[2023-06-30 06:33:22,294] [INFO] DFAST_QC pipeline started.
[2023-06-30 06:33:22,296] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 06:33:22,296] [INFO] DQC Reference Directory: /var/lib/cwl/stg93f63c66-3168-4e52-b805-1b0d7095ad95/dqc_reference
[2023-06-30 06:33:23,594] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 06:33:23,595] [INFO] Task started: Prodigal
[2023-06-30 06:33:23,595] [INFO] Running command: gunzip -c /var/lib/cwl/stga2178b39-ccbc-4f5f-9ffd-7d0030f80469/GCA_025359685.1_ASM2535968v1_genomic.fna.gz | prodigal -d GCA_025359685.1_ASM2535968v1_genomic.fna/cds.fna -a GCA_025359685.1_ASM2535968v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 06:33:30,883] [INFO] Task succeeded: Prodigal
[2023-06-30 06:33:30,883] [INFO] Task started: HMMsearch
[2023-06-30 06:33:30,884] [INFO] Running command: hmmsearch --tblout GCA_025359685.1_ASM2535968v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg93f63c66-3168-4e52-b805-1b0d7095ad95/dqc_reference/reference_markers.hmm GCA_025359685.1_ASM2535968v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 06:33:31,099] [INFO] Task succeeded: HMMsearch
[2023-06-30 06:33:31,100] [WARNING] Found 4/6 markers. [/var/lib/cwl/stga2178b39-ccbc-4f5f-9ffd-7d0030f80469/GCA_025359685.1_ASM2535968v1_genomic.fna.gz]
[2023-06-30 06:33:31,132] [INFO] Query marker FASTA was written to GCA_025359685.1_ASM2535968v1_genomic.fna/markers.fasta
[2023-06-30 06:33:31,133] [INFO] Task started: Blastn
[2023-06-30 06:33:31,133] [INFO] Running command: blastn -query GCA_025359685.1_ASM2535968v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg93f63c66-3168-4e52-b805-1b0d7095ad95/dqc_reference/reference_markers.fasta -out GCA_025359685.1_ASM2535968v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 06:33:31,970] [INFO] Task succeeded: Blastn
[2023-06-30 06:33:31,975] [INFO] Selected 16 target genomes.
[2023-06-30 06:33:31,976] [INFO] Target genome list was writen to GCA_025359685.1_ASM2535968v1_genomic.fna/target_genomes.txt
[2023-06-30 06:33:31,977] [INFO] Task started: fastANI
[2023-06-30 06:33:31,977] [INFO] Running command: fastANI --query /var/lib/cwl/stga2178b39-ccbc-4f5f-9ffd-7d0030f80469/GCA_025359685.1_ASM2535968v1_genomic.fna.gz --refList GCA_025359685.1_ASM2535968v1_genomic.fna/target_genomes.txt --output GCA_025359685.1_ASM2535968v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 06:33:42,758] [INFO] Task succeeded: fastANI
[2023-06-30 06:33:42,759] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg93f63c66-3168-4e52-b805-1b0d7095ad95/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 06:33:42,759] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg93f63c66-3168-4e52-b805-1b0d7095ad95/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 06:33:42,773] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 06:33:42,773] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 06:33:42,773] [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 kunmingense	strain=CGMCC 1.12274	GCA_002813245.1	1211806	1211806	type	True	79.7441	437	791	95	below_threshold
Novosphingobium arvoryzae	strain=KCTC 32422	GCA_014652615.1	1256514	1256514	type	True	79.5719	433	791	95	below_threshold
Novosphingobium ginsenosidimutans	strain=FW-6	GCA_007954425.1	1176536	1176536	type	True	79.3706	395	791	95	below_threshold
Novosphingobium lentum	strain=NBRC 107847	GCA_001590965.1	145287	145287	type	True	79.1853	375	791	95	below_threshold
Novosphingobium aerophilum	strain=4Y4	GCA_014230305.1	2839843	2839843	type	True	78.9323	337	791	95	below_threshold
Novosphingobium huizhouense	strain=c7	GCA_020179475.1	2866625	2866625	type	True	78.7006	367	791	95	below_threshold
Novosphingobium flavum	strain=NBRC 111647	GCA_014230315.1	1778672	1778672	type	True	78.6454	339	791	95	below_threshold
Novosphingobium colocasiae	strain=KCTC 32255	GCA_014652555.1	1256513	1256513	type	True	78.4731	304	791	95	below_threshold
Novosphingobium fuchskuhlense	strain=FNE08-7	GCA_001519075.1	1117702	1117702	type	True	78.4631	307	791	95	below_threshold
Novosphingobium percolationis	strain=c1	GCA_020179425.1	2871811	2871811	type	True	78.4573	344	791	95	below_threshold
Novosphingobium naphthalenivorans	strain=NBRC 102051	GCA_001590985.1	273168	273168	type	True	78.2284	300	791	95	below_threshold
Novosphingobium aureum	strain=YJ-S2-02	GCA_015865035.1	2792964	2792964	type	True	77.8822	280	791	95	below_threshold
Qipengyuania xiamenensis	strain=1XM1-15A	GCA_019711495.1	2867237	2867237	type	True	77.7731	225	791	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	77.725	261	791	95	below_threshold
Novosphingobium profundi	strain=F72	GCA_018491765.1	1774954	1774954	type	True	77.6574	268	791	95	below_threshold
Novosphingobium silvae	strain=FGD1	GCA_009856825.1	2692619	2692619	type	True	77.388	223	791	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 06:33:42,776] [INFO] DFAST Taxonomy check result was written to GCA_025359685.1_ASM2535968v1_genomic.fna/tc_result.tsv
[2023-06-30 06:33:42,777] [INFO] ===== Taxonomy check completed =====
[2023-06-30 06:33:42,777] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 06:33:42,778] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg93f63c66-3168-4e52-b805-1b0d7095ad95/dqc_reference/checkm_data
[2023-06-30 06:33:42,779] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 06:33:42,810] [INFO] Task started: CheckM
[2023-06-30 06:33:42,810] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_025359685.1_ASM2535968v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_025359685.1_ASM2535968v1_genomic.fna/checkm_input GCA_025359685.1_ASM2535968v1_genomic.fna/checkm_result
[2023-06-30 06:34:10,207] [INFO] Task succeeded: CheckM
[2023-06-30 06:34:10,208] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.61%
Contamintation: 7.41%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-30 06:34:10,234] [INFO] ===== Completeness check finished =====
[2023-06-30 06:34:10,235] [INFO] ===== Start GTDB Search =====
[2023-06-30 06:34:10,235] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_025359685.1_ASM2535968v1_genomic.fna/markers.fasta)
[2023-06-30 06:34:10,235] [INFO] Task started: Blastn
[2023-06-30 06:34:10,236] [INFO] Running command: blastn -query GCA_025359685.1_ASM2535968v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg93f63c66-3168-4e52-b805-1b0d7095ad95/dqc_reference/reference_markers_gtdb.fasta -out GCA_025359685.1_ASM2535968v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 06:34:11,686] [INFO] Task succeeded: Blastn
[2023-06-30 06:34:11,690] [INFO] Selected 16 target genomes.
[2023-06-30 06:34:11,690] [INFO] Target genome list was writen to GCA_025359685.1_ASM2535968v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 06:34:11,719] [INFO] Task started: fastANI
[2023-06-30 06:34:11,719] [INFO] Running command: fastANI --query /var/lib/cwl/stga2178b39-ccbc-4f5f-9ffd-7d0030f80469/GCA_025359685.1_ASM2535968v1_genomic.fna.gz --refList GCA_025359685.1_ASM2535968v1_genomic.fna/target_genomes_gtdb.txt --output GCA_025359685.1_ASM2535968v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 06:34:21,199] [INFO] Task succeeded: fastANI
[2023-06-30 06:34:21,216] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 06:34:21,217] [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
GCA_018334165.1	s__Novosphingobium sp018334165	80.6834	461	791	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	100.00	100.00	0.99	0.99	2	-
GCA_013822005.1	s__Novosphingobium sp013822005	80.6035	406	791	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002440635.1	s__Novosphingobium sp002440635	80.3654	493	791	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017302615.1	s__Novosphingobium sp017302615	80.2705	462	791	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015657645.1	s__Novosphingobium sp015657645	79.9378	400	791	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016719755.1	s__Novosphingobium sp016719755	79.8448	444	791	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	99.59	99.59	0.90	0.90	2	-
GCF_002813245.1	s__Novosphingobium kunmingense	79.7684	435	791	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013141325.1	s__Novosphingobium sp013141325	79.7317	364	791	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009926135.1	s__Novosphingobium sp009926135	79.6658	416	791	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002454125.1	s__Novosphingobium sp002454125	79.6065	370	791	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652615.1	s__Novosphingobium arvoryzae	79.5602	434	791	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017987575.1	s__Novosphingobium sp017987575	79.5494	344	791	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	99.30	99.30	0.83	0.83	2	-
GCA_009885425.1	s__Novosphingobium sp009885425	79.5468	273	791	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001590965.1	s__Novosphingobium lentum	79.1482	378	791	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240895.1	s__Novosphingobium sp018240895	78.7271	368	791	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902168115.1	s__Hansschlegelia sp902168115	76.1005	71	791	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methylopilaceae;g__Hansschlegelia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 06:34:21,218] [INFO] GTDB search result was written to GCA_025359685.1_ASM2535968v1_genomic.fna/result_gtdb.tsv
[2023-06-30 06:34:21,219] [INFO] ===== GTDB Search completed =====
[2023-06-30 06:34:21,223] [INFO] DFAST_QC result json was written to GCA_025359685.1_ASM2535968v1_genomic.fna/dqc_result.json
[2023-06-30 06:34:21,224] [INFO] DFAST_QC completed!
[2023-06-30 06:34:21,224] [INFO] Total running time: 0h0m59s