[2023-03-15 11:24:11,507] [INFO] DFAST_QC pipeline started.
[2023-03-15 11:24:11,508] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 11:24:11,508] [INFO] DQC Reference Directory: /var/lib/cwl/stg2c27b5d0-352a-4009-bbee-f9380390155c/dqc_reference
[2023-03-15 11:24:12,598] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 11:24:12,599] [INFO] Task started: Prodigal
[2023-03-15 11:24:12,599] [INFO] Running command: cat /var/lib/cwl/stgbbd16e90-a265-4b70-9ca4-1f6cc711ede5/OceanDNA-b32150.fa | prodigal -d OceanDNA-b32150/cds.fna -a OceanDNA-b32150/protein.faa -g 11 -q > /dev/null
[2023-03-15 11:24:39,033] [INFO] Task succeeded: Prodigal
[2023-03-15 11:24:39,033] [INFO] Task started: HMMsearch
[2023-03-15 11:24:39,033] [INFO] Running command: hmmsearch --tblout OceanDNA-b32150/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2c27b5d0-352a-4009-bbee-f9380390155c/dqc_reference/reference_markers.hmm OceanDNA-b32150/protein.faa > /dev/null
[2023-03-15 11:24:39,240] [INFO] Task succeeded: HMMsearch
[2023-03-15 11:24:39,240] [INFO] Found 6/6 markers.
[2023-03-15 11:24:39,266] [INFO] Query marker FASTA was written to OceanDNA-b32150/markers.fasta
[2023-03-15 11:24:39,266] [INFO] Task started: Blastn
[2023-03-15 11:24:39,266] [INFO] Running command: blastn -query OceanDNA-b32150/markers.fasta -db /var/lib/cwl/stg2c27b5d0-352a-4009-bbee-f9380390155c/dqc_reference/reference_markers.fasta -out OceanDNA-b32150/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:24:40,117] [INFO] Task succeeded: Blastn
[2023-03-15 11:24:40,118] [INFO] Selected 14 target genomes.
[2023-03-15 11:24:40,118] [INFO] Target genome list was writen to OceanDNA-b32150/target_genomes.txt
[2023-03-15 11:24:40,125] [INFO] Task started: fastANI
[2023-03-15 11:24:40,125] [INFO] Running command: fastANI --query /var/lib/cwl/stgbbd16e90-a265-4b70-9ca4-1f6cc711ede5/OceanDNA-b32150.fa --refList OceanDNA-b32150/target_genomes.txt --output OceanDNA-b32150/fastani_result.tsv --threads 1
[2023-03-15 11:24:52,222] [INFO] Task succeeded: fastANI
[2023-03-15 11:24:52,222] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2c27b5d0-352a-4009-bbee-f9380390155c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 11:24:52,223] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2c27b5d0-352a-4009-bbee-f9380390155c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 11:24:52,231] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 11:24:52,231] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 11:24:52,232] [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	88.7159	933	1411	95	below_threshold
Sphingopyxis bauzanensis	strain=DSM 22271	GCA_002205675.1	651663	651663	type	True	88.7033	938	1411	95	below_threshold
Sphingopyxis microcysteis	strain=Z10-6	GCA_012274265.1	2484145	2484145	type	True	87.3055	918	1411	95	below_threshold
Sphingopyxis solisilvae	strain=R366	GCA_015475875.1	1886788	1886788	type	True	86.6049	846	1411	95	below_threshold
Sphingopyxis italica	strain=DSM 25229	GCA_011926545.1	1129133	1129133	type	True	85.2344	932	1411	95	below_threshold
Sphingopyxis fribergensis	strain=Kp5.2	GCA_000803645.1	1515612	1515612	type	True	85.0885	932	1411	95	below_threshold
Sphingopyxis lindanitolerans	strain=WS5A3p	GCA_002993885.1	2054227	2054227	type	True	83.9623	828	1411	95	below_threshold
Sphingopyxis alaskensis	strain=RB2256	GCA_000013985.1	117207	117207	type	True	83.9425	826	1411	95	below_threshold
Sphingopyxis witflariensis	strain=DSM 14551	GCA_002205635.1	173675	173675	type	True	83.7989	835	1411	95	below_threshold
Sphingomonas cavernae	strain=K2R01-6	GCA_003590775.1	2320861	2320861	type	True	77.9566	368	1411	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	77.7431	375	1411	95	below_threshold
Sphingomonas psychrotolerans	strain=Cra20	GCA_002796605.1	1327635	1327635	type	True	77.625	350	1411	95	below_threshold
Novosphingobium huizhouense	strain=c7	GCA_020179475.1	2866625	2866625	type	True	77.5332	359	1411	95	below_threshold
Sphingomonas hylomeconis	strain=CCTCC AB 2013304	GCA_025370105.1	1395958	1395958	type	True	77.5321	371	1411	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 11:24:52,232] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32150/tc_result.tsv
[2023-03-15 11:24:52,232] [INFO] ===== Taxonomy check completed =====
[2023-03-15 11:24:52,232] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 11:24:52,232] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2c27b5d0-352a-4009-bbee-f9380390155c/dqc_reference/checkm_data
[2023-03-15 11:24:52,233] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 11:24:52,291] [INFO] Task started: CheckM
[2023-03-15 11:24:52,291] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32150/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32150/checkm_input OceanDNA-b32150/checkm_result
[2023-03-15 11:25:56,342] [INFO] Task succeeded: CheckM
[2023-03-15 11:25:56,343] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 11:25:56,351] [INFO] ===== Completeness check finished =====
[2023-03-15 11:25:56,351] [INFO] ===== Start GTDB Search =====
[2023-03-15 11:25:56,351] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32150/markers.fasta)
[2023-03-15 11:25:56,351] [INFO] Task started: Blastn
[2023-03-15 11:25:56,351] [INFO] Running command: blastn -query OceanDNA-b32150/markers.fasta -db /var/lib/cwl/stg2c27b5d0-352a-4009-bbee-f9380390155c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32150/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:25:58,015] [INFO] Task succeeded: Blastn
[2023-03-15 11:25:58,016] [INFO] Selected 12 target genomes.
[2023-03-15 11:25:58,016] [INFO] Target genome list was writen to OceanDNA-b32150/target_genomes_gtdb.txt
[2023-03-15 11:25:58,029] [INFO] Task started: fastANI
[2023-03-15 11:25:58,029] [INFO] Running command: fastANI --query /var/lib/cwl/stgbbd16e90-a265-4b70-9ca4-1f6cc711ede5/OceanDNA-b32150.fa --refList OceanDNA-b32150/target_genomes_gtdb.txt --output OceanDNA-b32150/fastani_result_gtdb.tsv --threads 1
[2023-03-15 11:26:09,796] [INFO] Task succeeded: fastANI
[2023-03-15 11:26:09,803] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 11:26:09,804] [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_016463225.1	s__Sphingopyxis sp016463225	89.9093	907	1411	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	89.1971	974	1411	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018823905.1	s__Sphingopyxis sp018823905	89.1219	862	1411	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	88.8032	947	1411	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	99.98	99.98	0.96	0.96	2	-
GCF_002205675.1	s__Sphingopyxis bauzanensis	88.7183	937	1411	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	99.99	99.99	1.00	1.00	2	-
GCA_016704835.1	s__Sphingopyxis sp016704835	87.7993	937	1411	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005503695.1	s__Sphingopyxis sp003609815	87.4442	931	1411	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	97.15	97.15	0.90	0.90	2	-
GCF_012274265.1	s__Sphingopyxis microcysteis	87.3006	919	1411	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	86.6049	846	1411	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	96.45	96.45	0.86	0.86	2	-
GCF_000803645.1	s__Sphingopyxis fribergensis	85.0778	934	1411	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016463645.1	s__Sphingopyxis sp016463645	84.1873	791	1411	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	83.9329	889	1411	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 11:26:09,804] [INFO] GTDB search result was written to OceanDNA-b32150/result_gtdb.tsv
[2023-03-15 11:26:09,805] [INFO] ===== GTDB Search completed =====
[2023-03-15 11:26:09,807] [INFO] DFAST_QC result json was written to OceanDNA-b32150/dqc_result.json
[2023-03-15 11:26:09,807] [INFO] DFAST_QC completed!
[2023-03-15 11:26:09,807] [INFO] Total running time: 0h1m58s