[2024-01-24 13:13:32,009] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:32,013] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:32,013] [INFO] DQC Reference Directory: /var/lib/cwl/stgfff9ebbb-ea8d-4856-acb2-2b999aa50970/dqc_reference
[2024-01-24 13:13:33,342] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:33,342] [INFO] Task started: Prodigal
[2024-01-24 13:13:33,343] [INFO] Running command: gunzip -c /var/lib/cwl/stg23eda7f7-39c2-4a3e-bf73-4c6c755a6a7c/GCF_022832435.1_ASM2283243v1_genomic.fna.gz | prodigal -d GCF_022832435.1_ASM2283243v1_genomic.fna/cds.fna -a GCF_022832435.1_ASM2283243v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:46,028] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:46,029] [INFO] Task started: HMMsearch
[2024-01-24 13:13:46,029] [INFO] Running command: hmmsearch --tblout GCF_022832435.1_ASM2283243v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfff9ebbb-ea8d-4856-acb2-2b999aa50970/dqc_reference/reference_markers.hmm GCF_022832435.1_ASM2283243v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:46,318] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:46,320] [INFO] Found 6/6 markers.
[2024-01-24 13:13:46,365] [INFO] Query marker FASTA was written to GCF_022832435.1_ASM2283243v1_genomic.fna/markers.fasta
[2024-01-24 13:13:46,366] [INFO] Task started: Blastn
[2024-01-24 13:13:46,366] [INFO] Running command: blastn -query GCF_022832435.1_ASM2283243v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfff9ebbb-ea8d-4856-acb2-2b999aa50970/dqc_reference/reference_markers.fasta -out GCF_022832435.1_ASM2283243v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:47,363] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:47,366] [INFO] Selected 14 target genomes.
[2024-01-24 13:13:47,366] [INFO] Target genome list was writen to GCF_022832435.1_ASM2283243v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:47,374] [INFO] Task started: fastANI
[2024-01-24 13:13:47,374] [INFO] Running command: fastANI --query /var/lib/cwl/stg23eda7f7-39c2-4a3e-bf73-4c6c755a6a7c/GCF_022832435.1_ASM2283243v1_genomic.fna.gz --refList GCF_022832435.1_ASM2283243v1_genomic.fna/target_genomes.txt --output GCF_022832435.1_ASM2283243v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:14:00,562] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:00,562] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfff9ebbb-ea8d-4856-acb2-2b999aa50970/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:14:00,563] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfff9ebbb-ea8d-4856-acb2-2b999aa50970/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:14:00,579] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:14:00,579] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:14:00,579] [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 profundi	strain=F72	GCA_018491765.1	1774954	1774954	type	True	83.9642	923	1401	95	below_threshold
Novosphingobium decolorationis	strain=502str22	GCA_018417475.1	2698673	2698673	type	True	83.6257	848	1401	95	below_threshold
Novosphingobium aureum	strain=YJ-S2-02	GCA_015865035.1	2792964	2792964	type	True	82.4747	750	1401	95	below_threshold
Novosphingobium naphthalenivorans	strain=NBRC 102051	GCA_001590985.1	273168	273168	type	True	81.272	648	1401	95	below_threshold
Novosphingobium pentaromativorans	strain=US6-1	GCA_000235975.2	205844	205844	type	True	80.8381	549	1401	95	below_threshold
Novosphingobium pentaromativorans	strain=US6-1	GCA_000767465.1	205844	205844	type	True	80.7174	571	1401	95	below_threshold
Novosphingobium mathurense	strain=SM117	GCA_900168325.1	428990	428990	type	True	80.5115	603	1401	95	below_threshold
Novosphingobium indicum	strain=CGMCC 1.6784	GCA_014645195.1	462949	462949	type	True	80.3997	605	1401	95	below_threshold
Novosphingobium malaysiense	strain=MUSC 273	GCA_000802225.1	1348853	1348853	type	True	80.3793	566	1401	95	below_threshold
Novosphingobium guangzhouense	strain=SA925	GCA_002896965.1	1850347	1850347	type	True	80.114	587	1401	95	below_threshold
Novosphingobium silvae	strain=FGD1	GCA_009856825.1	2692619	2692619	type	True	79.8355	561	1401	95	below_threshold
Novosphingobium huizhouense	strain=c7	GCA_020179475.1	2866625	2866625	type	True	79.678	509	1401	95	below_threshold
Novosphingobium aquimarinum	strain=M24A2M	GCA_009746585.1	2682494	2682494	type	True	79.6444	483	1401	95	below_threshold
Novosphingobium percolationis	strain=c1	GCA_020179425.1	2871811	2871811	type	True	79.3731	485	1401	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:14:00,581] [INFO] DFAST Taxonomy check result was written to GCF_022832435.1_ASM2283243v1_genomic.fna/tc_result.tsv
[2024-01-24 13:14:00,582] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:14:00,582] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:14:00,582] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfff9ebbb-ea8d-4856-acb2-2b999aa50970/dqc_reference/checkm_data
[2024-01-24 13:14:00,583] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:14:00,635] [INFO] Task started: CheckM
[2024-01-24 13:14:00,636] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022832435.1_ASM2283243v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022832435.1_ASM2283243v1_genomic.fna/checkm_input GCF_022832435.1_ASM2283243v1_genomic.fna/checkm_result
[2024-01-24 13:14:40,785] [INFO] Task succeeded: CheckM
[2024-01-24 13:14:40,791] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:14:40,815] [INFO] ===== Completeness check finished =====
[2024-01-24 13:14:40,816] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:14:40,816] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022832435.1_ASM2283243v1_genomic.fna/markers.fasta)
[2024-01-24 13:14:40,816] [INFO] Task started: Blastn
[2024-01-24 13:14:40,816] [INFO] Running command: blastn -query GCF_022832435.1_ASM2283243v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfff9ebbb-ea8d-4856-acb2-2b999aa50970/dqc_reference/reference_markers_gtdb.fasta -out GCF_022832435.1_ASM2283243v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:42,749] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:42,754] [INFO] Selected 12 target genomes.
[2024-01-24 13:14:42,754] [INFO] Target genome list was writen to GCF_022832435.1_ASM2283243v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:14:42,820] [INFO] Task started: fastANI
[2024-01-24 13:14:42,821] [INFO] Running command: fastANI --query /var/lib/cwl/stg23eda7f7-39c2-4a3e-bf73-4c6c755a6a7c/GCF_022832435.1_ASM2283243v1_genomic.fna.gz --refList GCF_022832435.1_ASM2283243v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022832435.1_ASM2283243v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:14:55,487] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:55,497] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:14:55,498] [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_018491765.1	s__Novosphingobium profundi	83.9533	925	1401	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018417475.1	s__Novosphingobium sp000813185	83.6197	847	1401	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	97.53	97.53	0.86	0.86	2	-
GCF_008107685.1	s__Novosphingobium sp008107685	82.7017	805	1401	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015865035.1	s__Novosphingobium sp015865035	82.4914	749	1401	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	81.2654	649	1401	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	81.0304	757	1401	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	98.32	98.32	0.81	0.81	2	-
GCF_000767465.1	s__Novosphingobium pentaromativorans	80.7076	572	1401	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	96.84	95.17	0.76	0.62	4	-
GCF_002149965.1	s__Novosphingobium panipatense	80.4645	693	1401	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	98.24	97.74	0.85	0.82	3	-
GCF_004341845.1	s__Novosphingobium sp004341845	80.4426	693	1401	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004342985.1	s__Novosphingobium sp004342985	80.4186	673	1401	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	97.88	97.88	0.88	0.88	2	-
GCF_000802225.1	s__Novosphingobium malaysiense	80.3958	564	1401	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002556635.1	s__Novosphingobium sp002556635	79.9644	585	1401	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:14:55,499] [INFO] GTDB search result was written to GCF_022832435.1_ASM2283243v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:14:55,500] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:14:55,503] [INFO] DFAST_QC result json was written to GCF_022832435.1_ASM2283243v1_genomic.fna/dqc_result.json
[2024-01-24 13:14:55,504] [INFO] DFAST_QC completed!
[2024-01-24 13:14:55,504] [INFO] Total running time: 0h1m23s