[2023-03-15 14:38:44,426] [INFO] DFAST_QC pipeline started.
[2023-03-15 14:38:44,426] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 14:38:44,426] [INFO] DQC Reference Directory: /var/lib/cwl/stgfb8b731a-9282-4047-9f48-b29ed6477868/dqc_reference
[2023-03-15 14:38:45,538] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 14:38:45,538] [INFO] Task started: Prodigal
[2023-03-15 14:38:45,538] [INFO] Running command: cat /var/lib/cwl/stg9bb98462-cf30-45de-9fb4-27e7ae4ee77a/OceanDNA-b32153.fa | prodigal -d OceanDNA-b32153/cds.fna -a OceanDNA-b32153/protein.faa -g 11 -q > /dev/null
[2023-03-15 14:39:04,385] [INFO] Task succeeded: Prodigal
[2023-03-15 14:39:04,385] [INFO] Task started: HMMsearch
[2023-03-15 14:39:04,385] [INFO] Running command: hmmsearch --tblout OceanDNA-b32153/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfb8b731a-9282-4047-9f48-b29ed6477868/dqc_reference/reference_markers.hmm OceanDNA-b32153/protein.faa > /dev/null
[2023-03-15 14:39:04,586] [INFO] Task succeeded: HMMsearch
[2023-03-15 14:39:04,587] [INFO] Found 6/6 markers.
[2023-03-15 14:39:04,606] [INFO] Query marker FASTA was written to OceanDNA-b32153/markers.fasta
[2023-03-15 14:39:04,607] [INFO] Task started: Blastn
[2023-03-15 14:39:04,608] [INFO] Running command: blastn -query OceanDNA-b32153/markers.fasta -db /var/lib/cwl/stgfb8b731a-9282-4047-9f48-b29ed6477868/dqc_reference/reference_markers.fasta -out OceanDNA-b32153/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 14:39:05,442] [INFO] Task succeeded: Blastn
[2023-03-15 14:39:05,443] [INFO] Selected 19 target genomes.
[2023-03-15 14:39:05,443] [INFO] Target genome list was writen to OceanDNA-b32153/target_genomes.txt
[2023-03-15 14:39:05,460] [INFO] Task started: fastANI
[2023-03-15 14:39:05,461] [INFO] Running command: fastANI --query /var/lib/cwl/stg9bb98462-cf30-45de-9fb4-27e7ae4ee77a/OceanDNA-b32153.fa --refList OceanDNA-b32153/target_genomes.txt --output OceanDNA-b32153/fastani_result.tsv --threads 1
[2023-03-15 14:39:21,658] [INFO] Task succeeded: fastANI
[2023-03-15 14:39:21,659] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfb8b731a-9282-4047-9f48-b29ed6477868/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 14:39:21,659] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfb8b731a-9282-4047-9f48-b29ed6477868/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 14:39:21,670] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2023-03-15 14:39:21,670] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-15 14:39:21,670] [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 alaskensis	strain=RB2256	GCA_000013985.1	117207	117207	type	True	99.6063	928	1019	95	conclusive
Sphingopyxis italica	strain=DSM 25229	GCA_011926545.1	1129133	1129133	type	True	86.0943	800	1019	95	below_threshold
Sphingopyxis fribergensis	strain=Kp5.2	GCA_000803645.1	1515612	1515612	type	True	85.6346	833	1019	95	below_threshold
Sphingopyxis solisilvae	strain=R366	GCA_015475875.1	1886788	1886788	type	True	84.8584	731	1019	95	below_threshold
Sphingopyxis macrogoltabida	strain=203	GCA_001314325.1	33050	33050	type	True	84.7992	793	1019	95	below_threshold
Sphingopyxis lindanitolerans	strain=WS5A3p	GCA_002993885.1	2054227	2054227	type	True	84.517	733	1019	95	below_threshold
Sphingopyxis soli	strain=BL03	GCA_018682675.1	592051	592051	type	True	84.4836	752	1019	95	below_threshold
Sphingopyxis terrae subsp. terrae	strain=203-1	GCA_001610975.1	2448440	33052	type	True	84.4389	753	1019	95	below_threshold
Sphingopyxis indica	strain=DS15	GCA_900188185.1	436663	436663	type	True	84.4058	735	1019	95	below_threshold
Sphingopyxis panaciterrae	strain=DSM 27164	GCA_011762125.1	363841	363841	type	True	84.2286	746	1019	95	below_threshold
Sphingopyxis terrae subsp. terrae	strain=NBRC 15098	GCA_001598815.1	2448440	33052	type	True	84.1975	744	1019	95	below_threshold
Sphingopyxis panaciterrulae	strain=DSM 27163	GCA_014199295.1	462372	462372	type	True	84.0201	744	1019	95	below_threshold
Sphingopyxis terrae subsp. ummariensis	strain=UI2	GCA_900177755.1	429001	33052	type	True	83.7814	713	1019	95	below_threshold
Sphingopyxis terrae subsp. ummariensis	strain=DSM 24316	GCA_002374275.1	429001	33052	type	True	83.7399	714	1019	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	78.062	359	1019	95	below_threshold
Sphingomonas psychrotolerans	strain=Cra20	GCA_002796605.1	1327635	1327635	type	True	77.6396	348	1019	95	below_threshold
Sphingomonas corticis	strain=36D10-4-7	GCA_012035195.1	2722791	2722791	type	True	77.5797	332	1019	95	below_threshold
Sphingomonas segetis	strain=YJ09	GCA_009720245.1	1104779	1104779	type	True	77.5647	164	1019	95	below_threshold
Novosphingobium aquimarinum	strain=M24A2M	GCA_009746585.1	2682494	2682494	type	True	77.1745	261	1019	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 14:39:21,675] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32153/tc_result.tsv
[2023-03-15 14:39:21,675] [INFO] ===== Taxonomy check completed =====
[2023-03-15 14:39:21,676] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 14:39:21,676] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfb8b731a-9282-4047-9f48-b29ed6477868/dqc_reference/checkm_data
[2023-03-15 14:39:21,676] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 14:39:21,782] [INFO] Task started: CheckM
[2023-03-15 14:39:21,782] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32153/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32153/checkm_input OceanDNA-b32153/checkm_result
[2023-03-15 14:40:09,224] [INFO] Task succeeded: CheckM
[2023-03-15 14:40:09,224] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 14:40:09,253] [INFO] ===== Completeness check finished =====
[2023-03-15 14:40:09,253] [INFO] ===== Start GTDB Search =====
[2023-03-15 14:40:09,253] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32153/markers.fasta)
[2023-03-15 14:40:09,254] [INFO] Task started: Blastn
[2023-03-15 14:40:09,254] [INFO] Running command: blastn -query OceanDNA-b32153/markers.fasta -db /var/lib/cwl/stgfb8b731a-9282-4047-9f48-b29ed6477868/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32153/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 14:40:10,860] [INFO] Task succeeded: Blastn
[2023-03-15 14:40:10,861] [INFO] Selected 14 target genomes.
[2023-03-15 14:40:10,861] [INFO] Target genome list was writen to OceanDNA-b32153/target_genomes_gtdb.txt
[2023-03-15 14:40:10,872] [INFO] Task started: fastANI
[2023-03-15 14:40:10,872] [INFO] Running command: fastANI --query /var/lib/cwl/stg9bb98462-cf30-45de-9fb4-27e7ae4ee77a/OceanDNA-b32153.fa --refList OceanDNA-b32153/target_genomes_gtdb.txt --output OceanDNA-b32153/fastani_result_gtdb.tsv --threads 1
[2023-03-15 14:40:24,764] [INFO] Task succeeded: fastANI
[2023-03-15 14:40:24,772] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 14:40:24,772] [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_000013985.1	s__Sphingopyxis alaskensis	99.6063	928	1019	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003609835.1	s__Sphingopyxis sp003609835	89.9811	876	1019	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014595975.1	s__Sphingopyxis sp014595975	89.1796	822	1019	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	86.526	846	1019	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900078365.1	s__Sphingopyxis sp900078365	86.4246	783	1019	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000756385.1	s__Sphingopyxis sp000756385	86.4206	816	1019	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	86.1042	799	1019	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001468465.1	s__Sphingopyxis sp001468465	85.7552	808	1019	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	85.7195	796	1019	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	99.44	99.44	0.94	0.94	2	-
GCF_015475875.1	s__Sphingopyxis solisilvae	84.8576	732	1019	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	96.45	96.45	0.86	0.86	2	-
GCF_018682675.1	s__Sphingopyxis soli	84.4995	750	1019	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001468395.1	s__Sphingopyxis sp001468395	84.1708	761	1019	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	99.27	97.10	0.97	0.89	9	-
GCA_016793775.1	s__Sphingopyxis sp016793775	84.0885	725	1019	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017309275.1	s__Sphingopyxis sp017309275	83.5892	730	1019	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 14:40:24,774] [INFO] GTDB search result was written to OceanDNA-b32153/result_gtdb.tsv
[2023-03-15 14:40:24,777] [INFO] ===== GTDB Search completed =====
[2023-03-15 14:40:24,783] [INFO] DFAST_QC result json was written to OceanDNA-b32153/dqc_result.json
[2023-03-15 14:40:24,783] [INFO] DFAST_QC completed!
[2023-03-15 14:40:24,783] [INFO] Total running time: 0h1m40s