[2024-01-24 14:05:29,069] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:29,071] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:29,071] [INFO] DQC Reference Directory: /var/lib/cwl/stg12e9b397-61f5-42a1-a519-b4e177d9c78c/dqc_reference
[2024-01-24 14:05:30,343] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:30,343] [INFO] Task started: Prodigal
[2024-01-24 14:05:30,344] [INFO] Running command: gunzip -c /var/lib/cwl/stg89941f2e-70b3-439f-b52b-87c3d5d1e631/GCF_002155425.1_ASM215542v1_genomic.fna.gz | prodigal -d GCF_002155425.1_ASM215542v1_genomic.fna/cds.fna -a GCF_002155425.1_ASM215542v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:05:40,422] [INFO] Task succeeded: Prodigal
[2024-01-24 14:05:40,423] [INFO] Task started: HMMsearch
[2024-01-24 14:05:40,423] [INFO] Running command: hmmsearch --tblout GCF_002155425.1_ASM215542v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg12e9b397-61f5-42a1-a519-b4e177d9c78c/dqc_reference/reference_markers.hmm GCF_002155425.1_ASM215542v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:05:40,665] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:05:40,667] [INFO] Found 6/6 markers.
[2024-01-24 14:05:40,697] [INFO] Query marker FASTA was written to GCF_002155425.1_ASM215542v1_genomic.fna/markers.fasta
[2024-01-24 14:05:40,697] [INFO] Task started: Blastn
[2024-01-24 14:05:40,698] [INFO] Running command: blastn -query GCF_002155425.1_ASM215542v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg12e9b397-61f5-42a1-a519-b4e177d9c78c/dqc_reference/reference_markers.fasta -out GCF_002155425.1_ASM215542v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:41,622] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:41,625] [INFO] Selected 13 target genomes.
[2024-01-24 14:05:41,626] [INFO] Target genome list was writen to GCF_002155425.1_ASM215542v1_genomic.fna/target_genomes.txt
[2024-01-24 14:05:41,654] [INFO] Task started: fastANI
[2024-01-24 14:05:41,654] [INFO] Running command: fastANI --query /var/lib/cwl/stg89941f2e-70b3-439f-b52b-87c3d5d1e631/GCF_002155425.1_ASM215542v1_genomic.fna.gz --refList GCF_002155425.1_ASM215542v1_genomic.fna/target_genomes.txt --output GCF_002155425.1_ASM215542v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:05:53,394] [INFO] Task succeeded: fastANI
[2024-01-24 14:05:53,394] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg12e9b397-61f5-42a1-a519-b4e177d9c78c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:05:53,395] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg12e9b397-61f5-42a1-a519-b4e177d9c78c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:05:53,406] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:05:53,406] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:05:53,406] [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 donghaensis	strain=DSM 16220	GCA_002155425.1	267135	267135	suspected-type	True	100.0	1115	1116	95	conclusive
Erythrobacter colymbi	strain=JCM 18338	GCA_002155685.1	1161202	1161202	type	True	85.7724	905	1116	95	below_threshold
Erythrobacter ramosus	strain=JCM 10282	GCA_009828055.1	35811	35811	type	True	84.7254	833	1116	95	below_threshold
Erythrobacter ramosus	strain=DSM 8510	GCA_014195675.1	35811	35811	type	True	84.7136	828	1116	95	below_threshold
Erythrobacter neustonensis	strain=DSM 9434	GCA_001663175.1	1112	1112	type	True	84.2251	790	1116	95	below_threshold
Erythrobacter tepidarius	strain=DSM 10594	GCA_002155695.1	60454	60454	type	True	83.5644	783	1116	95	below_threshold
Erythrobacter dokdonensis	strain=DSW-74	GCA_001677335.1	328225	328225	type	True	83.5571	774	1116	95	below_threshold
Erythrobacter sanguineus	strain=JCM 20691	GCA_002155655.1	198312	198312	type	True	82.8856	758	1116	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	79.5782	501	1116	95	below_threshold
Qipengyuania pelagi	strain=JCM 17468	GCA_009827295.1	994320	994320	type	True	79.2369	452	1116	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	79.2076	445	1116	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	79.0911	434	1116	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	78.6424	398	1116	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:05:53,408] [INFO] DFAST Taxonomy check result was written to GCF_002155425.1_ASM215542v1_genomic.fna/tc_result.tsv
[2024-01-24 14:05:53,408] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:05:53,409] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:05:53,409] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg12e9b397-61f5-42a1-a519-b4e177d9c78c/dqc_reference/checkm_data
[2024-01-24 14:05:53,410] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:05:53,444] [INFO] Task started: CheckM
[2024-01-24 14:05:53,444] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002155425.1_ASM215542v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002155425.1_ASM215542v1_genomic.fna/checkm_input GCF_002155425.1_ASM215542v1_genomic.fna/checkm_result
[2024-01-24 14:06:26,819] [INFO] Task succeeded: CheckM
[2024-01-24 14:06:26,820] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:06:26,846] [INFO] ===== Completeness check finished =====
[2024-01-24 14:06:26,846] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:06:26,847] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002155425.1_ASM215542v1_genomic.fna/markers.fasta)
[2024-01-24 14:06:26,847] [INFO] Task started: Blastn
[2024-01-24 14:06:26,847] [INFO] Running command: blastn -query GCF_002155425.1_ASM215542v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg12e9b397-61f5-42a1-a519-b4e177d9c78c/dqc_reference/reference_markers_gtdb.fasta -out GCF_002155425.1_ASM215542v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:28,601] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:28,604] [INFO] Selected 14 target genomes.
[2024-01-24 14:06:28,605] [INFO] Target genome list was writen to GCF_002155425.1_ASM215542v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:06:28,626] [INFO] Task started: fastANI
[2024-01-24 14:06:28,626] [INFO] Running command: fastANI --query /var/lib/cwl/stg89941f2e-70b3-439f-b52b-87c3d5d1e631/GCF_002155425.1_ASM215542v1_genomic.fna.gz --refList GCF_002155425.1_ASM215542v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002155425.1_ASM215542v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:06:40,196] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:40,208] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:06:40,209] [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_002155425.1	s__Erythrobacter donghaensis	100.0	1114	1116	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_006542605.1	s__Erythrobacter sp006542605	91.2172	983	1116	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	85.7773	904	1116	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001557325.1	s__Erythrobacter donghaensis_B	85.7172	748	1116	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	85.6056	535	1116	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	85.5317	780	1116	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	99.84	99.84	0.90	0.90	2	-
GCA_013822695.1	s__Erythrobacter sp013822695	85.5049	791	1116	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	99.78	99.78	0.82	0.82	2	-
GCF_000331285.1	s__Erythrobacter sp000331285	85.1464	806	1116	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	85.0731	849	1116	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009828055.1	s__Erythrobacter ramosus	84.7306	833	1116	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002952215.1	s__Erythrobacter sp002952215	84.7146	798	1116	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011054555.1	s__Erythrobacter sp011054555	84.4859	566	1116	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	83.9782	782	1116	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004292705.1	s__Erythrobacter sp004292705	83.9174	565	1116	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:06:40,211] [INFO] GTDB search result was written to GCF_002155425.1_ASM215542v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:06:40,211] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:06:40,215] [INFO] DFAST_QC result json was written to GCF_002155425.1_ASM215542v1_genomic.fna/dqc_result.json
[2024-01-24 14:06:40,215] [INFO] DFAST_QC completed!
[2024-01-24 14:06:40,215] [INFO] Total running time: 0h1m11s