[2024-01-24 11:09:50,717] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:09:50,795] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:09:50,796] [INFO] DQC Reference Directory: /var/lib/cwl/stg19d3f555-5d23-4ae0-b24d-6571a010e761/dqc_reference
[2024-01-24 11:09:53,303] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:09:53,304] [INFO] Task started: Prodigal
[2024-01-24 11:09:53,304] [INFO] Running command: gunzip -c /var/lib/cwl/stgfb65d5c5-fb18-4cd7-addf-d6c0b508fdb3/GCF_016027095.1_ASM1602709v1_genomic.fna.gz | prodigal -d GCF_016027095.1_ASM1602709v1_genomic.fna/cds.fna -a GCF_016027095.1_ASM1602709v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:10:06,125] [INFO] Task succeeded: Prodigal
[2024-01-24 11:10:06,125] [INFO] Task started: HMMsearch
[2024-01-24 11:10:06,125] [INFO] Running command: hmmsearch --tblout GCF_016027095.1_ASM1602709v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg19d3f555-5d23-4ae0-b24d-6571a010e761/dqc_reference/reference_markers.hmm GCF_016027095.1_ASM1602709v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:10:06,384] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:10:06,385] [INFO] Found 6/6 markers.
[2024-01-24 11:10:06,427] [INFO] Query marker FASTA was written to GCF_016027095.1_ASM1602709v1_genomic.fna/markers.fasta
[2024-01-24 11:10:06,428] [INFO] Task started: Blastn
[2024-01-24 11:10:06,428] [INFO] Running command: blastn -query GCF_016027095.1_ASM1602709v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg19d3f555-5d23-4ae0-b24d-6571a010e761/dqc_reference/reference_markers.fasta -out GCF_016027095.1_ASM1602709v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:10:07,401] [INFO] Task succeeded: Blastn
[2024-01-24 11:10:07,405] [INFO] Selected 11 target genomes.
[2024-01-24 11:10:07,405] [INFO] Target genome list was writen to GCF_016027095.1_ASM1602709v1_genomic.fna/target_genomes.txt
[2024-01-24 11:10:07,410] [INFO] Task started: fastANI
[2024-01-24 11:10:07,410] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb65d5c5-fb18-4cd7-addf-d6c0b508fdb3/GCF_016027095.1_ASM1602709v1_genomic.fna.gz --refList GCF_016027095.1_ASM1602709v1_genomic.fna/target_genomes.txt --output GCF_016027095.1_ASM1602709v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:10:18,399] [INFO] Task succeeded: fastANI
[2024-01-24 11:10:18,400] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg19d3f555-5d23-4ae0-b24d-6571a010e761/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:10:18,400] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg19d3f555-5d23-4ae0-b24d-6571a010e761/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:10:18,417] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:10:18,417] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:10:18,417] [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 paucimobilis	strain=FDAARGOS_908	GCA_016027095.1	13689	13689	type	True	100.0	1452	1454	95	conclusive
Sphingomonas paucimobilis	strain=NBRC 13935	GCA_000739895.2	13689	13689	type	True	99.9648	1392	1454	95	conclusive
Sphingomonas pseudosanguinis	strain=DSM 19512	GCA_017052355.1	413712	413712	type	True	89.2911	1015	1454	95	below_threshold
Sphingomonas pseudosanguinis	strain=DSM 19512	GCA_014196255.1	413712	413712	type	True	89.2909	1018	1454	95	below_threshold
Sphingomonas yabuuchiae	strain=DSM 14562	GCA_017052455.1	172044	172044	type	True	87.3411	973	1454	95	below_threshold
Sphingomonas sanguinis	strain=NBRC 13937	GCA_001591005.1	33051	33051	suspected-type	True	87.0854	945	1454	95	below_threshold
Sphingomonas panni	strain=DSM 15761	GCA_022664435.1	237612	237612	type	True	79.864	616	1454	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	79.4809	626	1454	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	79.4505	611	1454	95	below_threshold
Sphingomonas yunnanensis	strain=YIM 3	GCA_019898765.1	310400	310400	type	True	79.325	594	1454	95	below_threshold
Sphingomonas alpina	strain=DSM 22537	GCA_025370095.1	653931	653931	type	True	79.0841	522	1454	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:10:18,419] [INFO] DFAST Taxonomy check result was written to GCF_016027095.1_ASM1602709v1_genomic.fna/tc_result.tsv
[2024-01-24 11:10:18,419] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:10:18,419] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:10:18,420] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg19d3f555-5d23-4ae0-b24d-6571a010e761/dqc_reference/checkm_data
[2024-01-24 11:10:18,420] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:10:18,465] [INFO] Task started: CheckM
[2024-01-24 11:10:18,466] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016027095.1_ASM1602709v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016027095.1_ASM1602709v1_genomic.fna/checkm_input GCF_016027095.1_ASM1602709v1_genomic.fna/checkm_result
[2024-01-24 11:10:57,642] [INFO] Task succeeded: CheckM
[2024-01-24 11:10:57,645] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:10:57,663] [INFO] ===== Completeness check finished =====
[2024-01-24 11:10:57,664] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:10:57,664] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016027095.1_ASM1602709v1_genomic.fna/markers.fasta)
[2024-01-24 11:10:57,664] [INFO] Task started: Blastn
[2024-01-24 11:10:57,665] [INFO] Running command: blastn -query GCF_016027095.1_ASM1602709v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg19d3f555-5d23-4ae0-b24d-6571a010e761/dqc_reference/reference_markers_gtdb.fasta -out GCF_016027095.1_ASM1602709v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:10:59,558] [INFO] Task succeeded: Blastn
[2024-01-24 11:10:59,560] [INFO] Selected 9 target genomes.
[2024-01-24 11:10:59,561] [INFO] Target genome list was writen to GCF_016027095.1_ASM1602709v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:10:59,583] [INFO] Task started: fastANI
[2024-01-24 11:10:59,583] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb65d5c5-fb18-4cd7-addf-d6c0b508fdb3/GCF_016027095.1_ASM1602709v1_genomic.fna.gz --refList GCF_016027095.1_ASM1602709v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016027095.1_ASM1602709v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:11:09,271] [INFO] Task succeeded: fastANI
[2024-01-24 11:11:09,280] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:11:09,280] [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_000739895.2	s__Sphingomonas paucimobilis	99.9648	1392	1454	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.74	99.40	0.92	0.87	13	conclusive
GCF_014196255.1	s__Sphingomonas pseudosanguinis	89.2764	1019	1454	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000787715.1	s__Sphingomonas parapaucimobilis	87.3958	903	1454	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	97.90	97.90	0.87	0.87	2	-
GCF_014199595.1	s__Sphingomonas yabuuchiae	87.2346	979	1454	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	97.94	96.78	0.92	0.88	4	-
GCF_014197135.1	s__Sphingomonas zeae	87.1163	968	1454	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001591005.1	s__Sphingomonas sanguinis	87.0938	945	1454	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.09	96.84	0.89	0.83	8	-
GCF_001477495.1	s__Sphingomonas yabuuchiae_A	87.0318	885	1454	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019112965.1	s__Sphingomonas excrementigallinarum	86.9491	854	1454	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001476905.1	s__Sphingomonas sanguinis_B	86.8196	884	1454	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	96.13	96.11	0.83	0.82	3	-
--------------------------------------------------------------------------------
[2024-01-24 11:11:09,282] [INFO] GTDB search result was written to GCF_016027095.1_ASM1602709v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:11:09,282] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:11:09,289] [INFO] DFAST_QC result json was written to GCF_016027095.1_ASM1602709v1_genomic.fna/dqc_result.json
[2024-01-24 11:11:09,291] [INFO] DFAST_QC completed!
[2024-01-24 11:11:09,291] [INFO] Total running time: 0h1m19s