[2024-01-24 14:19:46,578] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:46,580] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:46,581] [INFO] DQC Reference Directory: /var/lib/cwl/stge1d4e89a-87a1-41f5-a1d4-f34d70eb0625/dqc_reference
[2024-01-24 14:19:47,976] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:47,977] [INFO] Task started: Prodigal
[2024-01-24 14:19:47,978] [INFO] Running command: gunzip -c /var/lib/cwl/stgfe674df1-d9fd-4602-8784-aa964cc68b3b/GCF_007830315.1_ASM783031v1_genomic.fna.gz | prodigal -d GCF_007830315.1_ASM783031v1_genomic.fna/cds.fna -a GCF_007830315.1_ASM783031v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:20:03,113] [INFO] Task succeeded: Prodigal
[2024-01-24 14:20:03,114] [INFO] Task started: HMMsearch
[2024-01-24 14:20:03,114] [INFO] Running command: hmmsearch --tblout GCF_007830315.1_ASM783031v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge1d4e89a-87a1-41f5-a1d4-f34d70eb0625/dqc_reference/reference_markers.hmm GCF_007830315.1_ASM783031v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:20:03,387] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:20:03,388] [INFO] Found 6/6 markers.
[2024-01-24 14:20:03,428] [INFO] Query marker FASTA was written to GCF_007830315.1_ASM783031v1_genomic.fna/markers.fasta
[2024-01-24 14:20:03,429] [INFO] Task started: Blastn
[2024-01-24 14:20:03,429] [INFO] Running command: blastn -query GCF_007830315.1_ASM783031v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge1d4e89a-87a1-41f5-a1d4-f34d70eb0625/dqc_reference/reference_markers.fasta -out GCF_007830315.1_ASM783031v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:04,452] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:04,455] [INFO] Selected 10 target genomes.
[2024-01-24 14:20:04,456] [INFO] Target genome list was writen to GCF_007830315.1_ASM783031v1_genomic.fna/target_genomes.txt
[2024-01-24 14:20:04,462] [INFO] Task started: fastANI
[2024-01-24 14:20:04,462] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe674df1-d9fd-4602-8784-aa964cc68b3b/GCF_007830315.1_ASM783031v1_genomic.fna.gz --refList GCF_007830315.1_ASM783031v1_genomic.fna/target_genomes.txt --output GCF_007830315.1_ASM783031v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:20:14,134] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:14,134] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge1d4e89a-87a1-41f5-a1d4-f34d70eb0625/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:20:14,134] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge1d4e89a-87a1-41f5-a1d4-f34d70eb0625/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:20:14,144] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:20:14,144] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:20:14,144] [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 taihuense	strain=CGMCC 1.3432	GCA_007830315.1	260085	260085	type	True	100.0	1474	1477	95	conclusive
Novosphingobium taihuense	strain=DSM 17507	GCA_014199635.1	260085	260085	type	True	99.9973	1453	1477	95	conclusive
Novosphingobium jiangmenense	strain=1Y9A	GCA_015694345.1	2791981	2791981	type	True	85.9102	1002	1477	95	below_threshold
Novosphingobium subterraneum	strain=NBRC 16086	GCA_001598575.1	48936	48936	type	True	85.113	955	1477	95	below_threshold
Novosphingobium subterraneum	strain=DSM 12447	GCA_000807925.1	48936	48936	type	True	85.1085	991	1477	95	below_threshold
Novosphingobium percolationis	strain=c1	GCA_020179425.1	2871811	2871811	type	True	81.1153	653	1477	95	below_threshold
Novosphingobium huizhouense	strain=c7	GCA_020179475.1	2866625	2866625	type	True	81.1015	634	1477	95	below_threshold
Novosphingobium decolorationis	strain=502str22	GCA_018417475.1	2698673	2698673	type	True	78.8962	394	1477	95	below_threshold
Novosphingobium silvae	strain=FGD1	GCA_009856825.1	2692619	2692619	type	True	78.7786	384	1477	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	78.2559	335	1477	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:20:14,145] [INFO] DFAST Taxonomy check result was written to GCF_007830315.1_ASM783031v1_genomic.fna/tc_result.tsv
[2024-01-24 14:20:14,146] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:20:14,146] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:20:14,146] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge1d4e89a-87a1-41f5-a1d4-f34d70eb0625/dqc_reference/checkm_data
[2024-01-24 14:20:14,147] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:20:14,190] [INFO] Task started: CheckM
[2024-01-24 14:20:14,190] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007830315.1_ASM783031v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007830315.1_ASM783031v1_genomic.fna/checkm_input GCF_007830315.1_ASM783031v1_genomic.fna/checkm_result
[2024-01-24 14:20:57,519] [INFO] Task succeeded: CheckM
[2024-01-24 14:20:57,520] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:20:57,537] [INFO] ===== Completeness check finished =====
[2024-01-24 14:20:57,537] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:20:57,538] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007830315.1_ASM783031v1_genomic.fna/markers.fasta)
[2024-01-24 14:20:57,538] [INFO] Task started: Blastn
[2024-01-24 14:20:57,538] [INFO] Running command: blastn -query GCF_007830315.1_ASM783031v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge1d4e89a-87a1-41f5-a1d4-f34d70eb0625/dqc_reference/reference_markers_gtdb.fasta -out GCF_007830315.1_ASM783031v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:59,225] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:59,228] [INFO] Selected 7 target genomes.
[2024-01-24 14:20:59,229] [INFO] Target genome list was writen to GCF_007830315.1_ASM783031v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:20:59,239] [INFO] Task started: fastANI
[2024-01-24 14:20:59,239] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe674df1-d9fd-4602-8784-aa964cc68b3b/GCF_007830315.1_ASM783031v1_genomic.fna.gz --refList GCF_007830315.1_ASM783031v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007830315.1_ASM783031v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:21:06,961] [INFO] Task succeeded: fastANI
[2024-01-24 14:21:06,968] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:21:06,969] [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_007830315.1	s__Novosphingobium taihuense	100.0	1474	1477	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	100.00	100.00	0.99	0.99	2	conclusive
GCF_015694345.1	s__Novosphingobium jiangmenense	85.9145	1003	1477	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003454795.1	s__Novosphingobium sp003454795	85.6599	1044	1477	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	98.02	97.88	0.92	0.91	3	-
GCF_000807925.1	s__Novosphingobium subterraneum	85.1222	989	1477	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	98.63	97.57	0.88	0.77	4	-
GCF_900176395.1	s__Novosphingobium sp900176395	83.9482	883	1477	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012641335.1	s__Novosphingobium sp012641335	83.3736	931	1477	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000013325.1	s__Novosphingobium aromaticivorans	83.3605	870	1477	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:21:06,970] [INFO] GTDB search result was written to GCF_007830315.1_ASM783031v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:21:06,971] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:21:06,973] [INFO] DFAST_QC result json was written to GCF_007830315.1_ASM783031v1_genomic.fna/dqc_result.json
[2024-01-24 14:21:06,974] [INFO] DFAST_QC completed!
[2024-01-24 14:21:06,974] [INFO] Total running time: 0h1m20s