[2024-01-24 11:35:34,259] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:35:34,261] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:35:34,261] [INFO] DQC Reference Directory: /var/lib/cwl/stge56ae466-d47c-4839-8963-5f4a316afcea/dqc_reference
[2024-01-24 11:35:35,477] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:35:35,478] [INFO] Task started: Prodigal
[2024-01-24 11:35:35,478] [INFO] Running command: gunzip -c /var/lib/cwl/stg57fa9257-c946-49d3-8faa-1300fbe994ba/GCF_017353515.1_ASM1735351v1_genomic.fna.gz | prodigal -d GCF_017353515.1_ASM1735351v1_genomic.fna/cds.fna -a GCF_017353515.1_ASM1735351v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:48,367] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:48,368] [INFO] Task started: HMMsearch
[2024-01-24 11:35:48,368] [INFO] Running command: hmmsearch --tblout GCF_017353515.1_ASM1735351v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge56ae466-d47c-4839-8963-5f4a316afcea/dqc_reference/reference_markers.hmm GCF_017353515.1_ASM1735351v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:48,675] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:48,677] [INFO] Found 6/6 markers.
[2024-01-24 11:35:48,720] [INFO] Query marker FASTA was written to GCF_017353515.1_ASM1735351v1_genomic.fna/markers.fasta
[2024-01-24 11:35:48,720] [INFO] Task started: Blastn
[2024-01-24 11:35:48,721] [INFO] Running command: blastn -query GCF_017353515.1_ASM1735351v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge56ae466-d47c-4839-8963-5f4a316afcea/dqc_reference/reference_markers.fasta -out GCF_017353515.1_ASM1735351v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:49,804] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:49,807] [INFO] Selected 11 target genomes.
[2024-01-24 11:35:49,808] [INFO] Target genome list was writen to GCF_017353515.1_ASM1735351v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:49,813] [INFO] Task started: fastANI
[2024-01-24 11:35:49,813] [INFO] Running command: fastANI --query /var/lib/cwl/stg57fa9257-c946-49d3-8faa-1300fbe994ba/GCF_017353515.1_ASM1735351v1_genomic.fna.gz --refList GCF_017353515.1_ASM1735351v1_genomic.fna/target_genomes.txt --output GCF_017353515.1_ASM1735351v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:36:02,686] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:02,687] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge56ae466-d47c-4839-8963-5f4a316afcea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:36:02,688] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge56ae466-d47c-4839-8963-5f4a316afcea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:36:02,700] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:36:02,700] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:36:02,701] [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
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	100.0	1676	1678	95	conclusive
Jiella endophytica	strain=CBS5Q-3	GCA_004519335.1	2558362	2558362	type	True	84.9632	1209	1678	95	below_threshold
Jiella pacifica	strain=40Bstr34	GCA_010500815.1	2696469	2696469	type	True	84.1507	1198	1678	95	below_threshold
Aurantimonas aggregata	strain=KCTC 52919	GCA_010500835.1	2047720	2047720	type	True	80.8573	802	1678	95	below_threshold
Aurantimonas manganoxydans	strain=SI85-9A1	GCA_000153465.1	651183	651183	type	True	80.8251	797	1678	95	below_threshold
Aurantimonas endophytica	strain=DSM 103570	GCA_014196845.1	1522175	1522175	type	True	80.8196	792	1678	95	below_threshold
Aurantimonas manganoxydans	strain=DSM 21871	GCA_001463865.1	651183	651183	type	True	80.8167	775	1678	95	below_threshold
Aurantimonas endophytica	strain=KCTC 52296	GCA_024105745.1	1522175	1522175	type	True	80.7461	798	1678	95	below_threshold
Aurantimonas marina	strain=SW136	GCA_017183135.1	2780508	2780508	type	True	79.7796	631	1678	95	below_threshold
Chelativorans intermedius	strain=LMG 28482	GCA_025398255.1	515947	515947	type	True	77.7627	390	1678	95	below_threshold
Microvirga splendida	strain=BT325	GCA_016427565.1	2795727	2795727	type	True	77.3592	278	1678	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:36:02,702] [INFO] DFAST Taxonomy check result was written to GCF_017353515.1_ASM1735351v1_genomic.fna/tc_result.tsv
[2024-01-24 11:36:02,703] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:36:02,703] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:36:02,703] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge56ae466-d47c-4839-8963-5f4a316afcea/dqc_reference/checkm_data
[2024-01-24 11:36:02,704] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:36:02,753] [INFO] Task started: CheckM
[2024-01-24 11:36:02,753] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017353515.1_ASM1735351v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017353515.1_ASM1735351v1_genomic.fna/checkm_input GCF_017353515.1_ASM1735351v1_genomic.fna/checkm_result
[2024-01-24 11:36:59,623] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:59,624] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:59,644] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:59,644] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:59,644] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017353515.1_ASM1735351v1_genomic.fna/markers.fasta)
[2024-01-24 11:36:59,645] [INFO] Task started: Blastn
[2024-01-24 11:36:59,645] [INFO] Running command: blastn -query GCF_017353515.1_ASM1735351v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge56ae466-d47c-4839-8963-5f4a316afcea/dqc_reference/reference_markers_gtdb.fasta -out GCF_017353515.1_ASM1735351v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:37:01,851] [INFO] Task succeeded: Blastn
[2024-01-24 11:37:01,855] [INFO] Selected 7 target genomes.
[2024-01-24 11:37:01,855] [INFO] Target genome list was writen to GCF_017353515.1_ASM1735351v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:37:01,862] [INFO] Task started: fastANI
[2024-01-24 11:37:01,862] [INFO] Running command: fastANI --query /var/lib/cwl/stg57fa9257-c946-49d3-8faa-1300fbe994ba/GCF_017353515.1_ASM1735351v1_genomic.fna.gz --refList GCF_017353515.1_ASM1735351v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017353515.1_ASM1735351v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:37:12,371] [INFO] Task succeeded: fastANI
[2024-01-24 11:37:12,385] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:37:12,385] [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_017353515.1	s__Jiella sp017353515	100.0	1676	1678	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004519335.1	s__Jiella endophytica	84.9752	1206	1678	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002088275.1	s__Jiella sp002088275	84.4774	1194	1678	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002700095.1	s__Jiella sp002700095	84.2582	1150	1678	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010500815.1	s__Jiella pacifica	84.1471	1199	1678	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017815135.1	s__Jiella sp017815135	83.2373	1081	1678	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017349315.1	s__Jiella sp017349315	81.86	905	1678	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:37:12,386] [INFO] GTDB search result was written to GCF_017353515.1_ASM1735351v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:37:12,387] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:37:12,390] [INFO] DFAST_QC result json was written to GCF_017353515.1_ASM1735351v1_genomic.fna/dqc_result.json
[2024-01-24 11:37:12,390] [INFO] DFAST_QC completed!
[2024-01-24 11:37:12,390] [INFO] Total running time: 0h1m38s