[2024-01-24 10:58:06,466] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:58:06,469] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:58:06,469] [INFO] DQC Reference Directory: /var/lib/cwl/stg706d161f-1489-473c-a35b-bba288ca83a0/dqc_reference
[2024-01-24 10:58:09,640] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:58:09,641] [INFO] Task started: Prodigal
[2024-01-24 10:58:09,641] [INFO] Running command: gunzip -c /var/lib/cwl/stg8ad253d1-a077-426b-a9fc-cfa33a8c2e27/GCF_010093385.1_ASM1009338v1_genomic.fna.gz | prodigal -d GCF_010093385.1_ASM1009338v1_genomic.fna/cds.fna -a GCF_010093385.1_ASM1009338v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:58:21,493] [INFO] Task succeeded: Prodigal
[2024-01-24 10:58:21,494] [INFO] Task started: HMMsearch
[2024-01-24 10:58:21,494] [INFO] Running command: hmmsearch --tblout GCF_010093385.1_ASM1009338v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg706d161f-1489-473c-a35b-bba288ca83a0/dqc_reference/reference_markers.hmm GCF_010093385.1_ASM1009338v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:58:21,809] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:58:21,810] [INFO] Found 6/6 markers.
[2024-01-24 10:58:21,843] [INFO] Query marker FASTA was written to GCF_010093385.1_ASM1009338v1_genomic.fna/markers.fasta
[2024-01-24 10:58:21,844] [INFO] Task started: Blastn
[2024-01-24 10:58:21,844] [INFO] Running command: blastn -query GCF_010093385.1_ASM1009338v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg706d161f-1489-473c-a35b-bba288ca83a0/dqc_reference/reference_markers.fasta -out GCF_010093385.1_ASM1009338v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:22,819] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:22,823] [INFO] Selected 16 target genomes.
[2024-01-24 10:58:22,824] [INFO] Target genome list was writen to GCF_010093385.1_ASM1009338v1_genomic.fna/target_genomes.txt
[2024-01-24 10:58:22,832] [INFO] Task started: fastANI
[2024-01-24 10:58:22,832] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ad253d1-a077-426b-a9fc-cfa33a8c2e27/GCF_010093385.1_ASM1009338v1_genomic.fna.gz --refList GCF_010093385.1_ASM1009338v1_genomic.fna/target_genomes.txt --output GCF_010093385.1_ASM1009338v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:36,781] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:36,782] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg706d161f-1489-473c-a35b-bba288ca83a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:36,782] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg706d161f-1489-473c-a35b-bba288ca83a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:36,805] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:58:36,805] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:58:36,806] [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
Pseudoxanthomonas mexicana	strain=DSM 17121	GCA_010093385.1	128785	128785	type	True	100.0	1257	1265	95	conclusive
Pseudoxanthomonas japonensis	strain=DSM 17109	GCA_010093445.1	69284	69284	type	True	87.5034	978	1265	95	below_threshold
Pseudoxanthomonas beigongshangi	strain=REN9	GCA_016820515.1	2782537	2782537	type	True	83.017	803	1265	95	below_threshold
Pseudoxanthomonas wuyuanensis	strain=CGMCC 1.10978	GCA_900215535.1	1073196	1073196	type	True	82.7578	803	1265	95	below_threshold
Pseudoxanthomonas wuyuanensis	strain=DSM 100640	GCA_010093325.1	1073196	1073196	type	True	82.7465	794	1265	95	below_threshold
Pseudoxanthomonas sangjuensis	strain=DSM 28345	GCA_010211755.1	1503750	1503750	type	True	82.5831	686	1265	95	below_threshold
Pseudoxanthomonas indica	strain=P15	GCA_900167565.1	428993	428993	type	True	82.1127	747	1265	95	below_threshold
Pseudoxanthomonas indica	strain=CCM 7430	GCA_014635165.1	428993	428993	type	True	82.0293	739	1265	95	below_threshold
Stenotrophomonas acidaminiphila	strain=DSM 13117	GCA_024221815.1	128780	128780	type	True	81.6879	689	1265	95	below_threshold
Xanthomonas translucens	strain=ATCC 19319	GCA_020880735.1	343	343	type	True	81.5406	593	1265	95	below_threshold
Pseudoxanthomonas sacheonensis	strain=DSM 19373	GCA_010093305.1	443615	443615	type	True	81.4818	733	1265	95	below_threshold
Pseudoxanthomonas composti	strain=GSS15	GCA_004122095.1	2137479	2137479	type	True	81.3974	668	1265	95	below_threshold
Lysobacter silvisoli	strain=zong2l5	GCA_003382365.1	2293254	2293254	type	True	81.1252	678	1265	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	80.5571	473	1265	95	below_threshold
Stenotrophomonas pennii	strain=Sa5BUN4	GCA_014836545.1	2762239	2762239	type	True	80.501	588	1265	95	below_threshold
Lysobacter capsici	strain=VKM B-2533	GCA_014779555.2	435897	435897	type	True	79.9036	646	1265	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:36,807] [INFO] DFAST Taxonomy check result was written to GCF_010093385.1_ASM1009338v1_genomic.fna/tc_result.tsv
[2024-01-24 10:58:36,808] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:36,808] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:36,808] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg706d161f-1489-473c-a35b-bba288ca83a0/dqc_reference/checkm_data
[2024-01-24 10:58:36,810] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:36,857] [INFO] Task started: CheckM
[2024-01-24 10:58:36,858] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010093385.1_ASM1009338v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010093385.1_ASM1009338v1_genomic.fna/checkm_input GCF_010093385.1_ASM1009338v1_genomic.fna/checkm_result
[2024-01-24 10:59:18,645] [INFO] Task succeeded: CheckM
[2024-01-24 10:59:18,647] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:59:18,667] [INFO] ===== Completeness check finished =====
[2024-01-24 10:59:18,668] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:59:18,669] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010093385.1_ASM1009338v1_genomic.fna/markers.fasta)
[2024-01-24 10:59:18,669] [INFO] Task started: Blastn
[2024-01-24 10:59:18,669] [INFO] Running command: blastn -query GCF_010093385.1_ASM1009338v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg706d161f-1489-473c-a35b-bba288ca83a0/dqc_reference/reference_markers_gtdb.fasta -out GCF_010093385.1_ASM1009338v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:59:20,548] [INFO] Task succeeded: Blastn
[2024-01-24 10:59:20,553] [INFO] Selected 12 target genomes.
[2024-01-24 10:59:20,553] [INFO] Target genome list was writen to GCF_010093385.1_ASM1009338v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:59:20,564] [INFO] Task started: fastANI
[2024-01-24 10:59:20,564] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ad253d1-a077-426b-a9fc-cfa33a8c2e27/GCF_010093385.1_ASM1009338v1_genomic.fna.gz --refList GCF_010093385.1_ASM1009338v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010093385.1_ASM1009338v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:59:32,705] [INFO] Task succeeded: fastANI
[2024-01-24 10:59:32,724] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:59:32,724] [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_010093385.1	s__Pseudoxanthomonas_A mexicana	100.0	1257	1265	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	96.97	96.88	0.87	0.86	4	conclusive
GCF_001427585.1	s__Pseudoxanthomonas_A sp001427585	88.2693	1032	1265	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104255.1	s__Pseudoxanthomonas_A sp900104255	87.9668	994	1265	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116385.1	s__Pseudoxanthomonas_A sp900116385	87.4844	985	1265	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_010093445.1	s__Pseudoxanthomonas_A japonensis	87.48	980	1265	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	96.78	96.68	0.83	0.68	4	-
GCF_006716465.1	s__Pseudoxanthomonas_A sp006716465	87.4423	1001	1265	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002863005.1	s__Pseudoxanthomonas_A sp002863005	87.261	946	1265	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014851815.1	s__Pseudoxanthomonas_A sp014851815	87.0332	977	1265	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001556105.1	s__Pseudoxanthomonas_A mexicana_A	86.881	905	1265	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	98.72	98.63	0.92	0.88	3	-
GCF_014851805.1	s__Pseudoxanthomonas_A sp014851805	86.8354	962	1265	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014852005.1	s__Pseudoxanthomonas_A sp014852005	86.7996	988	1265	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002862435.1	s__Macondimonas sp002862435	82.5505	136	1265	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA5335;f__UBA5335;g__Macondimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:59:32,726] [INFO] GTDB search result was written to GCF_010093385.1_ASM1009338v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:59:32,726] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:59:32,730] [INFO] DFAST_QC result json was written to GCF_010093385.1_ASM1009338v1_genomic.fna/dqc_result.json
[2024-01-24 10:59:32,730] [INFO] DFAST_QC completed!
[2024-01-24 10:59:32,730] [INFO] Total running time: 0h1m26s