[2023-03-15 21:24:36,519] [INFO] DFAST_QC pipeline started.
[2023-03-15 21:24:36,519] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 21:24:36,519] [INFO] DQC Reference Directory: /var/lib/cwl/stg927a2320-13c3-470a-a565-3924acede9f5/dqc_reference
[2023-03-15 21:24:37,606] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 21:24:37,606] [INFO] Task started: Prodigal
[2023-03-15 21:24:37,606] [INFO] Running command: cat /var/lib/cwl/stg6e487bb6-7636-47a6-8cde-c75905814695/OceanDNA-b32166.fa | prodigal -d OceanDNA-b32166/cds.fna -a OceanDNA-b32166/protein.faa -g 11 -q > /dev/null
[2023-03-15 21:24:58,104] [INFO] Task succeeded: Prodigal
[2023-03-15 21:24:58,105] [INFO] Task started: HMMsearch
[2023-03-15 21:24:58,105] [INFO] Running command: hmmsearch --tblout OceanDNA-b32166/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg927a2320-13c3-470a-a565-3924acede9f5/dqc_reference/reference_markers.hmm OceanDNA-b32166/protein.faa > /dev/null
[2023-03-15 21:24:58,296] [INFO] Task succeeded: HMMsearch
[2023-03-15 21:24:58,297] [INFO] Found 6/6 markers.
[2023-03-15 21:24:58,319] [INFO] Query marker FASTA was written to OceanDNA-b32166/markers.fasta
[2023-03-15 21:24:58,319] [INFO] Task started: Blastn
[2023-03-15 21:24:58,319] [INFO] Running command: blastn -query OceanDNA-b32166/markers.fasta -db /var/lib/cwl/stg927a2320-13c3-470a-a565-3924acede9f5/dqc_reference/reference_markers.fasta -out OceanDNA-b32166/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:24:59,206] [INFO] Task succeeded: Blastn
[2023-03-15 21:24:59,207] [INFO] Selected 13 target genomes.
[2023-03-15 21:24:59,207] [INFO] Target genome list was writen to OceanDNA-b32166/target_genomes.txt
[2023-03-15 21:24:59,215] [INFO] Task started: fastANI
[2023-03-15 21:24:59,215] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e487bb6-7636-47a6-8cde-c75905814695/OceanDNA-b32166.fa --refList OceanDNA-b32166/target_genomes.txt --output OceanDNA-b32166/fastani_result.tsv --threads 1
[2023-03-15 21:25:09,932] [INFO] Task succeeded: fastANI
[2023-03-15 21:25:09,933] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg927a2320-13c3-470a-a565-3924acede9f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 21:25:09,933] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg927a2320-13c3-470a-a565-3924acede9f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 21:25:09,941] [INFO] Found 13 fastANI hits (4 hits with ANI > threshold)
[2023-03-15 21:25:09,941] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-15 21:25:09,941] [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 terrae subsp. ummariensis	strain=DSM 24316	GCA_002374275.1	429001	33052	type	True	97.0834	965	1121	95	conclusive
Sphingopyxis terrae subsp. ummariensis	strain=UI2	GCA_900177755.1	429001	33052	type	True	97.0745	971	1121	95	conclusive
Sphingopyxis terrae subsp. terrae	strain=NBRC 15098	GCA_001598815.1	2448440	33052	type	True	96.9913	975	1121	95	conclusive
Sphingopyxis terrae subsp. terrae	strain=203-1	GCA_001610975.1	2448440	33052	type	True	95.8612	983	1121	95	conclusive
Sphingopyxis soli	strain=BL03	GCA_018682675.1	592051	592051	type	True	84.6104	775	1121	95	below_threshold
Sphingopyxis macrogoltabida	strain=203	GCA_001314325.1	33050	33050	type	True	84.2822	836	1121	95	below_threshold
Sphingopyxis granuli	strain=NBRC 100800	GCA_001591045.1	267128	267128	type	True	84.1337	727	1121	95	below_threshold
Sphingopyxis indica	strain=DS15	GCA_900188185.1	436663	436663	type	True	84.1286	760	1121	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	78.1915	373	1121	95	below_threshold
Sphingomonas panni	strain=DSM 15761	GCA_022664435.1	237612	237612	type	True	77.996	344	1121	95	below_threshold
Sphingomonas psychrotolerans	strain=Cra20	GCA_002796605.1	1327635	1327635	type	True	77.6526	347	1121	95	below_threshold
Sphingomonas aracearum	strain=WZY 27	GCA_003345355.1	2283317	2283317	type	True	77.5522	281	1121	95	below_threshold
Sphingomonas segetis	strain=YJ09	GCA_009720245.1	1104779	1104779	type	True	77.3138	176	1121	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 21:25:09,942] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32166/tc_result.tsv
[2023-03-15 21:25:09,942] [INFO] ===== Taxonomy check completed =====
[2023-03-15 21:25:09,942] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 21:25:09,942] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg927a2320-13c3-470a-a565-3924acede9f5/dqc_reference/checkm_data
[2023-03-15 21:25:09,943] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 21:25:09,949] [INFO] Task started: CheckM
[2023-03-15 21:25:09,949] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32166/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32166/checkm_input OceanDNA-b32166/checkm_result
[2023-03-15 21:26:01,330] [INFO] Task succeeded: CheckM
[2023-03-15 21:26:01,330] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 21:26:01,333] [INFO] ===== Completeness check finished =====
[2023-03-15 21:26:01,333] [INFO] ===== Start GTDB Search =====
[2023-03-15 21:26:01,333] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32166/markers.fasta)
[2023-03-15 21:26:01,333] [INFO] Task started: Blastn
[2023-03-15 21:26:01,333] [INFO] Running command: blastn -query OceanDNA-b32166/markers.fasta -db /var/lib/cwl/stg927a2320-13c3-470a-a565-3924acede9f5/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32166/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:26:03,105] [INFO] Task succeeded: Blastn
[2023-03-15 21:26:03,106] [INFO] Selected 18 target genomes.
[2023-03-15 21:26:03,106] [INFO] Target genome list was writen to OceanDNA-b32166/target_genomes_gtdb.txt
[2023-03-15 21:26:03,436] [INFO] Task started: fastANI
[2023-03-15 21:26:03,436] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e487bb6-7636-47a6-8cde-c75905814695/OceanDNA-b32166.fa --refList OceanDNA-b32166/target_genomes_gtdb.txt --output OceanDNA-b32166/fastani_result_gtdb.tsv --threads 1
[2023-03-15 21:26:19,929] [INFO] Task succeeded: fastANI
[2023-03-15 21:26:19,939] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 21:26:19,939] [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_001598815.1	s__Sphingopyxis terrae	97.0013	974	1121	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	96.70	95.58	0.84	0.76	19	conclusive
GCF_000756385.1	s__Sphingopyxis sp000756385	84.6627	821	1121	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018682675.1	s__Sphingopyxis soli	84.6104	775	1121	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	84.5862	841	1121	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013821905.1	s__Sphingopyxis sp013821905	84.4344	643	1121	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002277025.1	s__Sphingopyxis sp002277025	84.4312	817	1121	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	84.4308	816	1121	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	99.27	97.10	0.97	0.89	9	-
GCA_017309275.1	s__Sphingopyxis sp017309275	84.379	835	1121	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001314325.1	s__Sphingopyxis macrogoltabida	84.303	834	1121	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900188185.1	s__Sphingopyxis indica	84.1414	759	1121	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005503215.1	s__Sphingopyxis sp005503215	84.1393	833	1121	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	99.20	99.20	0.88	0.88	2	-
GCF_001591045.1	s__Sphingopyxis granuli	84.1319	727	1121	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	97.56	96.77	0.81	0.78	6	-
GCA_900078365.1	s__Sphingopyxis sp900078365	84.0973	805	1121	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	84.0776	816	1121	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	84.0572	735	1121	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000756375.1	s__Sphingopyxis sp000756375	83.7677	809	1121	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	83.6279	798	1121	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	99.44	99.44	0.94	0.94	2	-
GCF_014873485.1	s__Sphingopyxis sp014873485	83.615	796	1121	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 21:26:19,940] [INFO] GTDB search result was written to OceanDNA-b32166/result_gtdb.tsv
[2023-03-15 21:26:19,940] [INFO] ===== GTDB Search completed =====
[2023-03-15 21:26:19,941] [INFO] DFAST_QC result json was written to OceanDNA-b32166/dqc_result.json
[2023-03-15 21:26:19,942] [INFO] DFAST_QC completed!
[2023-03-15 21:26:19,942] [INFO] Total running time: 0h1m43s