[2023-03-16 03:23:49,908] [INFO] DFAST_QC pipeline started.
[2023-03-16 03:23:49,908] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 03:23:49,908] [INFO] DQC Reference Directory: /var/lib/cwl/stg8f12a54e-a2ec-4d05-aa4f-246306606818/dqc_reference
[2023-03-16 03:23:51,106] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 03:23:51,106] [INFO] Task started: Prodigal
[2023-03-16 03:23:51,107] [INFO] Running command: cat /var/lib/cwl/stgdc1232fb-992c-4b71-ba61-eedd908aed51/OceanDNA-b32130.fa | prodigal -d OceanDNA-b32130/cds.fna -a OceanDNA-b32130/protein.faa -g 11 -q > /dev/null
[2023-03-16 03:24:09,196] [INFO] Task succeeded: Prodigal
[2023-03-16 03:24:09,196] [INFO] Task started: HMMsearch
[2023-03-16 03:24:09,196] [INFO] Running command: hmmsearch --tblout OceanDNA-b32130/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8f12a54e-a2ec-4d05-aa4f-246306606818/dqc_reference/reference_markers.hmm OceanDNA-b32130/protein.faa > /dev/null
[2023-03-16 03:24:09,399] [INFO] Task succeeded: HMMsearch
[2023-03-16 03:24:09,400] [INFO] Found 6/6 markers.
[2023-03-16 03:24:09,416] [INFO] Query marker FASTA was written to OceanDNA-b32130/markers.fasta
[2023-03-16 03:24:09,417] [INFO] Task started: Blastn
[2023-03-16 03:24:09,417] [INFO] Running command: blastn -query OceanDNA-b32130/markers.fasta -db /var/lib/cwl/stg8f12a54e-a2ec-4d05-aa4f-246306606818/dqc_reference/reference_markers.fasta -out OceanDNA-b32130/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 03:24:10,134] [INFO] Task succeeded: Blastn
[2023-03-16 03:24:10,135] [INFO] Selected 13 target genomes.
[2023-03-16 03:24:10,135] [INFO] Target genome list was writen to OceanDNA-b32130/target_genomes.txt
[2023-03-16 03:24:10,144] [INFO] Task started: fastANI
[2023-03-16 03:24:10,144] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc1232fb-992c-4b71-ba61-eedd908aed51/OceanDNA-b32130.fa --refList OceanDNA-b32130/target_genomes.txt --output OceanDNA-b32130/fastani_result.tsv --threads 1
[2023-03-16 03:24:21,739] [INFO] Task succeeded: fastANI
[2023-03-16 03:24:21,739] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8f12a54e-a2ec-4d05-aa4f-246306606818/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 03:24:21,740] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8f12a54e-a2ec-4d05-aa4f-246306606818/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 03:24:21,748] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2023-03-16 03:24:21,748] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-16 03:24:21,748] [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 xenophagum	strain=NBRC 107872	GCA_000367345.1	121428	121428	type	True	97.5739	830	935	95	conclusive
Sphingobium terrigena	strain=EO9	GCA_003591655.1	2304063	2304063	type	True	89.873	754	935	95	below_threshold
Sphingobium cupriresistens	strain=CCTCC AB 2011146	GCA_004152865.1	1132417	1132417	type	True	84.3375	692	935	95	below_threshold
Sphingobium psychrophilum	strain=AR-3-1	GCA_012927105.1	2728834	2728834	type	True	83.8909	711	935	95	below_threshold
Sphingobium limneticum	strain=DSM 25076	GCA_008710155.1	1007511	1007511	type	True	83.5464	693	935	95	below_threshold
Sphingobium yanoikuyae	strain=ATCC 51230	GCA_000315525.1	13690	13690	suspected-type	True	82.9292	683	935	95	below_threshold
Sphingobium amiense	strain=NBRC 102518	GCA_001591305.1	135719	135719	type	True	82.3006	612	935	95	below_threshold
Sphingobium amiense	strain=DSM 16289	GCA_003967075.1	135719	135719	type	True	82.2687	628	935	95	below_threshold
Sphingobium indicum	strain=B90A	GCA_000264945.2	332055	332055	type	True	82.1144	633	935	95	below_threshold
Sphingobium sufflavum	strain=HL-25	GCA_021403115.1	1129547	1129547	type	True	78.9462	410	935	95	below_threshold
Sphingomonas hankookensis	strain=KCTC 22579	GCA_022664465.1	563996	563996	type	True	77.7665	310	935	95	below_threshold
Novosphingobium percolationis	strain=c1	GCA_020179425.1	2871811	2871811	type	True	77.3763	269	935	95	below_threshold
Novosphingobium umbonatum	strain=FSY-9	GCA_004005905.1	1908524	1908524	type	True	77.2569	219	935	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 03:24:21,748] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32130/tc_result.tsv
[2023-03-16 03:24:21,748] [INFO] ===== Taxonomy check completed =====
[2023-03-16 03:24:21,749] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 03:24:21,749] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8f12a54e-a2ec-4d05-aa4f-246306606818/dqc_reference/checkm_data
[2023-03-16 03:24:21,749] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 03:24:21,760] [INFO] Task started: CheckM
[2023-03-16 03:24:21,760] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32130/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32130/checkm_input OceanDNA-b32130/checkm_result
[2023-03-16 03:25:08,274] [INFO] Task succeeded: CheckM
[2023-03-16 03:25:08,275] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 03:25:08,277] [INFO] ===== Completeness check finished =====
[2023-03-16 03:25:08,277] [INFO] ===== Start GTDB Search =====
[2023-03-16 03:25:08,277] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32130/markers.fasta)
[2023-03-16 03:25:08,277] [INFO] Task started: Blastn
[2023-03-16 03:25:08,277] [INFO] Running command: blastn -query OceanDNA-b32130/markers.fasta -db /var/lib/cwl/stg8f12a54e-a2ec-4d05-aa4f-246306606818/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32130/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 03:25:09,508] [INFO] Task succeeded: Blastn
[2023-03-16 03:25:09,775] [INFO] Selected 6 target genomes.
[2023-03-16 03:25:09,775] [INFO] Target genome list was writen to OceanDNA-b32130/target_genomes_gtdb.txt
[2023-03-16 03:25:09,874] [INFO] Task started: fastANI
[2023-03-16 03:25:09,874] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc1232fb-992c-4b71-ba61-eedd908aed51/OceanDNA-b32130.fa --refList OceanDNA-b32130/target_genomes_gtdb.txt --output OceanDNA-b32130/fastani_result_gtdb.tsv --threads 1
[2023-03-16 03:25:15,443] [INFO] Task succeeded: fastANI
[2023-03-16 03:25:15,447] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 03:25:15,448] [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_000367345.1	s__Sphingobium xenophagum	97.5739	830	935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	97.29	96.67	0.79	0.71	22	conclusive
GCF_019097845.1	s__Sphingobium sp019097845	89.882	785	935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003591655.1	s__Sphingobium sp003591655	89.873	754	935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016463275.1	s__Sphingobium sp016463275	89.5836	566	935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000382885.1	s__Sphingobium japonicum_C	89.0511	696	935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014280435.1	s__Sphingobium sp014280435	84.7543	713	935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 03:25:15,448] [INFO] GTDB search result was written to OceanDNA-b32130/result_gtdb.tsv
[2023-03-16 03:25:15,448] [INFO] ===== GTDB Search completed =====
[2023-03-16 03:25:15,449] [INFO] DFAST_QC result json was written to OceanDNA-b32130/dqc_result.json
[2023-03-16 03:25:15,449] [INFO] DFAST_QC completed!
[2023-03-16 03:25:15,449] [INFO] Total running time: 0h1m26s