216] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 00:01:25,217] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg14ec554e-2108-41f1-91ce-05f6921ed36c/dqc_reference/checkm_data
[2023-03-19 00:01:25,217] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 00:01:25,221] [INFO] Task started: CheckM
[2023-03-19 00:01:25,221] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32148/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32148/checkm_input OceanDNA-b32148/checkm_result
[2023-03-19 00:01:53,924] [INFO] Task succeeded: CheckM
[2023-03-19 00:01:53,924] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 65.97%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 00:01:53,927] [INFO] ===== Completeness check finished =====
[2023-03-19 00:01:53,927] [INFO] ===== Start GTDB Search =====
[2023-03-19 00:01:53,927] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32148/markers.fasta)
[2023-03-19 00:01:53,927] [INFO] Task started: Blastn
[2023-03-19 00:01:53,927] [INFO] Running command: blastn -query OceanDNA-b32148/markers.fasta -db /var/lib/cwl/stg14ec554e-2108-41f1-91ce-05f6921ed36c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32148/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:01:55,175] [INFO] Task succeeded: Blastn
[2023-03-19 00:01:55,176] [INFO] Selected 9 target genomes.
[2023-03-19 00:01:55,176] [INFO] Target genome list was writen to OceanDNA-b32148/target_genomes_gtdb.txt
[2023-03-19 00:01:55,185] [INFO] Task started: fastANI
[2023-03-19 00:01:55,185] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb73a8bd-910c-4b74-84de-3d66701b2b12/OceanDNA-b32148.fa --refList OceanDNA-b32148/target_genomes_gtdb.txt --output OceanDNA-b32148/fastani_result_gtdb.tsv --threads 1
[2023-03-19 00:02:02,486] [INFO] Task succeeded: fastANI
[2023-03-19 00:02:02,492] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 00:02:02,492] [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_018823905.1	s__Sphingopyxis sp018823905	97.4828	467	501	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	99.80	99.78	0.95	0.94	3	conclusive
GCF_002205675.1	s__Sphingopyxis bauzanensis	90.1935	452	501	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	99.99	99.99	1.00	1.00	2	-
GCA_002454115.1	s__Sphingopyxis sp002454115	90.0625	478	501	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	99.98	99.98	0.96	0.96	2	-
GCA_016463225.1	s__Sphingopyxis sp016463225	89.3683	447	501	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005502465.1	s__Sphingopyxis sp005502465	88.7753	451	501	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016704835.1	s__Sphingopyxis sp016704835	88.1372	461	501	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001427105.1	s__Sphingopyxis sp001427105	85.3321	438	501	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003797775.2	s__Sphingopyxis sp001427085	84.6817	430	501	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	97.11	97.01	0.89	0.87	3	-
GCF_001990265.1	s__Sphingopyxis sp001990265	84.2586	413	501	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 00:02:02,493] [INFO] GTDB search result was written to OceanDNA-b32148/result_gtdb.tsv
[2023-03-19 00:02:02,493] [INFO] ===== GTDB Search completed =====
[2023-03-19 00:02:02,494] [INFO] DFAST_QC result json was written to OceanDNA-b32148/dqc_result.json
[2023-03-19 00:02:02,494] [INFO] DFAST_QC completed!
[2023-03-19 00:02:02,494] [INFO] Total running time: 0h0m59s