[2024-01-25 18:54:20,587] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:54:20,588] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:54:20,588] [INFO] DQC Reference Directory: /var/lib/cwl/stg714d7999-4132-41b7-b284-a48cd4159a0f/dqc_reference
[2024-01-25 18:54:21,725] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:54:21,726] [INFO] Task started: Prodigal
[2024-01-25 18:54:21,726] [INFO] Running command: gunzip -c /var/lib/cwl/stgb866ba19-9641-4a20-9256-50b1caeacf7e/GCF_009828055.1_ASM982805v1_genomic.fna.gz | prodigal -d GCF_009828055.1_ASM982805v1_genomic.fna/cds.fna -a GCF_009828055.1_ASM982805v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:54:30,626] [INFO] Task succeeded: Prodigal
[2024-01-25 18:54:30,627] [INFO] Task started: HMMsearch
[2024-01-25 18:54:30,627] [INFO] Running command: hmmsearch --tblout GCF_009828055.1_ASM982805v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg714d7999-4132-41b7-b284-a48cd4159a0f/dqc_reference/reference_markers.hmm GCF_009828055.1_ASM982805v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:54:30,834] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:54:30,835] [INFO] Found 6/6 markers.
[2024-01-25 18:54:30,864] [INFO] Query marker FASTA was written to GCF_009828055.1_ASM982805v1_genomic.fna/markers.fasta
[2024-01-25 18:54:30,864] [INFO] Task started: Blastn
[2024-01-25 18:54:30,864] [INFO] Running command: blastn -query GCF_009828055.1_ASM982805v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg714d7999-4132-41b7-b284-a48cd4159a0f/dqc_reference/reference_markers.fasta -out GCF_009828055.1_ASM982805v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:54:31,732] [INFO] Task succeeded: Blastn
[2024-01-25 18:54:31,735] [INFO] Selected 13 target genomes.
[2024-01-25 18:54:31,735] [INFO] Target genome list was writen to GCF_009828055.1_ASM982805v1_genomic.fna/target_genomes.txt
[2024-01-25 18:54:31,742] [INFO] Task started: fastANI
[2024-01-25 18:54:31,742] [INFO] Running command: fastANI --query /var/lib/cwl/stgb866ba19-9641-4a20-9256-50b1caeacf7e/GCF_009828055.1_ASM982805v1_genomic.fna.gz --refList GCF_009828055.1_ASM982805v1_genomic.fna/target_genomes.txt --output GCF_009828055.1_ASM982805v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:54:40,769] [INFO] Task succeeded: fastANI
[2024-01-25 18:54:40,769] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg714d7999-4132-41b7-b284-a48cd4159a0f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:54:40,769] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg714d7999-4132-41b7-b284-a48cd4159a0f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:54:40,778] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:54:40,778] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:54:40,778] [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
Erythrobacter ramosus	strain=JCM 10282	GCA_009828055.1	35811	35811	type	True	100.0	1073	1075	95	conclusive
Erythrobacter ramosus	strain=DSM 8510	GCA_014195675.1	35811	35811	type	True	99.993	1074	1075	95	conclusive
Erythrobacter donghaensis	strain=DSM 16220	GCA_002155425.1	267135	267135	suspected-type	True	84.7636	831	1075	95	below_threshold
Erythrobacter colymbi	strain=JCM 18338	GCA_002155685.1	1161202	1161202	type	True	84.455	830	1075	95	below_threshold
Erythrobacter neustonensis	strain=DSM 9434	GCA_001663175.1	1112	1112	type	True	83.0671	748	1075	95	below_threshold
Erythrobacter sanguineus	strain=JCM 20691	GCA_002155655.1	198312	198312	type	True	82.923	741	1075	95	below_threshold
Erythrobacter dokdonensis	strain=DSW-74	GCA_001677335.1	328225	328225	type	True	82.6231	726	1075	95	below_threshold
Erythrobacter tepidarius	strain=DSM 10594	GCA_002155695.1	60454	60454	type	True	82.6205	735	1075	95	below_threshold
Qipengyuania aurantiaca	strain=1NDH13	GCA_019711375.1	2867233	2867233	type	True	78.8015	406	1075	95	below_threshold
Qipengyuania pelagi	strain=JCM 17468	GCA_009827295.1	994320	994320	type	True	78.7965	387	1075	95	below_threshold
Alteriqipengyuania abyssalis	strain=NZ-12B	GCA_019857185.1	2860200	2860200	type	True	78.742	437	1075	95	below_threshold
Qipengyuania sphaerica	strain=GH29	GCA_019711595.1	2867243	2867243	type	True	78.691	381	1075	95	below_threshold
Qipengyuania huizhouensis	strain=YG19	GCA_019711635.1	2867245	2867245	type	True	78.5497	273	1075	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:54:40,779] [INFO] DFAST Taxonomy check result was written to GCF_009828055.1_ASM982805v1_genomic.fna/tc_result.tsv
[2024-01-25 18:54:40,780] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:54:40,780] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:54:40,780] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg714d7999-4132-41b7-b284-a48cd4159a0f/dqc_reference/checkm_data
[2024-01-25 18:54:40,781] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:54:40,815] [INFO] Task started: CheckM
[2024-01-25 18:54:40,815] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009828055.1_ASM982805v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009828055.1_ASM982805v1_genomic.fna/checkm_input GCF_009828055.1_ASM982805v1_genomic.fna/checkm_result
[2024-01-25 18:55:09,281] [INFO] Task succeeded: CheckM
[2024-01-25 18:55:09,282] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:55:09,303] [INFO] ===== Completeness check finished =====
[2024-01-25 18:55:09,304] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:55:09,304] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009828055.1_ASM982805v1_genomic.fna/markers.fasta)
[2024-01-25 18:55:09,304] [INFO] Task started: Blastn
[2024-01-25 18:55:09,304] [INFO] Running command: blastn -query GCF_009828055.1_ASM982805v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg714d7999-4132-41b7-b284-a48cd4159a0f/dqc_reference/reference_markers_gtdb.fasta -out GCF_009828055.1_ASM982805v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:55:11,003] [INFO] Task succeeded: Blastn
[2024-01-25 18:55:11,007] [INFO] Selected 14 target genomes.
[2024-01-25 18:55:11,007] [INFO] Target genome list was writen to GCF_009828055.1_ASM982805v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:55:11,034] [INFO] Task started: fastANI
[2024-01-25 18:55:11,034] [INFO] Running command: fastANI --query /var/lib/cwl/stgb866ba19-9641-4a20-9256-50b1caeacf7e/GCF_009828055.1_ASM982805v1_genomic.fna.gz --refList GCF_009828055.1_ASM982805v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009828055.1_ASM982805v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:55:22,066] [INFO] Task succeeded: fastANI
[2024-01-25 18:55:22,075] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:55:22,075] [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_009828055.1	s__Erythrobacter ramosus	100.0	1073	1075	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCA_002482865.1	s__Erythrobacter sp002482865	92.6516	633	1075	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009905735.1	s__Erythrobacter sp009905735	91.9327	922	1075	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003724185.1	s__Erythrobacter sp003724185	85.6719	849	1075	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002855495.1	s__Erythrobacter sp002855495	84.8792	779	1075	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002155425.1	s__Erythrobacter donghaensis	84.7636	831	1075	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006542605.1	s__Erythrobacter sp006542605	84.6817	812	1075	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013822695.1	s__Erythrobacter sp013822695	84.2212	753	1075	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	99.78	99.78	0.82	0.82	2	-
GCA_013911835.1	s__Erythrobacter sp013911835	84.0743	510	1075	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001557115.1	s__Erythrobacter sp001557115	83.8258	768	1075	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	99.84	99.84	0.90	0.90	2	-
GCF_002952215.1	s__Erythrobacter sp002952215	83.74	762	1075	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001556995.1	s__Erythrobacter sp001556995	83.5618	708	1075	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009995225.1	s__Erythrobacter sp009995225	83.4793	724	1075	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	99.97	99.95	0.97	0.95	3	-
GCF_001296025.1	s__Erythrobacter sp001296025	83.2535	760	1075	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:55:22,077] [INFO] GTDB search result was written to GCF_009828055.1_ASM982805v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:55:22,077] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:55:22,094] [INFO] DFAST_QC result json was written to GCF_009828055.1_ASM982805v1_genomic.fna/dqc_result.json
[2024-01-25 18:55:22,094] [INFO] DFAST_QC completed!
[2024-01-25 18:55:22,094] [INFO] Total running time: 0h1m2s