[2024-01-24 13:32:16,582] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:16,583] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:16,584] [INFO] DQC Reference Directory: /var/lib/cwl/stg37a6413c-21bf-444e-8ee1-77d96f08c3d1/dqc_reference
[2024-01-24 13:32:17,858] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:17,859] [INFO] Task started: Prodigal
[2024-01-24 13:32:17,859] [INFO] Running command: gunzip -c /var/lib/cwl/stg3ff78ed6-3e37-41f8-8d4e-249624705222/GCF_014201555.1_ASM1420155v1_genomic.fna.gz | prodigal -d GCF_014201555.1_ASM1420155v1_genomic.fna/cds.fna -a GCF_014201555.1_ASM1420155v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:29,820] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:29,821] [INFO] Task started: HMMsearch
[2024-01-24 13:32:29,821] [INFO] Running command: hmmsearch --tblout GCF_014201555.1_ASM1420155v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg37a6413c-21bf-444e-8ee1-77d96f08c3d1/dqc_reference/reference_markers.hmm GCF_014201555.1_ASM1420155v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:30,089] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:30,090] [INFO] Found 6/6 markers.
[2024-01-24 13:32:30,119] [INFO] Query marker FASTA was written to GCF_014201555.1_ASM1420155v1_genomic.fna/markers.fasta
[2024-01-24 13:32:30,119] [INFO] Task started: Blastn
[2024-01-24 13:32:30,119] [INFO] Running command: blastn -query GCF_014201555.1_ASM1420155v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg37a6413c-21bf-444e-8ee1-77d96f08c3d1/dqc_reference/reference_markers.fasta -out GCF_014201555.1_ASM1420155v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:31,166] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:31,169] [INFO] Selected 11 target genomes.
[2024-01-24 13:32:31,169] [INFO] Target genome list was writen to GCF_014201555.1_ASM1420155v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:31,174] [INFO] Task started: fastANI
[2024-01-24 13:32:31,174] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ff78ed6-3e37-41f8-8d4e-249624705222/GCF_014201555.1_ASM1420155v1_genomic.fna.gz --refList GCF_014201555.1_ASM1420155v1_genomic.fna/target_genomes.txt --output GCF_014201555.1_ASM1420155v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:41,026] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:41,027] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg37a6413c-21bf-444e-8ee1-77d96f08c3d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:41,027] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg37a6413c-21bf-444e-8ee1-77d96f08c3d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:41,038] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:32:41,038] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:41,038] [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
Oleiagrimonas soli	strain=DSM 107085	GCA_014201555.1	1543381	1543381	type	True	100.0	1123	1124	95	conclusive
Oleiagrimonas soli	strain=3.5X	GCA_000761445.1	1543381	1543381	type	True	99.9888	1120	1124	95	conclusive
Oleiagrimonas citrea	strain=MEBiC09124	GCA_012395255.1	1665687	1665687	type	True	87.6687	887	1124	95	below_threshold
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	81.0012	583	1124	95	below_threshold
Fulvimonas soli	strain=DSM 14263	GCA_003148905.1	155197	155197	type	True	80.9659	631	1124	95	below_threshold
Frateuria flava	strain=MAH-13	GCA_017837635.1	2821489	2821489	type	True	80.0685	553	1124	95	below_threshold
Dyella solisilvae	strain=DHG54	GCA_003351225.1	1920168	1920168	type	True	79.7283	520	1124	95	below_threshold
Dyella japonica	strain=DSM 16301	GCA_001010355.1	231455	231455	type	True	79.5592	405	1124	95	below_threshold
Dyella telluris	strain=G9	GCA_014297575.1	2763498	2763498	type	True	79.3932	506	1124	95	below_threshold
Dyella acidiphila	strain=7MK23	GCA_014863405.1	2775866	2775866	type	True	79.1668	497	1124	95	below_threshold
Tahibacter caeni	strain=BUT-6	GCA_024609805.1	1453545	1453545	type	True	78.5615	414	1124	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:41,048] [INFO] DFAST Taxonomy check result was written to GCF_014201555.1_ASM1420155v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:41,049] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:41,049] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:41,050] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg37a6413c-21bf-444e-8ee1-77d96f08c3d1/dqc_reference/checkm_data
[2024-01-24 13:32:41,052] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:41,121] [INFO] Task started: CheckM
[2024-01-24 13:32:41,122] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014201555.1_ASM1420155v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014201555.1_ASM1420155v1_genomic.fna/checkm_input GCF_014201555.1_ASM1420155v1_genomic.fna/checkm_result
[2024-01-24 13:33:28,496] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:28,498] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:28,518] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:28,518] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:28,518] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014201555.1_ASM1420155v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:28,519] [INFO] Task started: Blastn
[2024-01-24 13:33:28,519] [INFO] Running command: blastn -query GCF_014201555.1_ASM1420155v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg37a6413c-21bf-444e-8ee1-77d96f08c3d1/dqc_reference/reference_markers_gtdb.fasta -out GCF_014201555.1_ASM1420155v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:30,623] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:30,627] [INFO] Selected 14 target genomes.
[2024-01-24 13:33:30,628] [INFO] Target genome list was writen to GCF_014201555.1_ASM1420155v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:30,655] [INFO] Task started: fastANI
[2024-01-24 13:33:30,655] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ff78ed6-3e37-41f8-8d4e-249624705222/GCF_014201555.1_ASM1420155v1_genomic.fna.gz --refList GCF_014201555.1_ASM1420155v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014201555.1_ASM1420155v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:42,162] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:42,174] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:42,174] [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_000761445.1	s__Oleiagrimonas soli	99.9888	1120	1124	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Oleiagrimonas	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_012395255.1	s__Oleiagrimonas citrea	87.6687	887	1124	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Oleiagrimonas	95.0	98.37	98.37	0.90	0.90	2	-
GCF_003148905.1	s__Fulvimonas soli	80.9589	633	1124	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Fulvimonas	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000953855.2	s__Mizugakiibacter sediminis	80.6418	533	1124	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Mizugakiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002279065.1	s__Dyella_A sp002279065	80.6397	594	1124	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella_A	95.0	100.00	100.00	0.99	0.99	2	-
GCF_001428405.1	s__Frateuria_A sp001428405	80.6395	611	1124	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Frateuria_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017848855.1	s__Rhodanobacter denitrificans_B	80.5461	556	1124	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001182895.1	s__Frateuria_B defendens	80.5117	576	1124	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Frateuria_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013620825.1	s__Rhodanobacter sp001899565	80.3783	588	1124	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	98.48	98.45	0.90	0.89	4	-
GCF_900112865.1	s__Dyella marensis	80.3771	629	1124	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_012275375.1	s__Dyella sp012275375	80.3656	607	1124	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	96.64	95.58	0.92	0.90	4	-
GCF_011759385.1	s__Oleiagrimonas sp011759385	80.3253	558	1124	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Oleiagrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003332825.1	s__Dyella sp003332825	79.7568	540	1124	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003967035.1	s__Aerosticca soli	79.7386	453	1124	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Aerosticca	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:42,176] [INFO] GTDB search result was written to GCF_014201555.1_ASM1420155v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:42,176] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:42,181] [INFO] DFAST_QC result json was written to GCF_014201555.1_ASM1420155v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:42,181] [INFO] DFAST_QC completed!
[2024-01-24 13:33:42,181] [INFO] Total running time: 0h1m26s