[2024-01-24 14:19:17,490] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:17,492] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:17,492] [INFO] DQC Reference Directory: /var/lib/cwl/stgb107a7b4-a3d4-4bf6-89ce-bed7769e7a5b/dqc_reference
[2024-01-24 14:19:18,888] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:18,889] [INFO] Task started: Prodigal
[2024-01-24 14:19:18,889] [INFO] Running command: gunzip -c /var/lib/cwl/stg5d8b47d8-cd2a-4155-9a66-0c7e0d89271b/GCF_900182875.1_IMG-taxon_2706794921_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900182875.1_IMG-taxon_2706794921_annotated_assembly_genomic.fna/cds.fna -a GCF_900182875.1_IMG-taxon_2706794921_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:31,893] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:31,894] [INFO] Task started: HMMsearch
[2024-01-24 14:19:31,894] [INFO] Running command: hmmsearch --tblout GCF_900182875.1_IMG-taxon_2706794921_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb107a7b4-a3d4-4bf6-89ce-bed7769e7a5b/dqc_reference/reference_markers.hmm GCF_900182875.1_IMG-taxon_2706794921_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:32,184] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:32,185] [INFO] Found 6/6 markers.
[2024-01-24 14:19:32,232] [INFO] Query marker FASTA was written to GCF_900182875.1_IMG-taxon_2706794921_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:19:32,232] [INFO] Task started: Blastn
[2024-01-24 14:19:32,232] [INFO] Running command: blastn -query GCF_900182875.1_IMG-taxon_2706794921_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgb107a7b4-a3d4-4bf6-89ce-bed7769e7a5b/dqc_reference/reference_markers.fasta -out GCF_900182875.1_IMG-taxon_2706794921_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:33,175] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:33,179] [INFO] Selected 16 target genomes.
[2024-01-24 14:19:33,180] [INFO] Target genome list was writen to GCF_900182875.1_IMG-taxon_2706794921_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:19:33,285] [INFO] Task started: fastANI
[2024-01-24 14:19:33,286] [INFO] Running command: fastANI --query /var/lib/cwl/stg5d8b47d8-cd2a-4155-9a66-0c7e0d89271b/GCF_900182875.1_IMG-taxon_2706794921_annotated_assembly_genomic.fna.gz --refList GCF_900182875.1_IMG-taxon_2706794921_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900182875.1_IMG-taxon_2706794921_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:19:47,411] [INFO] Task succeeded: fastANI
[2024-01-24 14:19:47,411] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb107a7b4-a3d4-4bf6-89ce-bed7769e7a5b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:19:47,411] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb107a7b4-a3d4-4bf6-89ce-bed7769e7a5b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:19:47,436] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:19:47,437] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:19:47,437] [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	82.0263	712	1326	95	below_threshold
Novosphingobium silvae	strain=FGD1	GCA_009856825.1	2692619	2692619	type	True	80.7838	629	1326	95	below_threshold
Novosphingobium barchaimii	strain=LL02	GCA_001046635.1	1420591	1420591	type	True	80.6813	675	1326	95	below_threshold
Novosphingobium naphthalenivorans	strain=NBRC 102051	GCA_001590985.1	273168	273168	type	True	80.5692	490	1326	95	below_threshold
Novosphingobium pentaromativorans	strain=US6-1	GCA_000767465.1	205844	205844	type	True	80.3698	513	1326	95	below_threshold
Novosphingobium pentaromativorans	strain=US6-1	GCA_000235975.2	205844	205844	type	True	80.3669	519	1326	95	below_threshold
Novosphingobium lindaniclasticum	strain=LE124	GCA_000445125.1	1329895	1329895	type	True	80.2759	548	1326	95	below_threshold
Novosphingobium percolationis	strain=c1	GCA_020179425.1	2871811	2871811	type	True	79.9538	370	1326	95	below_threshold
Novosphingobium decolorationis	strain=502str22	GCA_018417475.1	2698673	2698673	type	True	79.7701	478	1326	95	below_threshold
Novosphingobium mathurense	strain=SM117	GCA_900168325.1	428990	428990	type	True	79.7359	485	1326	95	below_threshold
Novosphingobium aureum	strain=YJ-S2-02	GCA_015865035.1	2792964	2792964	type	True	79.685	467	1326	95	below_threshold
Novosphingobium indicum	strain=CGMCC 1.6784	GCA_014645195.1	462949	462949	type	True	79.5911	547	1326	95	below_threshold
Novosphingobium profundi	strain=F72	GCA_018491765.1	1774954	1774954	type	True	79.4872	480	1326	95	below_threshold
Novosphingobium endophyticum	strain=CGMCC 1.15095	GCA_014640675.1	1955250	1955250	type	True	79.3492	475	1326	95	below_threshold
Novosphingobium huizhouense	strain=c7	GCA_020179475.1	2866625	2866625	type	True	78.883	365	1326	95	below_threshold
Novosphingobium aquimarinum	strain=M24A2M	GCA_009746585.1	2682494	2682494	type	True	78.7947	369	1326	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:19:47,438] [INFO] DFAST Taxonomy check result was written to GCF_900182875.1_IMG-taxon_2706794921_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:19:47,439] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:19:47,439] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:19:47,440] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb107a7b4-a3d4-4bf6-89ce-bed7769e7a5b/dqc_reference/checkm_data
[2024-01-24 14:19:47,441] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:19:47,494] [INFO] Task started: CheckM
[2024-01-24 14:19:47,494] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900182875.1_IMG-taxon_2706794921_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900182875.1_IMG-taxon_2706794921_annotated_assembly_genomic.fna/checkm_input GCF_900182875.1_IMG-taxon_2706794921_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:20:28,476] [INFO] Task succeeded: CheckM
[2024-01-24 14:20:28,478] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:20:28,498] [INFO] ===== Completeness check finished =====
[2024-01-24 14:20:28,499] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:20:28,499] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900182875.1_IMG-taxon_2706794921_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:20:28,500] [INFO] Task started: Blastn
[2024-01-24 14:20:28,500] [INFO] Running command: blastn -query GCF_900182875.1_IMG-taxon_2706794921_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgb107a7b4-a3d4-4bf6-89ce-bed7769e7a5b/dqc_reference/reference_markers_gtdb.fasta -out GCF_900182875.1_IMG-taxon_2706794921_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:30,230] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:30,234] [INFO] Selected 14 target genomes.
[2024-01-24 14:20:30,234] [INFO] Target genome list was writen to GCF_900182875.1_IMG-taxon_2706794921_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:20:30,250] [INFO] Task started: fastANI
[2024-01-24 14:20:30,251] [INFO] Running command: fastANI --query /var/lib/cwl/stg5d8b47d8-cd2a-4155-9a66-0c7e0d89271b/GCF_900182875.1_IMG-taxon_2706794921_annotated_assembly_genomic.fna.gz --refList GCF_900182875.1_IMG-taxon_2706794921_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900182875.1_IMG-taxon_2706794921_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:20:43,735] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:43,747] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:20:43,748] [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_002916655.1	s__Novosphingobium sp002916655	98.351	1023	1326	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_002896965.1	s__Novosphingobium guangzhouense	82.0014	715	1326	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001742225.1	s__Novosphingobium resinovorum	81.6686	753	1326	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	98.22	97.83	0.80	0.78	4	-
GCF_000281975.1	s__Novosphingobium sp000281975	81.2313	655	1326	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	80.7898	628	1326	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	80.4748	622	1326	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_006874585.1	s__Novosphingobium sp006874585	80.4159	601	1326	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	80.3808	512	1326	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	96.84	95.17	0.76	0.62	4	-
GCF_007993975.1	s__Novosphingobium barchaimii_B	80.2201	577	1326	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017745295.1	s__Novosphingobium sp017745295	80.0999	535	1326	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900168325.1	s__Novosphingobium mathurense	79.725	486	1326	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	99.03	99.03	0.83	0.83	2	-
GCF_001421325.1	s__Novosphingobium sp001421325	79.6955	512	1326	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	79.6795	468	1326	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	79.5038	448	1326	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 14:20:43,749] [INFO] GTDB search result was written to GCF_900182875.1_IMG-taxon_2706794921_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:20:43,750] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:20:43,755] [INFO] DFAST_QC result json was written to GCF_900182875.1_IMG-taxon_2706794921_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:20:43,755] [INFO] DFAST_QC completed!
[2024-01-24 14:20:43,755] [INFO] Total running time: 0h1m26s