[2024-01-25 17:49:50,723] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:49:50,724] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:49:50,724] [INFO] DQC Reference Directory: /var/lib/cwl/stg25a1829e-bd09-4f70-bdb5-cc357ecf7997/dqc_reference
[2024-01-25 17:49:51,942] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:49:51,942] [INFO] Task started: Prodigal
[2024-01-25 17:49:51,943] [INFO] Running command: gunzip -c /var/lib/cwl/stge27330e6-6437-45f3-bf0e-34fee0db6015/GCF_002374855.1_ASM237485v1_genomic.fna.gz | prodigal -d GCF_002374855.1_ASM237485v1_genomic.fna/cds.fna -a GCF_002374855.1_ASM237485v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:50:01,733] [INFO] Task succeeded: Prodigal
[2024-01-25 17:50:01,734] [INFO] Task started: HMMsearch
[2024-01-25 17:50:01,734] [INFO] Running command: hmmsearch --tblout GCF_002374855.1_ASM237485v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg25a1829e-bd09-4f70-bdb5-cc357ecf7997/dqc_reference/reference_markers.hmm GCF_002374855.1_ASM237485v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:50:01,940] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:50:01,941] [INFO] Found 6/6 markers.
[2024-01-25 17:50:01,971] [INFO] Query marker FASTA was written to GCF_002374855.1_ASM237485v1_genomic.fna/markers.fasta
[2024-01-25 17:50:01,971] [INFO] Task started: Blastn
[2024-01-25 17:50:01,971] [INFO] Running command: blastn -query GCF_002374855.1_ASM237485v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg25a1829e-bd09-4f70-bdb5-cc357ecf7997/dqc_reference/reference_markers.fasta -out GCF_002374855.1_ASM237485v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:50:02,899] [INFO] Task succeeded: Blastn
[2024-01-25 17:50:02,903] [INFO] Selected 10 target genomes.
[2024-01-25 17:50:02,903] [INFO] Target genome list was writen to GCF_002374855.1_ASM237485v1_genomic.fna/target_genomes.txt
[2024-01-25 17:50:02,913] [INFO] Task started: fastANI
[2024-01-25 17:50:02,913] [INFO] Running command: fastANI --query /var/lib/cwl/stge27330e6-6437-45f3-bf0e-34fee0db6015/GCF_002374855.1_ASM237485v1_genomic.fna.gz --refList GCF_002374855.1_ASM237485v1_genomic.fna/target_genomes.txt --output GCF_002374855.1_ASM237485v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:50:13,023] [INFO] Task succeeded: fastANI
[2024-01-25 17:50:13,023] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg25a1829e-bd09-4f70-bdb5-cc357ecf7997/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:50:13,024] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg25a1829e-bd09-4f70-bdb5-cc357ecf7997/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:50:13,031] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 17:50:13,032] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:50:13,032] [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
Sphingomonas adhaesiva	strain=DSM 7418	GCA_002374855.1	28212	28212	type	True	100.0	1233	1238	95	conclusive
Sphingomonas adhaesiva	strain=NBRC 15099	GCA_001592345.1	28212	28212	type	True	99.6553	932	1238	95	conclusive
Sphingomonas ginsenosidimutans	strain=KACC 14949	GCA_002374835.1	862134	862134	type	True	92.7669	1018	1238	95	below_threshold
Sphingomonas endophytica	strain=DSM 101535	GCA_014199415.1	869719	869719	type	True	83.2013	709	1238	95	below_threshold
Sphingomonas phyllosphaerae	strain=FA2	GCA_000427645.1	257003	257003	type	True	82.8817	725	1238	95	below_threshold
Sphingomonas corticis	strain=36D10-4-7	GCA_012035195.1	2722791	2722791	type	True	82.6864	772	1238	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	82.5764	730	1238	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	82.443	738	1238	95	below_threshold
Sphingomonas yunnanensis	strain=YIM 3	GCA_019898765.1	310400	310400	type	True	82.1018	719	1238	95	below_threshold
Sphingomonas aracearum	strain=WZY 27	GCA_003345355.1	2283317	2283317	type	True	80.4403	589	1238	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:50:13,033] [INFO] DFAST Taxonomy check result was written to GCF_002374855.1_ASM237485v1_genomic.fna/tc_result.tsv
[2024-01-25 17:50:13,034] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:50:13,034] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:50:13,034] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg25a1829e-bd09-4f70-bdb5-cc357ecf7997/dqc_reference/checkm_data
[2024-01-25 17:50:13,035] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:50:13,077] [INFO] Task started: CheckM
[2024-01-25 17:50:13,077] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002374855.1_ASM237485v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002374855.1_ASM237485v1_genomic.fna/checkm_input GCF_002374855.1_ASM237485v1_genomic.fna/checkm_result
[2024-01-25 17:50:49,843] [INFO] Task succeeded: CheckM
[2024-01-25 17:50:49,844] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:50:49,862] [INFO] ===== Completeness check finished =====
[2024-01-25 17:50:49,862] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:50:49,863] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002374855.1_ASM237485v1_genomic.fna/markers.fasta)
[2024-01-25 17:50:49,863] [INFO] Task started: Blastn
[2024-01-25 17:50:49,863] [INFO] Running command: blastn -query GCF_002374855.1_ASM237485v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg25a1829e-bd09-4f70-bdb5-cc357ecf7997/dqc_reference/reference_markers_gtdb.fasta -out GCF_002374855.1_ASM237485v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:50:51,779] [INFO] Task succeeded: Blastn
[2024-01-25 17:50:51,785] [INFO] Selected 14 target genomes.
[2024-01-25 17:50:51,785] [INFO] Target genome list was writen to GCF_002374855.1_ASM237485v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:50:51,820] [INFO] Task started: fastANI
[2024-01-25 17:50:51,821] [INFO] Running command: fastANI --query /var/lib/cwl/stge27330e6-6437-45f3-bf0e-34fee0db6015/GCF_002374855.1_ASM237485v1_genomic.fna.gz --refList GCF_002374855.1_ASM237485v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002374855.1_ASM237485v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:51:05,630] [INFO] Task succeeded: fastANI
[2024-01-25 17:51:05,640] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:51:05,640] [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_002374855.1	s__Sphingomonas adhaesiva	100.0	1233	1238	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.76	99.56	0.89	0.87	3	conclusive
GCF_002374835.1	s__Sphingomonas ginsenosidimutans	92.7445	1020	1238	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.62	98.43	0.85	0.81	6	-
GCA_003243195.1	s__Sphingomonas taxi_B	84.0234	736	1238	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001476895.1	s__Sphingomonas endophytica_A	83.6434	699	1238	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199415.1	s__Sphingomonas endophytica	83.1495	714	1238	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.00	98.00	0.92	0.92	2	-
GCF_902506455.1	s__Sphingomonas sp902506455	82.8928	697	1238	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001421995.1	s__Sphingomonas sp001421995	82.8902	679	1238	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000427645.1	s__Sphingomonas phyllosphaerae	82.8608	726	1238	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425405.1	s__Sphingomonas sp001425405	82.6786	740	1238	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012035195.1	s__Sphingomonas sp012035195	82.6214	778	1238	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000419605.1	s__Sphingomonas phyllosphaerae_B	82.5514	688	1238	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004345855.1	s__Sphingomonas sp004345855	82.4404	774	1238	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014194975.1	s__Sphingomonas sp014194975	82.2173	744	1238	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014193845.1	s__Sphingomonas sp014193845	82.1905	733	1238	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.90	98.90	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2024-01-25 17:51:05,642] [INFO] GTDB search result was written to GCF_002374855.1_ASM237485v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:51:05,643] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:51:05,649] [INFO] DFAST_QC result json was written to GCF_002374855.1_ASM237485v1_genomic.fna/dqc_result.json
[2024-01-25 17:51:05,649] [INFO] DFAST_QC completed!
[2024-01-25 17:51:05,649] [INFO] Total running time: 0h1m15s