[2024-01-25 19:59:35,610] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:59:35,612] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:59:35,612] [INFO] DQC Reference Directory: /var/lib/cwl/stgec0a4921-b179-4338-84b4-4474bb18bf33/dqc_reference
[2024-01-25 19:59:36,856] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:59:36,857] [INFO] Task started: Prodigal
[2024-01-25 19:59:36,857] [INFO] Running command: gunzip -c /var/lib/cwl/stg9c4fb5d4-50d2-45b8-b4ec-6352e5b64a1e/GCF_015694345.1_ASM1569434v1_genomic.fna.gz | prodigal -d GCF_015694345.1_ASM1569434v1_genomic.fna/cds.fna -a GCF_015694345.1_ASM1569434v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:59:48,488] [INFO] Task succeeded: Prodigal
[2024-01-25 19:59:48,488] [INFO] Task started: HMMsearch
[2024-01-25 19:59:48,489] [INFO] Running command: hmmsearch --tblout GCF_015694345.1_ASM1569434v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgec0a4921-b179-4338-84b4-4474bb18bf33/dqc_reference/reference_markers.hmm GCF_015694345.1_ASM1569434v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:59:48,789] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:59:48,790] [INFO] Found 6/6 markers.
[2024-01-25 19:59:48,837] [INFO] Query marker FASTA was written to GCF_015694345.1_ASM1569434v1_genomic.fna/markers.fasta
[2024-01-25 19:59:48,837] [INFO] Task started: Blastn
[2024-01-25 19:59:48,837] [INFO] Running command: blastn -query GCF_015694345.1_ASM1569434v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgec0a4921-b179-4338-84b4-4474bb18bf33/dqc_reference/reference_markers.fasta -out GCF_015694345.1_ASM1569434v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:59:49,813] [INFO] Task succeeded: Blastn
[2024-01-25 19:59:49,816] [INFO] Selected 12 target genomes.
[2024-01-25 19:59:49,816] [INFO] Target genome list was writen to GCF_015694345.1_ASM1569434v1_genomic.fna/target_genomes.txt
[2024-01-25 19:59:49,831] [INFO] Task started: fastANI
[2024-01-25 19:59:49,831] [INFO] Running command: fastANI --query /var/lib/cwl/stg9c4fb5d4-50d2-45b8-b4ec-6352e5b64a1e/GCF_015694345.1_ASM1569434v1_genomic.fna.gz --refList GCF_015694345.1_ASM1569434v1_genomic.fna/target_genomes.txt --output GCF_015694345.1_ASM1569434v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:00:00,876] [INFO] Task succeeded: fastANI
[2024-01-25 20:00:00,877] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgec0a4921-b179-4338-84b4-4474bb18bf33/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:00:00,877] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgec0a4921-b179-4338-84b4-4474bb18bf33/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:00:00,885] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:00:00,886] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:00:00,886] [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 jiangmenense	strain=1Y9A	GCA_015694345.1	2791981	2791981	type	True	100.0	1345	1347	95	conclusive
Novosphingobium subterraneum	strain=DSM 12447	GCA_000807925.1	48936	48936	type	True	86.8949	1018	1347	95	below_threshold
Novosphingobium subterraneum	strain=NBRC 16086	GCA_001598575.1	48936	48936	type	True	86.8811	979	1347	95	below_threshold
Novosphingobium taihuense	strain=DSM 17507	GCA_014199635.1	260085	260085	type	True	86.098	988	1347	95	below_threshold
Novosphingobium taihuense	strain=CGMCC 1.3432	GCA_007830315.1	260085	260085	type	True	86.0605	999	1347	95	below_threshold
Novosphingobium aromaticivorans	strain=DSM 12444	GCA_000013325.1	48935	48935	type	True	83.8674	924	1347	95	below_threshold
Novosphingobium meiothermophilum	strain=SYSU G00007	GCA_003171715.1	2202251	2202251	type	True	82.3183	796	1347	95	below_threshold
Novosphingobium huizhouense	strain=c7	GCA_020179475.1	2866625	2866625	type	True	81.8096	674	1347	95	below_threshold
Novosphingobium percolationis	strain=c1	GCA_020179425.1	2871811	2871811	type	True	81.6284	698	1347	95	below_threshold
Novosphingobium silvae	strain=FGD1	GCA_009856825.1	2692619	2692619	type	True	78.9425	404	1347	95	below_threshold
Novosphingobium aquimarinum	strain=M24A2M	GCA_009746585.1	2682494	2682494	type	True	78.6921	410	1347	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	78.5268	378	1347	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:00:00,887] [INFO] DFAST Taxonomy check result was written to GCF_015694345.1_ASM1569434v1_genomic.fna/tc_result.tsv
[2024-01-25 20:00:00,888] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:00:00,888] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:00:00,888] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgec0a4921-b179-4338-84b4-4474bb18bf33/dqc_reference/checkm_data
[2024-01-25 20:00:00,889] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:00:00,931] [INFO] Task started: CheckM
[2024-01-25 20:00:00,931] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015694345.1_ASM1569434v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015694345.1_ASM1569434v1_genomic.fna/checkm_input GCF_015694345.1_ASM1569434v1_genomic.fna/checkm_result
[2024-01-25 20:00:38,148] [INFO] Task succeeded: CheckM
[2024-01-25 20:00:38,149] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:00:38,166] [INFO] ===== Completeness check finished =====
[2024-01-25 20:00:38,167] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:00:38,168] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015694345.1_ASM1569434v1_genomic.fna/markers.fasta)
[2024-01-25 20:00:38,168] [INFO] Task started: Blastn
[2024-01-25 20:00:38,168] [INFO] Running command: blastn -query GCF_015694345.1_ASM1569434v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgec0a4921-b179-4338-84b4-4474bb18bf33/dqc_reference/reference_markers_gtdb.fasta -out GCF_015694345.1_ASM1569434v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:00:40,031] [INFO] Task succeeded: Blastn
[2024-01-25 20:00:40,034] [INFO] Selected 7 target genomes.
[2024-01-25 20:00:40,035] [INFO] Target genome list was writen to GCF_015694345.1_ASM1569434v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:00:40,044] [INFO] Task started: fastANI
[2024-01-25 20:00:40,044] [INFO] Running command: fastANI --query /var/lib/cwl/stg9c4fb5d4-50d2-45b8-b4ec-6352e5b64a1e/GCF_015694345.1_ASM1569434v1_genomic.fna.gz --refList GCF_015694345.1_ASM1569434v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015694345.1_ASM1569434v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:00:47,376] [INFO] Task succeeded: fastANI
[2024-01-25 20:00:47,382] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:00:47,382] [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_015694345.1	s__Novosphingobium jiangmenense	100.0	1345	1347	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_003454795.1	s__Novosphingobium sp003454795	87.7765	1064	1347	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	86.9014	1018	1347	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	98.63	97.57	0.88	0.77	4	-
GCF_007830315.1	s__Novosphingobium taihuense	86.0583	999	1347	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900176395.1	s__Novosphingobium sp900176395	85.1826	862	1347	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	83.8489	924	1347	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_012641335.1	s__Novosphingobium sp012641335	82.6952	879	1347	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:00:47,383] [INFO] GTDB search result was written to GCF_015694345.1_ASM1569434v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:00:47,384] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:00:47,386] [INFO] DFAST_QC result json was written to GCF_015694345.1_ASM1569434v1_genomic.fna/dqc_result.json
[2024-01-25 20:00:47,387] [INFO] DFAST_QC completed!
[2024-01-25 20:00:47,387] [INFO] Total running time: 0h1m12s