[2024-01-24 11:19:55,270] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:19:55,272] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:19:55,272] [INFO] DQC Reference Directory: /var/lib/cwl/stgd4af0c05-1add-4488-a3ad-7407fb857367/dqc_reference
[2024-01-24 11:19:56,567] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:19:56,568] [INFO] Task started: Prodigal
[2024-01-24 11:19:56,568] [INFO] Running command: gunzip -c /var/lib/cwl/stg50bff31d-121e-465e-a159-f3e2d726a61f/GCF_000953855.2_ASM95385v3_genomic.fna.gz | prodigal -d GCF_000953855.2_ASM95385v3_genomic.fna/cds.fna -a GCF_000953855.2_ASM95385v3_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:20:04,695] [INFO] Task succeeded: Prodigal
[2024-01-24 11:20:04,696] [INFO] Task started: HMMsearch
[2024-01-24 11:20:04,696] [INFO] Running command: hmmsearch --tblout GCF_000953855.2_ASM95385v3_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd4af0c05-1add-4488-a3ad-7407fb857367/dqc_reference/reference_markers.hmm GCF_000953855.2_ASM95385v3_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:20:04,970] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:20:04,972] [INFO] Found 6/6 markers.
[2024-01-24 11:20:05,000] [INFO] Query marker FASTA was written to GCF_000953855.2_ASM95385v3_genomic.fna/markers.fasta
[2024-01-24 11:20:05,001] [INFO] Task started: Blastn
[2024-01-24 11:20:05,001] [INFO] Running command: blastn -query GCF_000953855.2_ASM95385v3_genomic.fna/markers.fasta -db /var/lib/cwl/stgd4af0c05-1add-4488-a3ad-7407fb857367/dqc_reference/reference_markers.fasta -out GCF_000953855.2_ASM95385v3_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:06,026] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:06,030] [INFO] Selected 22 target genomes.
[2024-01-24 11:20:06,031] [INFO] Target genome list was writen to GCF_000953855.2_ASM95385v3_genomic.fna/target_genomes.txt
[2024-01-24 11:20:06,041] [INFO] Task started: fastANI
[2024-01-24 11:20:06,042] [INFO] Running command: fastANI --query /var/lib/cwl/stg50bff31d-121e-465e-a159-f3e2d726a61f/GCF_000953855.2_ASM95385v3_genomic.fna.gz --refList GCF_000953855.2_ASM95385v3_genomic.fna/target_genomes.txt --output GCF_000953855.2_ASM95385v3_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:20:24,812] [INFO] Task succeeded: fastANI
[2024-01-24 11:20:24,813] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd4af0c05-1add-4488-a3ad-7407fb857367/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:20:24,813] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd4af0c05-1add-4488-a3ad-7407fb857367/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:20:24,830] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:20:24,830] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:20:24,831] [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
Fulvimonas soli	strain=DSM 14263	GCA_003148905.1	155197	155197	type	True	82.6765	630	981	95	below_threshold
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	82.4693	597	981	95	below_threshold
Rhodanobacter denitrificans	strain=2APBS1	GCA_000230695.3	666685	666685	type	True	81.5143	622	981	95	below_threshold
Frateuria flava	strain=MAH-13	GCA_017837635.1	2821489	2821489	type	True	80.6851	548	981	95	below_threshold
Frateuria terrea	strain=DSM 26515	GCA_900109025.1	529704	529704	type	True	80.6252	545	981	95	below_threshold
Frateuria terrea	strain=CGMCC 1.7053	GCA_900115705.1	529704	529704	type	True	80.6189	549	981	95	below_threshold
Dyella solisilvae	strain=DHG54	GCA_003351225.1	1920168	1920168	type	True	79.9944	526	981	95	below_threshold
Rhodanobacter panaciterrae	strain=KCTC 22232	GCA_014651895.1	490572	490572	type	True	79.9727	457	981	95	below_threshold
Vulcaniibacterium thermophilum	strain=KCTC 32020	GCA_007923255.1	1169913	1169913	type	True	79.9294	495	981	95	below_threshold
Vulcaniibacterium thermophilum	strain=KCTC 32020	GCA_014656335.1	1169913	1169913	type	True	79.8864	499	981	95	below_threshold
Dokdonella koreensis	strain=DS-123	GCA_001632775.1	323415	323415	type	True	79.8623	533	981	95	below_threshold
Dokdonella fugitiva	strain=A3	GCA_004342425.1	328517	328517	type	True	79.7559	554	981	95	below_threshold
Dyella kyungheensis	strain=THG-B117	GCA_016905005.1	1242174	1242174	type	True	79.639	494	981	95	below_threshold
Luteimonas marina	strain=FR1330	GCA_007859325.1	488485	488485	type	True	79.6134	489	981	95	below_threshold
Rhodanobacter fulvus	strain=Jip2	GCA_000264315.1	219571	219571	type	True	79.5987	484	981	95	below_threshold
Tahibacter caeni	strain=BUT-6	GCA_024609805.1	1453545	1453545	type	True	79.5333	537	981	95	below_threshold
Arenimonas malthae	strain=CC-JY-1	GCA_000747075.1	354197	354197	type	True	79.5034	450	981	95	below_threshold
Dyella acidiphila	strain=7MK23	GCA_014863405.1	2775866	2775866	type	True	79.4037	454	981	95	below_threshold
Dyella japonica	strain=DSM 16301	GCA_001010355.1	231455	231455	type	True	79.3366	424	981	95	below_threshold
Luteibacter yeojuensis	strain=DSM 17673	GCA_011742875.1	345309	345309	type	True	79.263	444	981	95	below_threshold
Dyella telluris	strain=G9	GCA_014297575.1	2763498	2763498	type	True	79.2402	484	981	95	below_threshold
Luteimonas huabeiensis	strain=HB2	GCA_000559025.1	1244513	1244513	type	True	79.0827	536	981	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:20:24,832] [INFO] DFAST Taxonomy check result was written to GCF_000953855.2_ASM95385v3_genomic.fna/tc_result.tsv
[2024-01-24 11:20:24,833] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:20:24,833] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:20:24,833] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd4af0c05-1add-4488-a3ad-7407fb857367/dqc_reference/checkm_data
[2024-01-24 11:20:24,835] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:20:24,869] [INFO] Task started: CheckM
[2024-01-24 11:20:24,870] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000953855.2_ASM95385v3_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000953855.2_ASM95385v3_genomic.fna/checkm_input GCF_000953855.2_ASM95385v3_genomic.fna/checkm_result
[2024-01-24 11:20:56,684] [INFO] Task succeeded: CheckM
[2024-01-24 11:20:56,686] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:20:56,711] [INFO] ===== Completeness check finished =====
[2024-01-24 11:20:56,711] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:20:56,712] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000953855.2_ASM95385v3_genomic.fna/markers.fasta)
[2024-01-24 11:20:56,712] [INFO] Task started: Blastn
[2024-01-24 11:20:56,712] [INFO] Running command: blastn -query GCF_000953855.2_ASM95385v3_genomic.fna/markers.fasta -db /var/lib/cwl/stgd4af0c05-1add-4488-a3ad-7407fb857367/dqc_reference/reference_markers_gtdb.fasta -out GCF_000953855.2_ASM95385v3_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:58,668] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:58,673] [INFO] Selected 21 target genomes.
[2024-01-24 11:20:58,674] [INFO] Target genome list was writen to GCF_000953855.2_ASM95385v3_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:20:58,692] [INFO] Task started: fastANI
[2024-01-24 11:20:58,692] [INFO] Running command: fastANI --query /var/lib/cwl/stg50bff31d-121e-465e-a159-f3e2d726a61f/GCF_000953855.2_ASM95385v3_genomic.fna.gz --refList GCF_000953855.2_ASM95385v3_genomic.fna/target_genomes_gtdb.txt --output GCF_000953855.2_ASM95385v3_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:21:17,154] [INFO] Task succeeded: fastANI
[2024-01-24 11:21:17,181] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:21:17,182] [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_000953855.2	s__Mizugakiibacter sediminis	100.0	970	981	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Mizugakiibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003148905.1	s__Fulvimonas soli	82.685	628	981	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Fulvimonas	95.0	99.99	99.99	0.99	0.99	2	-
GCF_001428405.1	s__Frateuria_A sp001428405	81.8583	631	981	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	81.539	579	981	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001617365.1	s__Rhodanobacter sp001617365	81.5365	607	981	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	99.98	99.98	0.98	0.97	3	-
GCF_001182895.1	s__Frateuria_B defendens	81.5184	605	981	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Frateuria_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009996615.1	s__Dokdonella_A sp009996615	81.4126	594	981	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013362045.1	s__Frateuria_A sp013362045	81.3981	472	981	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Frateuria_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112865.1	s__Dyella marensis	81.0723	611	981	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001428385.1	s__Rhodanobacter sp001428385	81.0565	574	981	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002001105.1	s__Rhodanobacter sp002001105	80.9162	582	981	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001641285.1	s__Dyella_A thiooxydans	80.9132	562	981	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014843005.1	s__Rhodanobacter sp014843005	80.6249	503	981	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744955.1	s__Dokdonella_A sp017744955	80.5168	613	981	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003241385.1	s__Dokdonella denitrificans_A	80.0308	554	981	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007923255.1	s__Lysobacter thermophilus	79.99	490	981	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	99.99	99.99	0.98	0.98	2	-
GCA_002483055.1	s__Dokdonella sp002483055	79.9614	489	981	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001632775.1	s__Dokdonella koreensis	79.8535	534	981	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000513995.1	s__Pseudoxanthomonas sp000513995	79.4608	484	981	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000513955.1	s__Pseudoxanthomonas suwonensis_C	79.3983	488	981	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	98.37	96.94	0.95	0.91	3	-
GCF_000559025.1	s__Luteimonas huabeiensis	79.1989	523	981	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:21:17,184] [INFO] GTDB search result was written to GCF_000953855.2_ASM95385v3_genomic.fna/result_gtdb.tsv
[2024-01-24 11:21:17,184] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:21:17,189] [INFO] DFAST_QC result json was written to GCF_000953855.2_ASM95385v3_genomic.fna/dqc_result.json
[2024-01-24 11:21:17,189] [INFO] DFAST_QC completed!
[2024-01-24 11:21:17,189] [INFO] Total running time: 0h1m22s