[2023-03-14 12:57:46,115] [INFO] DFAST_QC pipeline started.
[2023-03-14 12:57:46,115] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 12:57:46,116] [INFO] DQC Reference Directory: /var/lib/cwl/stg99648f36-5015-493c-b47f-de780c76674e/dqc_reference
[2023-03-14 12:57:48,865] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 12:57:48,865] [INFO] Task started: Prodigal
[2023-03-14 12:57:48,865] [INFO] Running command: cat /var/lib/cwl/stgf08583e6-18a4-4c50-a687-384439419c92/OceanDNA-b32042.fa | prodigal -d OceanDNA-b32042/cds.fna -a OceanDNA-b32042/protein.faa -g 11 -q > /dev/null
[2023-03-14 12:58:17,761] [INFO] Task succeeded: Prodigal
[2023-03-14 12:58:17,761] [INFO] Task started: HMMsearch
[2023-03-14 12:58:17,761] [INFO] Running command: hmmsearch --tblout OceanDNA-b32042/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg99648f36-5015-493c-b47f-de780c76674e/dqc_reference/reference_markers.hmm OceanDNA-b32042/protein.faa > /dev/null
[2023-03-14 12:58:18,326] [INFO] Task succeeded: HMMsearch
[2023-03-14 12:58:18,326] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgf08583e6-18a4-4c50-a687-384439419c92/OceanDNA-b32042.fa]
[2023-03-14 12:58:18,414] [INFO] Query marker FASTA was written to OceanDNA-b32042/markers.fasta
[2023-03-14 12:58:18,422] [INFO] Task started: Blastn
[2023-03-14 12:58:18,423] [INFO] Running command: blastn -query OceanDNA-b32042/markers.fasta -db /var/lib/cwl/stg99648f36-5015-493c-b47f-de780c76674e/dqc_reference/reference_markers.fasta -out OceanDNA-b32042/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:58:20,397] [INFO] Task succeeded: Blastn
[2023-03-14 12:58:20,406] [INFO] Selected 14 target genomes.
[2023-03-14 12:58:20,407] [INFO] Target genome list was writen to OceanDNA-b32042/target_genomes.txt
[2023-03-14 12:58:20,419] [INFO] Task started: fastANI
[2023-03-14 12:58:20,419] [INFO] Running command: fastANI --query /var/lib/cwl/stgf08583e6-18a4-4c50-a687-384439419c92/OceanDNA-b32042.fa --refList OceanDNA-b32042/target_genomes.txt --output OceanDNA-b32042/fastani_result.tsv --threads 1
[2023-03-14 12:58:38,062] [INFO] Task succeeded: fastANI
[2023-03-14 12:58:38,062] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg99648f36-5015-493c-b47f-de780c76674e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 12:58:38,063] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg99648f36-5015-493c-b47f-de780c76674e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 12:58:38,072] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2023-03-14 12:58:38,072] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-14 12:58:38,072] [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
Sphingobium limneticum	strain=DSM 25076	GCA_008710155.1	1007511	1007511	type	True	99.9099	1192	1262	95	conclusive
Sphingobium cupriresistens	strain=CCTCC AB 2011146	GCA_004152865.1	1132417	1132417	type	True	86.1483	797	1262	95	below_threshold
Sphingobium psychrophilum	strain=AR-3-1	GCA_012927105.1	2728834	2728834	type	True	85.8872	870	1262	95	below_threshold
Sphingobium yanoikuyae	strain=ATCC 51230	GCA_000315525.1	13690	13690	suspected-type	True	84.3845	786	1262	95	below_threshold
Sphingobium scionense	strain=DSM 19371	GCA_014197035.1	1404341	1404341	type	True	83.7488	812	1262	95	below_threshold
Sphingobium terrigena	strain=EO9	GCA_003591655.1	2304063	2304063	type	True	83.5262	749	1262	95	below_threshold
Sphingobium amiense	strain=NBRC 102518	GCA_001591305.1	135719	135719	type	True	82.8316	642	1262	95	below_threshold
Sphingobium amiense	strain=DSM 16289	GCA_003967075.1	135719	135719	type	True	82.812	647	1262	95	below_threshold
Sphingobium abikonense	strain=NBRC 16140	GCA_001598335.1	86193	86193	type	True	82.7341	648	1262	95	below_threshold
Sphingobium lactosutens	strain=DS20	GCA_000445105.1	522773	522773	type	True	82.6571	655	1262	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	77.6707	334	1262	95	below_threshold
Sphingomonas aracearum	strain=WZY 27	GCA_003345355.1	2283317	2283317	type	True	77.4534	282	1262	95	below_threshold
Sphingomonas profundi	strain=LMO-1	GCA_009739515.1	2681549	2681549	type	True	77.0996	342	1262	95	below_threshold
Sphingomonas morindae	strain=NBD5	GCA_023822065.1	1541170	1541170	type	True	76.9778	334	1262	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 12:58:38,073] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32042/tc_result.tsv
[2023-03-14 12:58:38,073] [INFO] ===== Taxonomy check completed =====
[2023-03-14 12:58:38,073] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 12:58:38,073] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg99648f36-5015-493c-b47f-de780c76674e/dqc_reference/checkm_data
[2023-03-14 12:58:38,074] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 12:58:38,154] [INFO] Task started: CheckM
[2023-03-14 12:58:38,154] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32042/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32042/checkm_input OceanDNA-b32042/checkm_result
[2023-03-14 12:59:56,380] [INFO] Task succeeded: CheckM
[2023-03-14 12:59:56,380] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 12:59:56,383] [INFO] ===== Completeness check finished =====
[2023-03-14 12:59:56,383] [INFO] ===== Start GTDB Search =====
[2023-03-14 12:59:56,384] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32042/markers.fasta)
[2023-03-14 12:59:56,386] [INFO] Task started: Blastn
[2023-03-14 12:59:56,386] [INFO] Running command: blastn -query OceanDNA-b32042/markers.fasta -db /var/lib/cwl/stg99648f36-5015-493c-b47f-de780c76674e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32042/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:59:57,790] [INFO] Task succeeded: Blastn
[2023-03-14 12:59:57,791] [INFO] Selected 9 target genomes.
[2023-03-14 12:59:57,791] [INFO] Target genome list was writen to OceanDNA-b32042/target_genomes_gtdb.txt
[2023-03-14 12:59:57,806] [INFO] Task started: fastANI
[2023-03-14 12:59:57,806] [INFO] Running command: fastANI --query /var/lib/cwl/stgf08583e6-18a4-4c50-a687-384439419c92/OceanDNA-b32042.fa --refList OceanDNA-b32042/target_genomes_gtdb.txt --output OceanDNA-b32042/fastani_result_gtdb.tsv --threads 1
[2023-03-14 13:00:08,205] [INFO] Task succeeded: fastANI
[2023-03-14 13:00:08,211] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 13:00:08,211] [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_008710155.1	s__Sphingobium limneticum	99.9099	1192	1262	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	98.69	97.69	0.91	0.88	5	conclusive
GCF_001421665.1	s__Sphingobium sp001421665	88.9487	937	1262	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203965.1	s__Sphingobium sp014203965	88.8857	932	1262	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900111125.1	s__Sphingobium sp900111125	86.2092	878	1262	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004152865.1	s__Sphingobium cupriresistens	86.143	797	1262	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	98.64	98.49	0.81	0.81	3	-
GCF_009720145.1	s__Sphingobium sp009720145	85.9423	783	1262	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109095.1	s__Sphingobium sp900109095	85.8493	884	1262	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013393185.1	s__Sphingobium lactosutens_A	85.448	862	1262	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002457415.1	s__Sphingobium sp002457415	83.9542	659	1262	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 13:00:08,212] [INFO] GTDB search result was written to OceanDNA-b32042/result_gtdb.tsv
[2023-03-14 13:00:08,212] [INFO] ===== GTDB Search completed =====
[2023-03-14 13:00:08,213] [INFO] DFAST_QC result json was written to OceanDNA-b32042/dqc_result.json
[2023-03-14 13:00:08,213] [INFO] DFAST_QC completed!
[2023-03-14 13:00:08,214] [INFO] Total running time: 0h2m22s