[2023-06-29 13:18:19,945] [INFO] DFAST_QC pipeline started.
[2023-06-29 13:18:19,948] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 13:18:19,948] [INFO] DQC Reference Directory: /var/lib/cwl/stg31e28970-6b69-40af-b6ce-68d8cdc442d9/dqc_reference
[2023-06-29 13:18:21,219] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 13:18:21,220] [INFO] Task started: Prodigal
[2023-06-29 13:18:21,220] [INFO] Running command: gunzip -c /var/lib/cwl/stg5339d674-276d-4454-b0e7-621a1380479a/GCA_023653175.1_ASM2365317v1_genomic.fna.gz | prodigal -d GCA_023653175.1_ASM2365317v1_genomic.fna/cds.fna -a GCA_023653175.1_ASM2365317v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 13:18:30,952] [INFO] Task succeeded: Prodigal
[2023-06-29 13:18:30,953] [INFO] Task started: HMMsearch
[2023-06-29 13:18:30,953] [INFO] Running command: hmmsearch --tblout GCA_023653175.1_ASM2365317v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg31e28970-6b69-40af-b6ce-68d8cdc442d9/dqc_reference/reference_markers.hmm GCA_023653175.1_ASM2365317v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 13:18:31,223] [INFO] Task succeeded: HMMsearch
[2023-06-29 13:18:31,224] [INFO] Found 6/6 markers.
[2023-06-29 13:18:31,269] [INFO] Query marker FASTA was written to GCA_023653175.1_ASM2365317v1_genomic.fna/markers.fasta
[2023-06-29 13:18:31,269] [INFO] Task started: Blastn
[2023-06-29 13:18:31,269] [INFO] Running command: blastn -query GCA_023653175.1_ASM2365317v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg31e28970-6b69-40af-b6ce-68d8cdc442d9/dqc_reference/reference_markers.fasta -out GCA_023653175.1_ASM2365317v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 13:18:32,133] [INFO] Task succeeded: Blastn
[2023-06-29 13:18:32,137] [INFO] Selected 13 target genomes.
[2023-06-29 13:18:32,138] [INFO] Target genome list was writen to GCA_023653175.1_ASM2365317v1_genomic.fna/target_genomes.txt
[2023-06-29 13:18:32,176] [INFO] Task started: fastANI
[2023-06-29 13:18:32,176] [INFO] Running command: fastANI --query /var/lib/cwl/stg5339d674-276d-4454-b0e7-621a1380479a/GCA_023653175.1_ASM2365317v1_genomic.fna.gz --refList GCA_023653175.1_ASM2365317v1_genomic.fna/target_genomes.txt --output GCA_023653175.1_ASM2365317v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 13:18:41,287] [INFO] Task succeeded: fastANI
[2023-06-29 13:18:41,288] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg31e28970-6b69-40af-b6ce-68d8cdc442d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 13:18:41,289] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg31e28970-6b69-40af-b6ce-68d8cdc442d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 13:18:41,305] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 13:18:41,305] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 13:18:41,306] [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 colymbi	strain=JCM 18338	GCA_002155685.1	1161202	1161202	type	True	86.665	840	1084	95	below_threshold
Erythrobacter donghaensis	strain=DSM 16220	GCA_002155425.1	267135	267135	suspected-type	True	85.3613	783	1084	95	below_threshold
Erythrobacter ramosus	strain=JCM 10282	GCA_009828055.1	35811	35811	type	True	84.0008	734	1084	95	below_threshold
Erythrobacter ramosus	strain=DSM 8510	GCA_014195675.1	35811	35811	type	True	83.9405	739	1084	95	below_threshold
Erythrobacter neustonensis	strain=DSM 9434	GCA_001663175.1	1112	1112	type	True	83.7222	703	1084	95	below_threshold
Erythrobacter tepidarius	strain=DSM 10594	GCA_002155695.1	60454	60454	type	True	83.4113	676	1084	95	below_threshold
Erythrobacter dokdonensis	strain=DSM 17193	GCA_002155305.1	328225	328225	type	True	83.0243	658	1084	95	below_threshold
Erythrobacter dokdonensis	strain=DSW-74	GCA_001677335.1	328225	328225	type	True	82.9872	655	1084	95	below_threshold
Qipengyuania aurantiaca	strain=1NDH13	GCA_019711375.1	2867233	2867233	type	True	78.9551	396	1084	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	78.7605	399	1084	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	78.6864	403	1084	95	below_threshold
Qipengyuania pelagi	strain=JCM 17468	GCA_009827295.1	994320	994320	type	True	78.6823	376	1084	95	below_threshold
Qipengyuania huizhouensis	strain=YG19	GCA_019711635.1	2867245	2867245	type	True	78.1227	266	1084	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 13:18:41,308] [INFO] DFAST Taxonomy check result was written to GCA_023653175.1_ASM2365317v1_genomic.fna/tc_result.tsv
[2023-06-29 13:18:41,309] [INFO] ===== Taxonomy check completed =====
[2023-06-29 13:18:41,309] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 13:18:41,309] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg31e28970-6b69-40af-b6ce-68d8cdc442d9/dqc_reference/checkm_data
[2023-06-29 13:18:41,311] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 13:18:41,357] [INFO] Task started: CheckM
[2023-06-29 13:18:41,357] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_023653175.1_ASM2365317v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_023653175.1_ASM2365317v1_genomic.fna/checkm_input GCA_023653175.1_ASM2365317v1_genomic.fna/checkm_result
[2023-06-29 13:19:13,613] [INFO] Task succeeded: CheckM
[2023-06-29 13:19:13,614] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.12%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 13:19:13,634] [INFO] ===== Completeness check finished =====
[2023-06-29 13:19:13,635] [INFO] ===== Start GTDB Search =====
[2023-06-29 13:19:13,635] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_023653175.1_ASM2365317v1_genomic.fna/markers.fasta)
[2023-06-29 13:19:13,636] [INFO] Task started: Blastn
[2023-06-29 13:19:13,636] [INFO] Running command: blastn -query GCA_023653175.1_ASM2365317v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg31e28970-6b69-40af-b6ce-68d8cdc442d9/dqc_reference/reference_markers_gtdb.fasta -out GCA_023653175.1_ASM2365317v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 13:19:15,162] [INFO] Task succeeded: Blastn
[2023-06-29 13:19:15,166] [INFO] Selected 13 target genomes.
[2023-06-29 13:19:15,166] [INFO] Target genome list was writen to GCA_023653175.1_ASM2365317v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 13:19:15,184] [INFO] Task started: fastANI
[2023-06-29 13:19:15,184] [INFO] Running command: fastANI --query /var/lib/cwl/stg5339d674-276d-4454-b0e7-621a1380479a/GCA_023653175.1_ASM2365317v1_genomic.fna.gz --refList GCA_023653175.1_ASM2365317v1_genomic.fna/target_genomes_gtdb.txt --output GCA_023653175.1_ASM2365317v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 13:19:25,865] [INFO] Task succeeded: fastANI
[2023-06-29 13:19:25,883] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 13:19:25,883] [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_013822695.1	s__Erythrobacter sp013822695	89.2943	762	1084	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	99.78	99.78	0.82	0.82	2	-
GCF_001557325.1	s__Erythrobacter donghaensis_B	89.0506	778	1084	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	99.70	99.64	0.86	0.85	7	-
GCA_013911835.1	s__Erythrobacter sp013911835	88.87	546	1084	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	88.3168	798	1084	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	99.84	99.84	0.90	0.90	2	-
GCF_000331285.1	s__Erythrobacter sp000331285	87.9322	753	1084	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002155685.1	s__Erythrobacter colymbi	86.6506	841	1084	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002215495.1	s__Erythrobacter sp002215495	86.1634	788	1084	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	85.3507	784	1084	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	85.3172	805	1084	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	84.2935	749	1084	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002952215.1	s__Erythrobacter sp002952215	83.8961	712	1084	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002482865.1	s__Erythrobacter sp002482865	83.4522	537	1084	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002155695.1	s__Erythrobacter tepidarius	83.4055	676	1084	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 13:19:25,885] [INFO] GTDB search result was written to GCA_023653175.1_ASM2365317v1_genomic.fna/result_gtdb.tsv
[2023-06-29 13:19:25,886] [INFO] ===== GTDB Search completed =====
[2023-06-29 13:19:25,889] [INFO] DFAST_QC result json was written to GCA_023653175.1_ASM2365317v1_genomic.fna/dqc_result.json
[2023-06-29 13:19:25,890] [INFO] DFAST_QC completed!
[2023-06-29 13:19:25,890] [INFO] Total running time: 0h1m6s