[2023-03-17 05:43:46,029] [INFO] DFAST_QC pipeline started.
[2023-03-17 05:43:46,036] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 05:43:46,036] [INFO] DQC Reference Directory: /var/lib/cwl/stg411a1cbb-41a5-4ae2-8c8c-444e0b494636/dqc_reference
[2023-03-17 05:43:49,664] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 05:43:49,666] [INFO] Task started: Prodigal
[2023-03-17 05:43:49,666] [INFO] Running command: cat /var/lib/cwl/stg66af38a7-4921-41a8-9c41-cd3ff3a515bc/OceanDNA-b32156.fa | prodigal -d OceanDNA-b32156/cds.fna -a OceanDNA-b32156/protein.faa -g 11 -q > /dev/null
[2023-03-17 05:44:11,322] [INFO] Task succeeded: Prodigal
[2023-03-17 05:44:11,322] [INFO] Task started: HMMsearch
[2023-03-17 05:44:11,322] [INFO] Running command: hmmsearch --tblout OceanDNA-b32156/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg411a1cbb-41a5-4ae2-8c8c-444e0b494636/dqc_reference/reference_markers.hmm OceanDNA-b32156/protein.faa > /dev/null
[2023-03-17 05:44:11,581] [INFO] Task succeeded: HMMsearch
[2023-03-17 05:44:11,581] [INFO] Found 6/6 markers.
[2023-03-17 05:44:11,677] [INFO] Query marker FASTA was written to OceanDNA-b32156/markers.fasta
[2023-03-17 05:44:11,679] [INFO] Task started: Blastn
[2023-03-17 05:44:11,679] [INFO] Running command: blastn -query OceanDNA-b32156/markers.fasta -db /var/lib/cwl/stg411a1cbb-41a5-4ae2-8c8c-444e0b494636/dqc_reference/reference_markers.fasta -out OceanDNA-b32156/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:44:12,724] [INFO] Task succeeded: Blastn
[2023-03-17 05:44:12,751] [INFO] Selected 16 target genomes.
[2023-03-17 05:44:12,751] [INFO] Target genome list was writen to OceanDNA-b32156/target_genomes.txt
[2023-03-17 05:44:12,823] [INFO] Task started: fastANI
[2023-03-17 05:44:12,823] [INFO] Running command: fastANI --query /var/lib/cwl/stg66af38a7-4921-41a8-9c41-cd3ff3a515bc/OceanDNA-b32156.fa --refList OceanDNA-b32156/target_genomes.txt --output OceanDNA-b32156/fastani_result.tsv --threads 1
[2023-03-17 05:44:26,325] [INFO] Task succeeded: fastANI
[2023-03-17 05:44:26,325] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg411a1cbb-41a5-4ae2-8c8c-444e0b494636/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 05:44:26,326] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg411a1cbb-41a5-4ae2-8c8c-444e0b494636/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 05:44:26,381] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2023-03-17 05:44:26,381] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-17 05:44:26,381] [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=CGMCC 1.8959	GCA_014645635.1	651663	651663	type	True	95.4133	908	1172	95	conclusive
Sphingopyxis bauzanensis	strain=DSM 22271	GCA_002205675.1	651663	651663	type	True	95.2643	926	1172	95	conclusive
Sphingopyxis microcysteis	strain=Z10-6	GCA_012274265.1	2484145	2484145	type	True	87.2022	799	1172	95	below_threshold
Sphingopyxis solisilvae	strain=R366	GCA_015475875.1	1886788	1886788	type	True	86.5208	787	1172	95	below_threshold
Sphingopyxis italica	strain=DSM 25229	GCA_011926545.1	1129133	1129133	type	True	84.6596	815	1172	95	below_threshold
Sphingopyxis fribergensis	strain=Kp5.2	GCA_000803645.1	1515612	1515612	type	True	84.5129	819	1172	95	below_threshold
Sphingopyxis lindanitolerans	strain=WS5A3p	GCA_002993885.1	2054227	2054227	type	True	83.9497	743	1172	95	below_threshold
Sphingopyxis alaskensis	strain=RB2256	GCA_000013985.1	117207	117207	type	True	83.8971	712	1172	95	below_threshold
Sphingopyxis panaciterrae	strain=DSM 27164	GCA_011762125.1	363841	363841	type	True	83.7639	748	1172	95	below_threshold
Sphingopyxis macrogoltabida	strain=203	GCA_001314325.1	33050	33050	type	True	83.755	794	1172	95	below_threshold
Sphingopyxis witflariensis	strain=DSM 14551	GCA_002205635.1	173675	173675	type	True	83.3809	759	1172	95	below_threshold
Sphingomonas cavernae	strain=K2R01-6	GCA_003590775.1	2320861	2320861	type	True	77.761	304	1172	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	77.5142	286	1172	95	below_threshold
Sphingomonas alpina	strain=DSM 22537	GCA_025370095.1	653931	653931	type	True	77.4846	300	1172	95	below_threshold
Novosphingobium huizhouense	strain=c7	GCA_020179475.1	2866625	2866625	type	True	77.4308	311	1172	95	below_threshold
Sphingomonas hylomeconis	strain=CCTCC AB 2013304	GCA_025370105.1	1395958	1395958	type	True	77.3586	314	1172	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 05:44:26,391] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32156/tc_result.tsv
[2023-03-17 05:44:26,412] [INFO] ===== Taxonomy check completed =====
[2023-03-17 05:44:26,412] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 05:44:26,412] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg411a1cbb-41a5-4ae2-8c8c-444e0b494636/dqc_reference/checkm_data
[2023-03-17 05:44:26,413] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 05:44:26,418] [INFO] Task started: CheckM
[2023-03-17 05:44:26,418] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32156/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32156/checkm_input OceanDNA-b32156/checkm_result
[2023-03-17 05:45:25,414] [INFO] Task succeeded: CheckM
[2023-03-17 05:45:25,415] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 05:45:25,418] [INFO] ===== Completeness check finished =====
[2023-03-17 05:45:25,419] [INFO] ===== Start GTDB Search =====
[2023-03-17 05:45:25,419] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32156/markers.fasta)
[2023-03-17 05:45:25,420] [INFO] Task started: Blastn
[2023-03-17 05:45:25,420] [INFO] Running command: blastn -query OceanDNA-b32156/markers.fasta -db /var/lib/cwl/stg411a1cbb-41a5-4ae2-8c8c-444e0b494636/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32156/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:45:27,526] [INFO] Task succeeded: Blastn
[2023-03-17 05:45:27,527] [INFO] Selected 11 target genomes.
[2023-03-17 05:45:27,527] [INFO] Target genome list was writen to OceanDNA-b32156/target_genomes_gtdb.txt
[2023-03-17 05:45:27,720] [INFO] Task started: fastANI
[2023-03-17 05:45:27,720] [INFO] Running command: fastANI --query /var/lib/cwl/stg66af38a7-4921-41a8-9c41-cd3ff3a515bc/OceanDNA-b32156.fa --refList OceanDNA-b32156/target_genomes_gtdb.txt --output OceanDNA-b32156/fastani_result_gtdb.tsv --threads 1
[2023-03-17 05:45:38,175] [INFO] Task succeeded: fastANI
[2023-03-17 05:45:38,182] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 05:45:38,183] [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_002205675.1	s__Sphingopyxis bauzanensis	95.2884	925	1172	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCA_018823905.1	s__Sphingopyxis sp018823905	89.8986	764	1172	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	99.80	99.78	0.95	0.94	3	-
GCA_002454115.1	s__Sphingopyxis sp002454115	88.9434	820	1172	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	88.5999	798	1172	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	88.0708	839	1172	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	87.7435	826	1172	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012274265.1	s__Sphingopyxis microcysteis	87.1962	800	1172	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	96.26	96.26	0.86	0.86	2	-
GCF_015475875.1	s__Sphingopyxis solisilvae	86.5637	784	1172	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	96.45	96.45	0.86	0.86	2	-
GCF_000756375.1	s__Sphingopyxis sp000756375	84.8589	802	1172	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000803645.1	s__Sphingopyxis fribergensis	84.5252	818	1172	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108295.1	s__Sphingopyxis sp900108295	83.7911	752	1172	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 05:45:38,183] [INFO] GTDB search result was written to OceanDNA-b32156/result_gtdb.tsv
[2023-03-17 05:45:38,183] [INFO] ===== GTDB Search completed =====
[2023-03-17 05:45:38,185] [INFO] DFAST_QC result json was written to OceanDNA-b32156/dqc_result.json
[2023-03-17 05:45:38,185] [INFO] DFAST_QC completed!
[2023-03-17 05:45:38,185] [INFO] Total running time: 0h1m52s