[2024-01-24 13:28:01,793] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:01,802] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:01,802] [INFO] DQC Reference Directory: /var/lib/cwl/stgc026386d-8cbc-4850-bf3d-febf3e1453d4/dqc_reference
[2024-01-24 13:28:03,126] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:03,126] [INFO] Task started: Prodigal
[2024-01-24 13:28:03,126] [INFO] Running command: gunzip -c /var/lib/cwl/stgfe8221a3-0c45-4348-9552-7a1f52ad3120/GCF_000427645.1_ASM42764v1_genomic.fna.gz | prodigal -d GCF_000427645.1_ASM42764v1_genomic.fna/cds.fna -a GCF_000427645.1_ASM42764v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:14,499] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:14,499] [INFO] Task started: HMMsearch
[2024-01-24 13:28:14,500] [INFO] Running command: hmmsearch --tblout GCF_000427645.1_ASM42764v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc026386d-8cbc-4850-bf3d-febf3e1453d4/dqc_reference/reference_markers.hmm GCF_000427645.1_ASM42764v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:14,734] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:14,736] [INFO] Found 6/6 markers.
[2024-01-24 13:28:14,773] [INFO] Query marker FASTA was written to GCF_000427645.1_ASM42764v1_genomic.fna/markers.fasta
[2024-01-24 13:28:14,774] [INFO] Task started: Blastn
[2024-01-24 13:28:14,774] [INFO] Running command: blastn -query GCF_000427645.1_ASM42764v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc026386d-8cbc-4850-bf3d-febf3e1453d4/dqc_reference/reference_markers.fasta -out GCF_000427645.1_ASM42764v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:15,809] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:15,812] [INFO] Selected 13 target genomes.
[2024-01-24 13:28:15,813] [INFO] Target genome list was writen to GCF_000427645.1_ASM42764v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:15,814] [INFO] Task started: fastANI
[2024-01-24 13:28:15,814] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe8221a3-0c45-4348-9552-7a1f52ad3120/GCF_000427645.1_ASM42764v1_genomic.fna.gz --refList GCF_000427645.1_ASM42764v1_genomic.fna/target_genomes.txt --output GCF_000427645.1_ASM42764v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:30,014] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:30,014] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc026386d-8cbc-4850-bf3d-febf3e1453d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:30,014] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc026386d-8cbc-4850-bf3d-febf3e1453d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:30,025] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:28:30,025] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:30,026] [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 phyllosphaerae	strain=FA2	GCA_000427645.1	257003	257003	type	True	100.0	1306	1306	95	conclusive
Sphingomonas endophytica	strain=DSM 101535	GCA_014199415.1	869719	869719	type	True	90.3835	967	1306	95	below_threshold
Sphingomonas adhaesiva	strain=NBRC 15099	GCA_001592345.1	28212	28212	type	True	83.1699	583	1306	95	below_threshold
Sphingomonas adhaesiva	strain=DSM 7418	GCA_002374855.1	28212	28212	type	True	82.9743	715	1306	95	below_threshold
Sphingomonas ginsenosidimutans	strain=KACC 14949	GCA_002374835.1	862134	862134	type	True	82.8087	721	1306	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	82.7493	807	1306	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	82.6247	819	1306	95	below_threshold
Sphingomonas yunnanensis	strain=YIM 3	GCA_019898765.1	310400	310400	type	True	82.4856	807	1306	95	below_threshold
Sphingomonas citricola	strain=RHCKR47	GCA_019429535.1	2862498	2862498	type	True	81.2344	655	1306	95	below_threshold
Sphingomonas corticis	strain=36D10-4-7	GCA_012035195.1	2722791	2722791	type	True	81.137	678	1306	95	below_threshold
Sphingomonas metalli	strain=CGMCC 1.15330	GCA_014641735.1	1779358	1779358	type	True	80.7801	599	1306	95	below_threshold
Sphingomonas melonis	strain=DAPP-PG 224	GCA_000379045.1	152682	152682	type	True	80.6742	614	1306	95	below_threshold
Sphingomonas pseudosanguinis	strain=DSM 19512	GCA_014196255.1	413712	413712	type	True	80.3347	626	1306	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:30,028] [INFO] DFAST Taxonomy check result was written to GCF_000427645.1_ASM42764v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:30,029] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:30,029] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:30,029] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc026386d-8cbc-4850-bf3d-febf3e1453d4/dqc_reference/checkm_data
[2024-01-24 13:28:30,030] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:30,070] [INFO] Task started: CheckM
[2024-01-24 13:28:30,070] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000427645.1_ASM42764v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000427645.1_ASM42764v1_genomic.fna/checkm_input GCF_000427645.1_ASM42764v1_genomic.fna/checkm_result
[2024-01-24 13:29:06,138] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:06,139] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:06,156] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:06,156] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:06,157] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000427645.1_ASM42764v1_genomic.fna/markers.fasta)
[2024-01-24 13:29:06,157] [INFO] Task started: Blastn
[2024-01-24 13:29:06,157] [INFO] Running command: blastn -query GCF_000427645.1_ASM42764v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc026386d-8cbc-4850-bf3d-febf3e1453d4/dqc_reference/reference_markers_gtdb.fasta -out GCF_000427645.1_ASM42764v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:08,037] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:08,040] [INFO] Selected 10 target genomes.
[2024-01-24 13:29:08,040] [INFO] Target genome list was writen to GCF_000427645.1_ASM42764v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:08,044] [INFO] Task started: fastANI
[2024-01-24 13:29:08,044] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe8221a3-0c45-4348-9552-7a1f52ad3120/GCF_000427645.1_ASM42764v1_genomic.fna.gz --refList GCF_000427645.1_ASM42764v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000427645.1_ASM42764v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:18,525] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:18,534] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:18,534] [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_000427645.1	s__Sphingomonas phyllosphaerae	100.0	1306	1306	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014199415.1	s__Sphingomonas endophytica	90.3806	967	1306	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	89.5721	1017	1306	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	85.467	833	1306	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	85.1495	921	1306	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003243195.1	s__Sphingomonas taxi_B	84.9106	807	1306	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	84.5789	882	1306	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002374855.1	s__Sphingomonas adhaesiva	82.9563	715	1306	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.76	99.56	0.89	0.87	3	-
GCF_002374835.1	s__Sphingomonas ginsenosidimutans	82.8225	720	1306	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.62	98.43	0.85	0.81	6	-
GCF_014193845.1	s__Sphingomonas sp014193845	82.4808	818	1306	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.90	98.90	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:29:18,536] [INFO] GTDB search result was written to GCF_000427645.1_ASM42764v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:18,536] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:18,540] [INFO] DFAST_QC result json was written to GCF_000427645.1_ASM42764v1_genomic.fna/dqc_result.json
[2024-01-24 13:29:18,540] [INFO] DFAST_QC completed!
[2024-01-24 13:29:18,540] [INFO] Total running time: 0h1m17s