[2024-01-24 12:14:09,982] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:09,989] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:09,989] [INFO] DQC Reference Directory: /var/lib/cwl/stg2e3316a6-0544-49a9-9713-e7a7f6dac8ce/dqc_reference
[2024-01-24 12:14:11,454] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:11,455] [INFO] Task started: Prodigal
[2024-01-24 12:14:11,455] [INFO] Running command: gunzip -c /var/lib/cwl/stg3db31249-2901-4da9-84c8-ee5eec412134/GCF_032334595.1_ASM3233459v1_genomic.fna.gz | prodigal -d GCF_032334595.1_ASM3233459v1_genomic.fna/cds.fna -a GCF_032334595.1_ASM3233459v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:25,834] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:25,835] [INFO] Task started: HMMsearch
[2024-01-24 12:14:25,835] [INFO] Running command: hmmsearch --tblout GCF_032334595.1_ASM3233459v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2e3316a6-0544-49a9-9713-e7a7f6dac8ce/dqc_reference/reference_markers.hmm GCF_032334595.1_ASM3233459v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:26,147] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:26,149] [INFO] Found 6/6 markers.
[2024-01-24 12:14:26,205] [INFO] Query marker FASTA was written to GCF_032334595.1_ASM3233459v1_genomic.fna/markers.fasta
[2024-01-24 12:14:26,206] [INFO] Task started: Blastn
[2024-01-24 12:14:26,206] [INFO] Running command: blastn -query GCF_032334595.1_ASM3233459v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2e3316a6-0544-49a9-9713-e7a7f6dac8ce/dqc_reference/reference_markers.fasta -out GCF_032334595.1_ASM3233459v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:27,262] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:27,265] [INFO] Selected 14 target genomes.
[2024-01-24 12:14:27,266] [INFO] Target genome list was writen to GCF_032334595.1_ASM3233459v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:27,272] [INFO] Task started: fastANI
[2024-01-24 12:14:27,272] [INFO] Running command: fastANI --query /var/lib/cwl/stg3db31249-2901-4da9-84c8-ee5eec412134/GCF_032334595.1_ASM3233459v1_genomic.fna.gz --refList GCF_032334595.1_ASM3233459v1_genomic.fna/target_genomes.txt --output GCF_032334595.1_ASM3233459v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:41,620] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:41,620] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2e3316a6-0544-49a9-9713-e7a7f6dac8ce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:41,621] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2e3316a6-0544-49a9-9713-e7a7f6dac8ce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:41,633] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:14:41,633] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:14:41,633] [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 naasensis	strain=DSM 100060	GCA_011762145.1	1344951	1344951	type	True	85.6868	1028	1487	95	below_threshold
Sphingomonas gei	strain=ZFGT-11	GCA_004792685.1	1395960	1395960	type	True	85.6351	1057	1487	95	below_threshold
Sphingomonas naasensis	strain=KIS18-15	GCA_004792695.1	1344951	1344951	type	True	85.6227	1035	1487	95	below_threshold
Sphingomonas psychrotolerans	strain=Cra20	GCA_002796605.1	1327635	1327635	type	True	85.611	1064	1487	95	below_threshold
Sphingomonas hengshuiensis	strain=WHSC-8	GCA_000935025.1	1609977	1609977	type	True	81.4176	793	1487	95	below_threshold
Sphingomonas trueperi	strain=DSM 7225	GCA_011927635.1	53317	53317	type	True	81.0695	748	1487	95	below_threshold
Sphingomonas pituitosa	strain=NBRC 102491	GCA_001598435.1	99597	99597	type	True	80.9989	736	1487	95	below_threshold
Sphingomonas azotifigens	strain=NBRC 15497	GCA_002091475.1	330920	330920	type	True	80.9563	733	1487	95	below_threshold
Sphingomonas soli	strain=NBRC 100801	GCA_001591025.1	266127	266127	type	True	80.4735	671	1487	95	below_threshold
Sphingomonas koreensis	strain=NBRC 16723	GCA_001598395.1	93064	93064	type	True	80.0699	615	1487	95	below_threshold
Sphingomonas suaedae	strain=XS-10	GCA_007833215.1	2599297	2599297	type	True	79.4489	604	1487	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	79.1069	591	1487	95	below_threshold
Sphingomonas yunnanensis	strain=YIM 3	GCA_019898765.1	310400	310400	type	True	79.0834	561	1487	95	below_threshold
Sphingomonas corticis	strain=36D10-4-7	GCA_012035195.1	2722791	2722791	type	True	78.5168	502	1487	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:41,635] [INFO] DFAST Taxonomy check result was written to GCF_032334595.1_ASM3233459v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:41,636] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:41,636] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:41,636] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2e3316a6-0544-49a9-9713-e7a7f6dac8ce/dqc_reference/checkm_data
[2024-01-24 12:14:41,637] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:41,679] [INFO] Task started: CheckM
[2024-01-24 12:14:41,680] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_032334595.1_ASM3233459v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_032334595.1_ASM3233459v1_genomic.fna/checkm_input GCF_032334595.1_ASM3233459v1_genomic.fna/checkm_result
[2024-01-24 12:15:25,148] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:25,149] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 1.04%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:25,184] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:25,185] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:25,186] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_032334595.1_ASM3233459v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:25,186] [INFO] Task started: Blastn
[2024-01-24 12:15:25,186] [INFO] Running command: blastn -query GCF_032334595.1_ASM3233459v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2e3316a6-0544-49a9-9713-e7a7f6dac8ce/dqc_reference/reference_markers_gtdb.fasta -out GCF_032334595.1_ASM3233459v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:27,125] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:27,128] [INFO] Selected 12 target genomes.
[2024-01-24 12:15:27,128] [INFO] Target genome list was writen to GCF_032334595.1_ASM3233459v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:27,140] [INFO] Task started: fastANI
[2024-01-24 12:15:27,141] [INFO] Running command: fastANI --query /var/lib/cwl/stg3db31249-2901-4da9-84c8-ee5eec412134/GCF_032334595.1_ASM3233459v1_genomic.fna.gz --refList GCF_032334595.1_ASM3233459v1_genomic.fna/target_genomes_gtdb.txt --output GCF_032334595.1_ASM3233459v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:39,822] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:39,839] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:15:39,840] [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_004792685.1	s__Sphingomonas gei	85.656	1054	1487	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002796605.1	s__Sphingomonas sp002796605	85.6191	1063	1487	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004792695.1	s__Sphingomonas naasensis	85.6191	1036	1487	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001428865.1	s__Sphingomonas sp001428865	85.2684	981	1487	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000712135.1	s__Sphingomonas sp000712135	84.9835	1015	1487	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002002925.1	s__Sphingomonas sp002002925	84.6451	1007	1487	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744835.1	s__Sphingomonas sp017744835	82.6116	869	1487	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204495.1	s__Sphingomonas kyeonggiensis_A	81.7473	862	1487	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000935025.1	s__Sphingomonas hengshuiensis	81.449	789	1487	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011927635.1	s__Sphingomonas trueperi	81.0946	745	1487	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.33	98.84	0.92	0.91	3	-
GCF_002091475.1	s__Sphingomonas azotifigens	80.9388	734	1487	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000282895.1	s__Sphingomonas sp000282895	80.1936	661	1487	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:15:39,842] [INFO] GTDB search result was written to GCF_032334595.1_ASM3233459v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:39,843] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:39,847] [INFO] DFAST_QC result json was written to GCF_032334595.1_ASM3233459v1_genomic.fna/dqc_result.json
[2024-01-24 12:15:39,847] [INFO] DFAST_QC completed!
[2024-01-24 12:15:39,847] [INFO] Total running time: 0h1m30s