[2023-06-29 08:44:34,353] [INFO] DFAST_QC pipeline started.
[2023-06-29 08:44:34,355] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 08:44:34,356] [INFO] DQC Reference Directory: /var/lib/cwl/stg905cd87f-9513-40fa-bb5b-7480766bf28f/dqc_reference
[2023-06-29 08:44:35,632] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 08:44:35,633] [INFO] Task started: Prodigal
[2023-06-29 08:44:35,634] [INFO] Running command: gunzip -c /var/lib/cwl/stgabdbf34b-d828-4ec1-9fd3-d0ba912b93da/GCA_020852005.1_ASM2085200v1_genomic.fna.gz | prodigal -d GCA_020852005.1_ASM2085200v1_genomic.fna/cds.fna -a GCA_020852005.1_ASM2085200v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 08:44:43,446] [INFO] Task succeeded: Prodigal
[2023-06-29 08:44:43,446] [INFO] Task started: HMMsearch
[2023-06-29 08:44:43,447] [INFO] Running command: hmmsearch --tblout GCA_020852005.1_ASM2085200v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg905cd87f-9513-40fa-bb5b-7480766bf28f/dqc_reference/reference_markers.hmm GCA_020852005.1_ASM2085200v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 08:44:43,693] [INFO] Task succeeded: HMMsearch
[2023-06-29 08:44:43,695] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgabdbf34b-d828-4ec1-9fd3-d0ba912b93da/GCA_020852005.1_ASM2085200v1_genomic.fna.gz]
[2023-06-29 08:44:43,729] [INFO] Query marker FASTA was written to GCA_020852005.1_ASM2085200v1_genomic.fna/markers.fasta
[2023-06-29 08:44:43,730] [INFO] Task started: Blastn
[2023-06-29 08:44:43,730] [INFO] Running command: blastn -query GCA_020852005.1_ASM2085200v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg905cd87f-9513-40fa-bb5b-7480766bf28f/dqc_reference/reference_markers.fasta -out GCA_020852005.1_ASM2085200v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 08:44:44,437] [INFO] Task succeeded: Blastn
[2023-06-29 08:44:44,441] [INFO] Selected 13 target genomes.
[2023-06-29 08:44:44,441] [INFO] Target genome list was writen to GCA_020852005.1_ASM2085200v1_genomic.fna/target_genomes.txt
[2023-06-29 08:44:44,445] [INFO] Task started: fastANI
[2023-06-29 08:44:44,446] [INFO] Running command: fastANI --query /var/lib/cwl/stgabdbf34b-d828-4ec1-9fd3-d0ba912b93da/GCA_020852005.1_ASM2085200v1_genomic.fna.gz --refList GCA_020852005.1_ASM2085200v1_genomic.fna/target_genomes.txt --output GCA_020852005.1_ASM2085200v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 08:44:54,187] [INFO] Task succeeded: fastANI
[2023-06-29 08:44:54,188] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg905cd87f-9513-40fa-bb5b-7480766bf28f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 08:44:54,188] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg905cd87f-9513-40fa-bb5b-7480766bf28f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 08:44:54,200] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 08:44:54,200] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 08:44:54,200] [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
Dokdonella fugitiva	strain=A3	GCA_004342425.1	328517	328517	type	True	80.1859	433	738	95	below_threshold
Dokdonella koreensis	strain=DS-123	GCA_001632775.1	323415	323415	type	True	78.7333	308	738	95	below_threshold
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	78.3617	255	738	95	below_threshold
Fulvimonas soli	strain=DSM 14263	GCA_003148905.1	155197	155197	type	True	78.3238	275	738	95	below_threshold
Dokdonella immobilis	strain=CGMCC 1.7659	GCA_900115085.1	578942	578942	type	True	78.1587	290	738	95	below_threshold
Rudaea cellulosilytica	strain=DSM 22992	GCA_000378125.1	540746	540746	type	True	77.9652	274	738	95	below_threshold
Oleiagrimonas citrea	strain=MEBiC09124	GCA_012395255.1	1665687	1665687	type	True	77.9461	212	738	95	below_threshold
Tahibacter caeni	strain=BUT-6	GCA_024609805.1	1453545	1453545	type	True	77.9221	284	738	95	below_threshold
Dyella solisilvae	strain=DHG54	GCA_003351225.1	1920168	1920168	type	True	77.9127	223	738	95	below_threshold
Rhodanobacter fulvus	strain=Jip2	GCA_000264315.1	219571	219571	type	True	77.8037	216	738	95	below_threshold
Tahibacter aquaticus	strain=DSM 21667	GCA_004363655.1	520092	520092	type	True	77.7962	265	738	95	below_threshold
Dyella japonica	strain=DSM 16301	GCA_001010355.1	231455	231455	type	True	77.6582	185	738	95	below_threshold
Dyella acidiphila	strain=7MK23	GCA_014863405.1	2775866	2775866	type	True	77.5985	209	738	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 08:44:54,203] [INFO] DFAST Taxonomy check result was written to GCA_020852005.1_ASM2085200v1_genomic.fna/tc_result.tsv
[2023-06-29 08:44:54,203] [INFO] ===== Taxonomy check completed =====
[2023-06-29 08:44:54,203] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 08:44:54,204] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg905cd87f-9513-40fa-bb5b-7480766bf28f/dqc_reference/checkm_data
[2023-06-29 08:44:54,205] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 08:44:54,234] [INFO] Task started: CheckM
[2023-06-29 08:44:54,234] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020852005.1_ASM2085200v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020852005.1_ASM2085200v1_genomic.fna/checkm_input GCA_020852005.1_ASM2085200v1_genomic.fna/checkm_result
[2023-06-29 08:45:41,022] [INFO] Task succeeded: CheckM
[2023-06-29 08:45:41,023] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.04%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 08:45:41,046] [INFO] ===== Completeness check finished =====
[2023-06-29 08:45:41,047] [INFO] ===== Start GTDB Search =====
[2023-06-29 08:45:41,047] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020852005.1_ASM2085200v1_genomic.fna/markers.fasta)
[2023-06-29 08:45:41,048] [INFO] Task started: Blastn
[2023-06-29 08:45:41,048] [INFO] Running command: blastn -query GCA_020852005.1_ASM2085200v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg905cd87f-9513-40fa-bb5b-7480766bf28f/dqc_reference/reference_markers_gtdb.fasta -out GCA_020852005.1_ASM2085200v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 08:45:42,054] [INFO] Task succeeded: Blastn
[2023-06-29 08:45:42,059] [INFO] Selected 8 target genomes.
[2023-06-29 08:45:42,060] [INFO] Target genome list was writen to GCA_020852005.1_ASM2085200v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 08:45:42,065] [INFO] Task started: fastANI
[2023-06-29 08:45:42,066] [INFO] Running command: fastANI --query /var/lib/cwl/stgabdbf34b-d828-4ec1-9fd3-d0ba912b93da/GCA_020852005.1_ASM2085200v1_genomic.fna.gz --refList GCA_020852005.1_ASM2085200v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020852005.1_ASM2085200v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 08:45:48,264] [INFO] Task succeeded: fastANI
[2023-06-29 08:45:48,278] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 08:45:48,278] [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
GCA_002632325.1	s__Dokdonella_A sp002632325	99.4953	712	738	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_014338185.1	s__Dokdonella_A sp014338185	81.4192	494	738	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella_A	95.0	96.24	96.24	0.88	0.88	2	-
GCF_004342425.1	s__Dokdonella_A fugitiva	80.1973	432	738	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella_A	95.0	99.45	99.45	0.96	0.96	2	-
GCA_017744955.1	s__Dokdonella_A sp017744955	79.9329	440	738	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014138265.1	s__Dokdonella_A fugitiva_A	79.9274	448	738	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_002297645.1	s__Dokdonella_A sp002297645	79.5719	356	738	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella_A	95.0	99.81	99.81	0.89	0.89	2	-
GCA_004143945.1	s__Dokdonella_A sp004143945	79.2873	410	738	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001632775.1	s__Dokdonella koreensis	78.7316	308	738	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 08:45:48,280] [INFO] GTDB search result was written to GCA_020852005.1_ASM2085200v1_genomic.fna/result_gtdb.tsv
[2023-06-29 08:45:48,281] [INFO] ===== GTDB Search completed =====
[2023-06-29 08:45:48,284] [INFO] DFAST_QC result json was written to GCA_020852005.1_ASM2085200v1_genomic.fna/dqc_result.json
[2023-06-29 08:45:48,284] [INFO] DFAST_QC completed!
[2023-06-29 08:45:48,285] [INFO] Total running time: 0h1m14s