[2023-03-17 01:44:57,466] [INFO] DFAST_QC pipeline started.
[2023-03-17 01:44:57,466] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 01:44:57,466] [INFO] DQC Reference Directory: /var/lib/cwl/stgb3d47534-cc73-4f11-bd31-05faf4caca44/dqc_reference
[2023-03-17 01:44:59,094] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 01:44:59,094] [INFO] Task started: Prodigal
[2023-03-17 01:44:59,094] [INFO] Running command: cat /var/lib/cwl/stg9673d54c-6b5f-475e-bf44-ff204907f7d4/OceanDNA-b32152.fa | prodigal -d OceanDNA-b32152/cds.fna -a OceanDNA-b32152/protein.faa -g 11 -q > /dev/null
[2023-03-17 01:45:26,117] [INFO] Task succeeded: Prodigal
[2023-03-17 01:45:26,117] [INFO] Task started: HMMsearch
[2023-03-17 01:45:26,117] [INFO] Running command: hmmsearch --tblout OceanDNA-b32152/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb3d47534-cc73-4f11-bd31-05faf4caca44/dqc_reference/reference_markers.hmm OceanDNA-b32152/protein.faa > /dev/null
[2023-03-17 01:45:26,321] [INFO] Task succeeded: HMMsearch
[2023-03-17 01:45:26,322] [INFO] Found 6/6 markers.
[2023-03-17 01:45:26,348] [INFO] Query marker FASTA was written to OceanDNA-b32152/markers.fasta
[2023-03-17 01:45:26,348] [INFO] Task started: Blastn
[2023-03-17 01:45:26,348] [INFO] Running command: blastn -query OceanDNA-b32152/markers.fasta -db /var/lib/cwl/stgb3d47534-cc73-4f11-bd31-05faf4caca44/dqc_reference/reference_markers.fasta -out OceanDNA-b32152/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 01:45:27,167] [INFO] Task succeeded: Blastn
[2023-03-17 01:45:27,167] [INFO] Selected 16 target genomes.
[2023-03-17 01:45:27,168] [INFO] Target genome list was writen to OceanDNA-b32152/target_genomes.txt
[2023-03-17 01:45:27,178] [INFO] Task started: fastANI
[2023-03-17 01:45:27,179] [INFO] Running command: fastANI --query /var/lib/cwl/stg9673d54c-6b5f-475e-bf44-ff204907f7d4/OceanDNA-b32152.fa --refList OceanDNA-b32152/target_genomes.txt --output OceanDNA-b32152/fastani_result.tsv --threads 1
[2023-03-17 01:45:41,457] [INFO] Task succeeded: fastANI
[2023-03-17 01:45:41,458] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb3d47534-cc73-4f11-bd31-05faf4caca44/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 01:45:41,458] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb3d47534-cc73-4f11-bd31-05faf4caca44/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 01:45:41,467] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 01:45:41,467] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 01:45:41,467] [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 fribergensis	strain=Kp5.2	GCA_000803645.1	1515612	1515612	type	True	88.4854	1019	1446	95	below_threshold
Sphingopyxis italica	strain=DSM 25229	GCA_011926545.1	1129133	1129133	type	True	87.2856	949	1446	95	below_threshold
Sphingopyxis microcysteis	strain=Z10-6	GCA_012274265.1	2484145	2484145	type	True	85.0741	794	1446	95	below_threshold
Sphingopyxis alaskensis	strain=RB2256	GCA_000013985.1	117207	117207	type	True	85.0204	809	1446	95	below_threshold
Sphingopyxis bauzanensis	strain=CGMCC 1.8959	GCA_014645635.1	651663	651663	type	True	85.0172	843	1446	95	below_threshold
Sphingopyxis bauzanensis	strain=DSM 22271	GCA_002205675.1	651663	651663	type	True	85.0089	835	1446	95	below_threshold
Sphingopyxis lindanitolerans	strain=WS5A3p	GCA_002993885.1	2054227	2054227	type	True	84.8374	805	1446	95	below_threshold
Sphingopyxis panaciterrae	strain=DSM 27164	GCA_011762125.1	363841	363841	type	True	84.7061	849	1446	95	below_threshold
Sphingopyxis macrogoltabida	strain=203	GCA_001314325.1	33050	33050	type	True	84.6664	905	1446	95	below_threshold
Sphingopyxis solisilvae	strain=R366	GCA_015475875.1	1886788	1886788	type	True	84.3573	768	1446	95	below_threshold
Sphingopyxis witflariensis	strain=DSM 14551	GCA_002205635.1	173675	173675	type	True	84.3333	829	1446	95	below_threshold
Sphingomonas cavernae	strain=K2R01-6	GCA_003590775.1	2320861	2320861	type	True	78.0226	338	1446	95	below_threshold
Sphingomonas alpina	strain=DSM 22537	GCA_025370095.1	653931	653931	type	True	77.5962	345	1446	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	77.3964	307	1446	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	77.2977	255	1446	95	below_threshold
Novosphingobium huizhouense	strain=c7	GCA_020179475.1	2866625	2866625	type	True	77.2954	330	1446	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 01:45:41,468] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32152/tc_result.tsv
[2023-03-17 01:45:41,468] [INFO] ===== Taxonomy check completed =====
[2023-03-17 01:45:41,468] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 01:45:41,468] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb3d47534-cc73-4f11-bd31-05faf4caca44/dqc_reference/checkm_data
[2023-03-17 01:45:41,469] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 01:45:41,474] [INFO] Task started: CheckM
[2023-03-17 01:45:41,474] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32152/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32152/checkm_input OceanDNA-b32152/checkm_result
[2023-03-17 01:46:46,586] [INFO] Task succeeded: CheckM
[2023-03-17 01:46:46,586] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 01:46:46,589] [INFO] ===== Completeness check finished =====
[2023-03-17 01:46:46,589] [INFO] ===== Start GTDB Search =====
[2023-03-17 01:46:46,589] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32152/markers.fasta)
[2023-03-17 01:46:46,590] [INFO] Task started: Blastn
[2023-03-17 01:46:46,590] [INFO] Running command: blastn -query OceanDNA-b32152/markers.fasta -db /var/lib/cwl/stgb3d47534-cc73-4f11-bd31-05faf4caca44/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32152/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 01:46:48,211] [INFO] Task succeeded: Blastn
[2023-03-17 01:46:48,212] [INFO] Selected 14 target genomes.
[2023-03-17 01:46:48,212] [INFO] Target genome list was writen to OceanDNA-b32152/target_genomes_gtdb.txt
[2023-03-17 01:46:48,548] [INFO] Task started: fastANI
[2023-03-17 01:46:48,548] [INFO] Running command: fastANI --query /var/lib/cwl/stg9673d54c-6b5f-475e-bf44-ff204907f7d4/OceanDNA-b32152.fa --refList OceanDNA-b32152/target_genomes_gtdb.txt --output OceanDNA-b32152/fastani_result_gtdb.tsv --threads 1
[2023-03-17 01:47:02,722] [INFO] Task succeeded: fastANI
[2023-03-17 01:47:02,731] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 01:47:02,731] [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_005503215.1	s__Sphingopyxis sp005503215	89.1591	1054	1446	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	99.20	99.20	0.88	0.88	2	-
GCF_001468225.1	s__Sphingopyxis sp001468225	89.1018	1036	1446	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	99.99	99.97	0.98	0.96	8	-
GCF_000756375.1	s__Sphingopyxis sp000756375	88.4906	931	1446	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	88.4854	1019	1446	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	88.4181	926	1446	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014873485.1	s__Sphingopyxis sp014873485	87.3683	972	1446	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011926545.1	s__Sphingopyxis italica	87.2479	952	1446	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410105.1	s__Sphingopyxis sp013410105	86.653	946	1446	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	99.44	99.44	0.94	0.94	2	-
GCF_900108295.1	s__Sphingopyxis sp900108295	86.5289	892	1446	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001047015.1	s__Sphingopyxis sp001047015	86.1612	954	1446	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004795895.1	s__Sphingopyxis sp004795895	85.9879	939	1446	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002454115.1	s__Sphingopyxis sp002454115	85.2196	832	1446	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	99.98	99.98	0.96	0.96	2	-
GCF_001468265.1	s__Sphingopyxis sp001468265	84.5169	842	1446	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003797775.2	s__Sphingopyxis sp001427085	84.3056	853	1446	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	97.11	97.01	0.89	0.87	3	-
--------------------------------------------------------------------------------
[2023-03-17 01:47:02,731] [INFO] GTDB search result was written to OceanDNA-b32152/result_gtdb.tsv
[2023-03-17 01:47:02,731] [INFO] ===== GTDB Search completed =====
[2023-03-17 01:47:02,733] [INFO] DFAST_QC result json was written to OceanDNA-b32152/dqc_result.json
[2023-03-17 01:47:02,733] [INFO] DFAST_QC completed!
[2023-03-17 01:47:02,733] [INFO] Total running time: 0h2m5s