[2023-06-29 00:19:31,480] [INFO] DFAST_QC pipeline started.
[2023-06-29 00:19:31,482] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 00:19:31,482] [INFO] DQC Reference Directory: /var/lib/cwl/stgd115e3d2-a6aa-46a3-afe4-f89d859040e9/dqc_reference
[2023-06-29 00:19:32,715] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 00:19:32,716] [INFO] Task started: Prodigal
[2023-06-29 00:19:32,716] [INFO] Running command: gunzip -c /var/lib/cwl/stg69d31f23-d9f7-44c2-ad43-cbe19557d987/GCA_002708035.1_ASM270803v1_genomic.fna.gz | prodigal -d GCA_002708035.1_ASM270803v1_genomic.fna/cds.fna -a GCA_002708035.1_ASM270803v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 00:19:39,416] [INFO] Task succeeded: Prodigal
[2023-06-29 00:19:39,417] [INFO] Task started: HMMsearch
[2023-06-29 00:19:39,417] [INFO] Running command: hmmsearch --tblout GCA_002708035.1_ASM270803v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd115e3d2-a6aa-46a3-afe4-f89d859040e9/dqc_reference/reference_markers.hmm GCA_002708035.1_ASM270803v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 00:19:39,626] [INFO] Task succeeded: HMMsearch
[2023-06-29 00:19:39,628] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg69d31f23-d9f7-44c2-ad43-cbe19557d987/GCA_002708035.1_ASM270803v1_genomic.fna.gz]
[2023-06-29 00:19:39,658] [INFO] Query marker FASTA was written to GCA_002708035.1_ASM270803v1_genomic.fna/markers.fasta
[2023-06-29 00:19:39,658] [INFO] Task started: Blastn
[2023-06-29 00:19:39,658] [INFO] Running command: blastn -query GCA_002708035.1_ASM270803v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd115e3d2-a6aa-46a3-afe4-f89d859040e9/dqc_reference/reference_markers.fasta -out GCA_002708035.1_ASM270803v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 00:19:40,174] [INFO] Task succeeded: Blastn
[2023-06-29 00:19:40,177] [INFO] Selected 12 target genomes.
[2023-06-29 00:19:40,178] [INFO] Target genome list was writen to GCA_002708035.1_ASM270803v1_genomic.fna/target_genomes.txt
[2023-06-29 00:19:40,185] [INFO] Task started: fastANI
[2023-06-29 00:19:40,185] [INFO] Running command: fastANI --query /var/lib/cwl/stg69d31f23-d9f7-44c2-ad43-cbe19557d987/GCA_002708035.1_ASM270803v1_genomic.fna.gz --refList GCA_002708035.1_ASM270803v1_genomic.fna/target_genomes.txt --output GCA_002708035.1_ASM270803v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 00:19:49,238] [INFO] Task succeeded: fastANI
[2023-06-29 00:19:49,239] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd115e3d2-a6aa-46a3-afe4-f89d859040e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 00:19:49,240] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd115e3d2-a6aa-46a3-afe4-f89d859040e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 00:19:49,253] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 00:19:49,254] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 00:19:49,254] [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
Sphingobium abikonense	strain=NBRC 16140	GCA_001598335.1	86193	86193	type	True	89.3791	606	732	95	below_threshold
Sphingobium lactosutens	strain=DS20	GCA_000445105.1	522773	522773	type	True	89.3513	624	732	95	below_threshold
Sphingobium cupriresistens	strain=CCTCC AB 2011146	GCA_004152865.1	1132417	1132417	type	True	82.5902	482	732	95	below_threshold
Sphingobium limneticum	strain=DSM 25076	GCA_008710155.1	1007511	1007511	type	True	82.5004	509	732	95	below_threshold
Sphingobium yanoikuyae	strain=ATCC 51230	GCA_000315525.1	13690	13690	suspected-type	True	82.4765	499	732	95	below_threshold
Sphingobium terrigena	strain=EO9	GCA_003591655.1	2304063	2304063	type	True	81.832	453	732	95	below_threshold
Sphingobium chlorophenolicum	strain=NBRC 16172	GCA_000722875.1	46429	46429	type	True	81.263	409	732	95	below_threshold
Sphingobium chlorophenolicum	strain=NBRC 16172	GCA_001598515.1	46429	46429	type	True	81.2524	382	732	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	77.7984	223	732	95	below_threshold
Sphingomonas cavernae	strain=K2R01-6	GCA_003590775.1	2320861	2320861	type	True	77.6717	192	732	95	below_threshold
Sphingomonas morindae	strain=NBD5	GCA_023822065.1	1541170	1541170	type	True	77.3898	207	732	95	below_threshold
Sphingomonas aracearum	strain=WZY 27	GCA_003345355.1	2283317	2283317	type	True	77.3311	186	732	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 00:19:49,256] [INFO] DFAST Taxonomy check result was written to GCA_002708035.1_ASM270803v1_genomic.fna/tc_result.tsv
[2023-06-29 00:19:49,257] [INFO] ===== Taxonomy check completed =====
[2023-06-29 00:19:49,257] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 00:19:49,257] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd115e3d2-a6aa-46a3-afe4-f89d859040e9/dqc_reference/checkm_data
[2023-06-29 00:19:49,258] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 00:19:49,282] [INFO] Task started: CheckM
[2023-06-29 00:19:49,282] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002708035.1_ASM270803v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002708035.1_ASM270803v1_genomic.fna/checkm_input GCA_002708035.1_ASM270803v1_genomic.fna/checkm_result
[2023-06-29 00:20:14,221] [INFO] Task succeeded: CheckM
[2023-06-29 00:20:14,222] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 84.38%
Contamintation: 2.78%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-29 00:20:14,280] [INFO] ===== Completeness check finished =====
[2023-06-29 00:20:14,281] [INFO] ===== Start GTDB Search =====
[2023-06-29 00:20:14,281] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002708035.1_ASM270803v1_genomic.fna/markers.fasta)
[2023-06-29 00:20:14,281] [INFO] Task started: Blastn
[2023-06-29 00:20:14,281] [INFO] Running command: blastn -query GCA_002708035.1_ASM270803v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd115e3d2-a6aa-46a3-afe4-f89d859040e9/dqc_reference/reference_markers_gtdb.fasta -out GCA_002708035.1_ASM270803v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 00:20:14,797] [INFO] Task succeeded: Blastn
[2023-06-29 00:20:14,801] [INFO] Selected 9 target genomes.
[2023-06-29 00:20:14,801] [INFO] Target genome list was writen to GCA_002708035.1_ASM270803v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 00:20:14,809] [INFO] Task started: fastANI
[2023-06-29 00:20:14,809] [INFO] Running command: fastANI --query /var/lib/cwl/stg69d31f23-d9f7-44c2-ad43-cbe19557d987/GCA_002708035.1_ASM270803v1_genomic.fna.gz --refList GCA_002708035.1_ASM270803v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002708035.1_ASM270803v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 00:20:22,455] [INFO] Task succeeded: fastANI
[2023-06-29 00:20:22,471] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 00:20:22,471] [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_000153545.1	s__Sphingobium sp000153545	98.0035	668	732	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	97.72	97.49	0.82	0.71	9	conclusive
GCF_001598335.1	s__Sphingobium abikonense	89.3788	607	732	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.3976	N/A	N/A	N/A	N/A	1	-
GCF_000445105.1	s__Sphingobium lactosutens	89.3621	622	732	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.3976	N/A	N/A	N/A	N/A	1	-
GCA_002457415.1	s__Sphingobium sp002457415	86.0487	526	732	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001650725.1	s__Sphingobium sp001650725	83.0606	513	732	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	99.12	99.12	0.95	0.95	2	-
GCF_009720145.1	s__Sphingobium sp009720145	83.0486	485	732	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013393185.1	s__Sphingobium lactosutens_A	82.9953	523	732	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008710155.1	s__Sphingobium limneticum	82.5046	509	732	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	98.69	97.69	0.91	0.88	5	-
GCF_001556865.1	s__Sphingobium sp001556865	81.9868	451	732	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 00:20:22,473] [INFO] GTDB search result was written to GCA_002708035.1_ASM270803v1_genomic.fna/result_gtdb.tsv
[2023-06-29 00:20:22,473] [INFO] ===== GTDB Search completed =====
[2023-06-29 00:20:22,477] [INFO] DFAST_QC result json was written to GCA_002708035.1_ASM270803v1_genomic.fna/dqc_result.json
[2023-06-29 00:20:22,477] [INFO] DFAST_QC completed!
[2023-06-29 00:20:22,477] [INFO] Total running time: 0h0m51s