[2024-01-24 12:15:18,439] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:15:18,441] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:15:18,441] [INFO] DQC Reference Directory: /var/lib/cwl/stg22c3b3c0-a348-4e5e-b151-cfa987b2b4da/dqc_reference
[2024-01-24 12:15:19,764] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:15:19,765] [INFO] Task started: Prodigal
[2024-01-24 12:15:19,765] [INFO] Running command: gunzip -c /var/lib/cwl/stg8dabfb34-ccf4-466e-a9c6-9325b1d1a479/GCF_009856825.1_ASM985682v1_genomic.fna.gz | prodigal -d GCF_009856825.1_ASM985682v1_genomic.fna/cds.fna -a GCF_009856825.1_ASM985682v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:15:33,376] [INFO] Task succeeded: Prodigal
[2024-01-24 12:15:33,376] [INFO] Task started: HMMsearch
[2024-01-24 12:15:33,377] [INFO] Running command: hmmsearch --tblout GCF_009856825.1_ASM985682v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg22c3b3c0-a348-4e5e-b151-cfa987b2b4da/dqc_reference/reference_markers.hmm GCF_009856825.1_ASM985682v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:15:33,621] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:15:33,622] [INFO] Found 6/6 markers.
[2024-01-24 12:15:33,664] [INFO] Query marker FASTA was written to GCF_009856825.1_ASM985682v1_genomic.fna/markers.fasta
[2024-01-24 12:15:33,664] [INFO] Task started: Blastn
[2024-01-24 12:15:33,664] [INFO] Running command: blastn -query GCF_009856825.1_ASM985682v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg22c3b3c0-a348-4e5e-b151-cfa987b2b4da/dqc_reference/reference_markers.fasta -out GCF_009856825.1_ASM985682v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:34,658] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:34,661] [INFO] Selected 17 target genomes.
[2024-01-24 12:15:34,662] [INFO] Target genome list was writen to GCF_009856825.1_ASM985682v1_genomic.fna/target_genomes.txt
[2024-01-24 12:15:34,668] [INFO] Task started: fastANI
[2024-01-24 12:15:34,668] [INFO] Running command: fastANI --query /var/lib/cwl/stg8dabfb34-ccf4-466e-a9c6-9325b1d1a479/GCF_009856825.1_ASM985682v1_genomic.fna.gz --refList GCF_009856825.1_ASM985682v1_genomic.fna/target_genomes.txt --output GCF_009856825.1_ASM985682v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:50,084] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:50,085] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg22c3b3c0-a348-4e5e-b151-cfa987b2b4da/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:50,085] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg22c3b3c0-a348-4e5e-b151-cfa987b2b4da/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:50,099] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:15:50,099] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:15:50,099] [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 silvae	strain=FGD1	GCA_009856825.1	2692619	2692619	type	True	100.0	1485	1491	95	conclusive
Novosphingobium guangzhouense	strain=SA925	GCA_002896965.1	1850347	1850347	type	True	82.1787	801	1491	95	below_threshold
Novosphingobium barchaimii	strain=LL02	GCA_001046635.1	1420591	1420591	type	True	81.7252	826	1491	95	below_threshold
Novosphingobium lindaniclasticum	strain=LE124	GCA_000445125.1	1329895	1329895	type	True	81.4308	673	1491	95	below_threshold
Novosphingobium naphthalenivorans	strain=NBRC 102051	GCA_001590985.1	273168	273168	type	True	80.8575	621	1491	95	below_threshold
Novosphingobium decolorationis	strain=502str22	GCA_018417475.1	2698673	2698673	type	True	80.7687	608	1491	95	below_threshold
Novosphingobium profundi	strain=F72	GCA_018491765.1	1774954	1774954	type	True	80.5359	621	1491	95	below_threshold
Novosphingobium pentaromativorans	strain=US6-1	GCA_000767465.1	205844	205844	type	True	80.486	558	1491	95	below_threshold
Novosphingobium mathurense	strain=SM117	GCA_900168325.1	428990	428990	type	True	80.4695	552	1491	95	below_threshold
Novosphingobium aureum	strain=YJ-S2-02	GCA_015865035.1	2792964	2792964	type	True	80.4382	628	1491	95	below_threshold
Novosphingobium pentaromativorans	strain=US6-1	GCA_000235975.2	205844	205844	type	True	80.4366	551	1491	95	below_threshold
Novosphingobium indicum	strain=CGMCC 1.6784	GCA_014645195.1	462949	462949	type	True	80.2887	628	1491	95	below_threshold
Novosphingobium endophyticum	strain=CGMCC 1.15095	GCA_014640675.1	1955250	1955250	type	True	80.1263	554	1491	95	below_threshold
Novosphingobium colocasiae	strain=KCTC 32255	GCA_014652555.1	1256513	1256513	type	True	79.7896	516	1491	95	below_threshold
Novosphingobium huizhouense	strain=c7	GCA_020179475.1	2866625	2866625	type	True	79.1837	453	1491	95	below_threshold
Novosphingobium percolationis	strain=c1	GCA_020179425.1	2871811	2871811	type	True	79.072	437	1491	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	78.3669	343	1491	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:50,101] [INFO] DFAST Taxonomy check result was written to GCF_009856825.1_ASM985682v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:50,102] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:50,102] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:50,102] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg22c3b3c0-a348-4e5e-b151-cfa987b2b4da/dqc_reference/checkm_data
[2024-01-24 12:15:50,103] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:50,147] [INFO] Task started: CheckM
[2024-01-24 12:15:50,147] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009856825.1_ASM985682v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009856825.1_ASM985682v1_genomic.fna/checkm_input GCF_009856825.1_ASM985682v1_genomic.fna/checkm_result
[2024-01-24 12:16:29,849] [INFO] Task succeeded: CheckM
[2024-01-24 12:16:29,851] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:16:29,873] [INFO] ===== Completeness check finished =====
[2024-01-24 12:16:29,873] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:16:29,873] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009856825.1_ASM985682v1_genomic.fna/markers.fasta)
[2024-01-24 12:16:29,874] [INFO] Task started: Blastn
[2024-01-24 12:16:29,874] [INFO] Running command: blastn -query GCF_009856825.1_ASM985682v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg22c3b3c0-a348-4e5e-b151-cfa987b2b4da/dqc_reference/reference_markers_gtdb.fasta -out GCF_009856825.1_ASM985682v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:31,578] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:31,581] [INFO] Selected 19 target genomes.
[2024-01-24 12:16:31,581] [INFO] Target genome list was writen to GCF_009856825.1_ASM985682v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:16:31,594] [INFO] Task started: fastANI
[2024-01-24 12:16:31,594] [INFO] Running command: fastANI --query /var/lib/cwl/stg8dabfb34-ccf4-466e-a9c6-9325b1d1a479/GCF_009856825.1_ASM985682v1_genomic.fna.gz --refList GCF_009856825.1_ASM985682v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009856825.1_ASM985682v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:50,842] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:50,856] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:16:50,856] [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_009856825.1	s__Novosphingobium sp009856825	100.0	1485	1491	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_000281975.1	s__Novosphingobium sp000281975	83.5425	872	1491	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002149965.1	s__Novosphingobium panipatense	82.6218	804	1491	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	98.24	97.74	0.85	0.82	3	-
GCF_001742225.1	s__Novosphingobium resinovorum	82.4823	884	1491	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	98.22	97.83	0.80	0.78	4	-
GCF_002896965.1	s__Novosphingobium guangzhouense	82.1409	806	1491	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	81.9142	797	1491	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000876675.2	s__Novosphingobium sp000876675	81.91	840	1491	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	81.722	826	1491	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	81.7214	749	1491	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	98.32	98.32	0.81	0.81	2	-
GCF_002916655.1	s__Novosphingobium sp002916655	81.3763	650	1491	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	81.0951	668	1491	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007993975.1	s__Novosphingobium barchaimii_B	80.9155	718	1491	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	80.8333	711	1491	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	97.88	97.88	0.88	0.88	2	-
GCF_018417475.1	s__Novosphingobium sp000813185	80.7778	608	1491	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	97.53	97.53	0.86	0.86	2	-
GCF_900113255.1	s__Novosphingobium sp900113255	80.7325	582	1491	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	80.4692	560	1491	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	96.84	95.17	0.76	0.62	4	-
GCF_015865035.1	s__Novosphingobium sp015865035	80.4439	627	1491	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014640675.1	s__Novosphingobium endophyticum	80.1469	552	1491	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	79.7195	563	1491	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 12:16:50,858] [INFO] GTDB search result was written to GCF_009856825.1_ASM985682v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:50,860] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:50,864] [INFO] DFAST_QC result json was written to GCF_009856825.1_ASM985682v1_genomic.fna/dqc_result.json
[2024-01-24 12:16:50,864] [INFO] DFAST_QC completed!
[2024-01-24 12:16:50,864] [INFO] Total running time: 0h1m32s