[2024-01-24 15:18:27,614] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:27,615] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:27,616] [INFO] DQC Reference Directory: /var/lib/cwl/stgb798fcbb-3ae6-46a4-bd6a-5643378f294b/dqc_reference
[2024-01-24 15:18:29,036] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:29,037] [INFO] Task started: Prodigal
[2024-01-24 15:18:29,037] [INFO] Running command: gunzip -c /var/lib/cwl/stg51562699-1976-49cf-8539-7d5ae99b3a43/GCF_016905005.1_ASM1690500v1_genomic.fna.gz | prodigal -d GCF_016905005.1_ASM1690500v1_genomic.fna/cds.fna -a GCF_016905005.1_ASM1690500v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:46,379] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:46,380] [INFO] Task started: HMMsearch
[2024-01-24 15:18:46,380] [INFO] Running command: hmmsearch --tblout GCF_016905005.1_ASM1690500v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb798fcbb-3ae6-46a4-bd6a-5643378f294b/dqc_reference/reference_markers.hmm GCF_016905005.1_ASM1690500v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:46,705] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:46,706] [INFO] Found 6/6 markers.
[2024-01-24 15:18:46,758] [INFO] Query marker FASTA was written to GCF_016905005.1_ASM1690500v1_genomic.fna/markers.fasta
[2024-01-24 15:18:46,759] [INFO] Task started: Blastn
[2024-01-24 15:18:46,759] [INFO] Running command: blastn -query GCF_016905005.1_ASM1690500v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb798fcbb-3ae6-46a4-bd6a-5643378f294b/dqc_reference/reference_markers.fasta -out GCF_016905005.1_ASM1690500v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:47,883] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:47,886] [INFO] Selected 9 target genomes.
[2024-01-24 15:18:47,886] [INFO] Target genome list was writen to GCF_016905005.1_ASM1690500v1_genomic.fna/target_genomes.txt
[2024-01-24 15:18:47,891] [INFO] Task started: fastANI
[2024-01-24 15:18:47,891] [INFO] Running command: fastANI --query /var/lib/cwl/stg51562699-1976-49cf-8539-7d5ae99b3a43/GCF_016905005.1_ASM1690500v1_genomic.fna.gz --refList GCF_016905005.1_ASM1690500v1_genomic.fna/target_genomes.txt --output GCF_016905005.1_ASM1690500v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:18:59,718] [INFO] Task succeeded: fastANI
[2024-01-24 15:18:59,718] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb798fcbb-3ae6-46a4-bd6a-5643378f294b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:18:59,719] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb798fcbb-3ae6-46a4-bd6a-5643378f294b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:18:59,727] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:18:59,727] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:18:59,727] [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
Dyella kyungheensis	strain=THG-B117	GCA_016905005.1	1242174	1242174	type	True	100.0	1601	1602	95	conclusive
Dyella japonica	strain=DSM 16301	GCA_001010355.1	231455	231455	type	True	87.6541	1070	1602	95	below_threshold
Dyella telluris	strain=G9	GCA_014297575.1	2763498	2763498	type	True	85.2116	1136	1602	95	below_threshold
Dyella amyloliquefaciens	strain=DHC06	GCA_004296575.1	1770545	1770545	type	True	83.9642	1040	1602	95	below_threshold
Dyella solisilvae	strain=DHG54	GCA_003351225.1	1920168	1920168	type	True	83.8296	978	1602	95	below_threshold
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	81.9537	717	1602	95	below_threshold
Frateuria flava	strain=MAH-13	GCA_017837635.1	2821489	2821489	type	True	80.9834	654	1602	95	below_threshold
Dyella acidiphila	strain=7MK23	GCA_014863405.1	2775866	2775866	type	True	80.8356	773	1602	95	below_threshold
Tahibacter caeni	strain=BUT-6	GCA_024609805.1	1453545	1453545	type	True	78.3582	365	1602	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:18:59,729] [INFO] DFAST Taxonomy check result was written to GCF_016905005.1_ASM1690500v1_genomic.fna/tc_result.tsv
[2024-01-24 15:18:59,729] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:18:59,730] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:18:59,730] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb798fcbb-3ae6-46a4-bd6a-5643378f294b/dqc_reference/checkm_data
[2024-01-24 15:18:59,731] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:18:59,776] [INFO] Task started: CheckM
[2024-01-24 15:18:59,777] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016905005.1_ASM1690500v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016905005.1_ASM1690500v1_genomic.fna/checkm_input GCF_016905005.1_ASM1690500v1_genomic.fna/checkm_result
[2024-01-24 15:19:57,287] [INFO] Task succeeded: CheckM
[2024-01-24 15:19:57,288] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:19:57,310] [INFO] ===== Completeness check finished =====
[2024-01-24 15:19:57,310] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:19:57,311] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016905005.1_ASM1690500v1_genomic.fna/markers.fasta)
[2024-01-24 15:19:57,311] [INFO] Task started: Blastn
[2024-01-24 15:19:57,312] [INFO] Running command: blastn -query GCF_016905005.1_ASM1690500v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb798fcbb-3ae6-46a4-bd6a-5643378f294b/dqc_reference/reference_markers_gtdb.fasta -out GCF_016905005.1_ASM1690500v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:59,313] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:59,325] [INFO] Selected 11 target genomes.
[2024-01-24 15:19:59,326] [INFO] Target genome list was writen to GCF_016905005.1_ASM1690500v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:19:59,334] [INFO] Task started: fastANI
[2024-01-24 15:19:59,335] [INFO] Running command: fastANI --query /var/lib/cwl/stg51562699-1976-49cf-8539-7d5ae99b3a43/GCF_016905005.1_ASM1690500v1_genomic.fna.gz --refList GCF_016905005.1_ASM1690500v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016905005.1_ASM1690500v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:20:14,213] [INFO] Task succeeded: fastANI
[2024-01-24 15:20:14,226] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:20:14,227] [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_016905005.1	s__Dyella kyungheensis	100.0	1601	1602	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001010355.1	s__Dyella japonica	87.6762	1068	1602	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003688835.1	s__Dyella sp003688835	87.3236	1225	1602	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003201105.1	s__Dyella jiangningensis_B	85.9211	1147	1602	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000725385.1	s__Dyella japonica_C	85.2809	1141	1602	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014297575.1	s__Dyella sp014297575	85.2151	1136	1602	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003121485.1	s__Dyella sp003121485	85.1417	1135	1602	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016586165.1	s__Dyella sp016586165	84.229	1023	1602	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002878475.1	s__Dyella sp002878475	84.0313	1089	1602	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004296575.1	s__Dyella sp004296575	83.9694	1039	1602	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016428905.1	s__Dyella sp016428905	83.9292	1021	1602	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:20:14,229] [INFO] GTDB search result was written to GCF_016905005.1_ASM1690500v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:20:14,229] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:20:14,233] [INFO] DFAST_QC result json was written to GCF_016905005.1_ASM1690500v1_genomic.fna/dqc_result.json
[2024-01-24 15:20:14,233] [INFO] DFAST_QC completed!
[2024-01-24 15:20:14,233] [INFO] Total running time: 0h1m47s