[2024-01-25 19:48:50,518] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:48:50,519] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:48:50,520] [INFO] DQC Reference Directory: /var/lib/cwl/stg554319c4-9aa5-480a-a30e-4f01aa7561e5/dqc_reference
[2024-01-25 19:48:51,659] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:48:51,660] [INFO] Task started: Prodigal
[2024-01-25 19:48:51,660] [INFO] Running command: gunzip -c /var/lib/cwl/stg80ad3343-2e9c-4db8-9d38-9785430dceb4/GCF_002896965.1_ASM289696v1_genomic.fna.gz | prodigal -d GCF_002896965.1_ASM289696v1_genomic.fna/cds.fna -a GCF_002896965.1_ASM289696v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:49:07,418] [INFO] Task succeeded: Prodigal
[2024-01-25 19:49:07,419] [INFO] Task started: HMMsearch
[2024-01-25 19:49:07,419] [INFO] Running command: hmmsearch --tblout GCF_002896965.1_ASM289696v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg554319c4-9aa5-480a-a30e-4f01aa7561e5/dqc_reference/reference_markers.hmm GCF_002896965.1_ASM289696v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:49:07,705] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:49:07,706] [INFO] Found 6/6 markers.
[2024-01-25 19:49:07,756] [INFO] Query marker FASTA was written to GCF_002896965.1_ASM289696v1_genomic.fna/markers.fasta
[2024-01-25 19:49:07,757] [INFO] Task started: Blastn
[2024-01-25 19:49:07,757] [INFO] Running command: blastn -query GCF_002896965.1_ASM289696v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg554319c4-9aa5-480a-a30e-4f01aa7561e5/dqc_reference/reference_markers.fasta -out GCF_002896965.1_ASM289696v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:49:08,631] [INFO] Task succeeded: Blastn
[2024-01-25 19:49:08,633] [INFO] Selected 16 target genomes.
[2024-01-25 19:49:08,634] [INFO] Target genome list was writen to GCF_002896965.1_ASM289696v1_genomic.fna/target_genomes.txt
[2024-01-25 19:49:08,644] [INFO] Task started: fastANI
[2024-01-25 19:49:08,644] [INFO] Running command: fastANI --query /var/lib/cwl/stg80ad3343-2e9c-4db8-9d38-9785430dceb4/GCF_002896965.1_ASM289696v1_genomic.fna.gz --refList GCF_002896965.1_ASM289696v1_genomic.fna/target_genomes.txt --output GCF_002896965.1_ASM289696v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:49:25,005] [INFO] Task succeeded: fastANI
[2024-01-25 19:49:25,006] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg554319c4-9aa5-480a-a30e-4f01aa7561e5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:49:25,006] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg554319c4-9aa5-480a-a30e-4f01aa7561e5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:49:25,016] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:49:25,016] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:49:25,016] [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
Novosphingobium guangzhouense	strain=SA925	GCA_002896965.1	1850347	1850347	type	True	100.0	1925	1932	95	conclusive
Novosphingobium barchaimii	strain=LL02	GCA_001046635.1	1420591	1420591	type	True	82.0877	932	1932	95	below_threshold
Novosphingobium silvae	strain=FGD1	GCA_009856825.1	2692619	2692619	type	True	82.0495	828	1932	95	below_threshold
Novosphingobium lindaniclasticum	strain=LE124	GCA_000445125.1	1329895	1329895	type	True	81.8374	753	1932	95	below_threshold
Novosphingobium indicum	strain=CGMCC 1.6784	GCA_014645195.1	462949	462949	type	True	80.6508	716	1932	95	below_threshold
Novosphingobium decolorationis	strain=502str22	GCA_018417475.1	2698673	2698673	type	True	80.6068	628	1932	95	below_threshold
Novosphingobium profundi	strain=F72	GCA_018491765.1	1774954	1774954	type	True	80.5244	704	1932	95	below_threshold
Novosphingobium mathurense	strain=SM117	GCA_900168325.1	428990	428990	type	True	80.4658	609	1932	95	below_threshold
Novosphingobium pentaromativorans	strain=US6-1	GCA_000235975.2	205844	205844	type	True	80.4196	599	1932	95	below_threshold
Novosphingobium pentaromativorans	strain=US6-1	GCA_000767465.1	205844	205844	type	True	80.3646	612	1932	95	below_threshold
Novosphingobium colocasiae	strain=KCTC 32255	GCA_014652555.1	1256513	1256513	type	True	80.3432	561	1932	95	below_threshold
Novosphingobium endophyticum	strain=CGMCC 1.15095	GCA_014640675.1	1955250	1955250	type	True	80.0843	569	1932	95	below_threshold
Novosphingobium aureum	strain=YJ-S2-02	GCA_015865035.1	2792964	2792964	type	True	80.0527	639	1932	95	below_threshold
Novosphingobium percolationis	strain=c1	GCA_020179425.1	2871811	2871811	type	True	79.2143	491	1932	95	below_threshold
Novosphingobium huizhouense	strain=c7	GCA_020179475.1	2866625	2866625	type	True	79.1086	444	1932	95	below_threshold
Novosphingobium aquimarinum	strain=M24A2M	GCA_009746585.1	2682494	2682494	type	True	78.783	486	1932	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:49:25,018] [INFO] DFAST Taxonomy check result was written to GCF_002896965.1_ASM289696v1_genomic.fna/tc_result.tsv
[2024-01-25 19:49:25,018] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:49:25,018] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:49:25,018] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg554319c4-9aa5-480a-a30e-4f01aa7561e5/dqc_reference/checkm_data
[2024-01-25 19:49:25,019] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:49:25,074] [INFO] Task started: CheckM
[2024-01-25 19:49:25,074] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002896965.1_ASM289696v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002896965.1_ASM289696v1_genomic.fna/checkm_input GCF_002896965.1_ASM289696v1_genomic.fna/checkm_result
[2024-01-25 19:50:12,226] [INFO] Task succeeded: CheckM
[2024-01-25 19:50:12,227] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:50:12,245] [INFO] ===== Completeness check finished =====
[2024-01-25 19:50:12,245] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:50:12,246] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002896965.1_ASM289696v1_genomic.fna/markers.fasta)
[2024-01-25 19:50:12,247] [INFO] Task started: Blastn
[2024-01-25 19:50:12,247] [INFO] Running command: blastn -query GCF_002896965.1_ASM289696v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg554319c4-9aa5-480a-a30e-4f01aa7561e5/dqc_reference/reference_markers_gtdb.fasta -out GCF_002896965.1_ASM289696v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:50:13,974] [INFO] Task succeeded: Blastn
[2024-01-25 19:50:13,977] [INFO] Selected 16 target genomes.
[2024-01-25 19:50:13,977] [INFO] Target genome list was writen to GCF_002896965.1_ASM289696v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:50:13,995] [INFO] Task started: fastANI
[2024-01-25 19:50:13,995] [INFO] Running command: fastANI --query /var/lib/cwl/stg80ad3343-2e9c-4db8-9d38-9785430dceb4/GCF_002896965.1_ASM289696v1_genomic.fna.gz --refList GCF_002896965.1_ASM289696v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002896965.1_ASM289696v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:50:32,115] [INFO] Task succeeded: fastANI
[2024-01-25 19:50:32,126] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:50:32,126] [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_002896965.1	s__Novosphingobium guangzhouense	100.0	1925	1932	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001742225.1	s__Novosphingobium resinovorum	86.5486	1219	1932	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	98.22	97.83	0.80	0.78	4	-
GCF_002149965.1	s__Novosphingobium panipatense	82.2331	862	1932	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	98.24	97.74	0.85	0.82	3	-
GCF_000281975.1	s__Novosphingobium sp000281975	82.1523	925	1932	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001046635.1	s__Novosphingobium barchaimii	82.0821	932	1932	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009856825.1	s__Novosphingobium sp009856825	82.0546	828	1932	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000876675.2	s__Novosphingobium sp000876675	82.0229	949	1932	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902706195.1	s__Novosphingobium sp902706195	82.0147	898	1932	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_002916655.1	s__Novosphingobium sp002916655	81.7538	704	1932	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006874585.1	s__Novosphingobium sp006874585	81.6637	810	1932	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	98.32	98.32	0.81	0.81	2	-
GCF_007993975.1	s__Novosphingobium barchaimii_B	81.4498	797	1932	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001590985.1	s__Novosphingobium naphthalenivorans	81.0342	647	1932	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004341845.1	s__Novosphingobium sp004341845	81.0085	753	1932	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001421325.1	s__Novosphingobium sp001421325	80.939	690	1932	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000272475.1	s__Novosphingobium sp000272475	80.4774	616	1932	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000767465.1	s__Novosphingobium pentaromativorans	80.3855	612	1932	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	96.84	95.17	0.76	0.62	4	-
--------------------------------------------------------------------------------
[2024-01-25 19:50:32,128] [INFO] GTDB search result was written to GCF_002896965.1_ASM289696v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:50:32,128] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:50:32,131] [INFO] DFAST_QC result json was written to GCF_002896965.1_ASM289696v1_genomic.fna/dqc_result.json
[2024-01-25 19:50:32,131] [INFO] DFAST_QC completed!
[2024-01-25 19:50:32,132] [INFO] Total running time: 0h1m42s