[2024-01-24 10:47:54,174] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:54,175] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:54,175] [INFO] DQC Reference Directory: /var/lib/cwl/stg4f622c2c-a69b-4ee1-b7a3-044fd9184610/dqc_reference
[2024-01-24 10:48:03,342] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:48:03,344] [INFO] Task started: Prodigal
[2024-01-24 10:48:03,344] [INFO] Running command: gunzip -c /var/lib/cwl/stg44e52e42-5626-44df-bb4a-df100f8f9cee/GCF_000714795.1_Ery_DSM_8509_v1_genomic.fna.gz | prodigal -d GCF_000714795.1_Ery_DSM_8509_v1_genomic.fna/cds.fna -a GCF_000714795.1_Ery_DSM_8509_v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:48:12,512] [INFO] Task succeeded: Prodigal
[2024-01-24 10:48:12,513] [INFO] Task started: HMMsearch
[2024-01-24 10:48:12,513] [INFO] Running command: hmmsearch --tblout GCF_000714795.1_Ery_DSM_8509_v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4f622c2c-a69b-4ee1-b7a3-044fd9184610/dqc_reference/reference_markers.hmm GCF_000714795.1_Ery_DSM_8509_v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:48:12,776] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:48:12,778] [INFO] Found 6/6 markers.
[2024-01-24 10:48:12,809] [INFO] Query marker FASTA was written to GCF_000714795.1_Ery_DSM_8509_v1_genomic.fna/markers.fasta
[2024-01-24 10:48:12,810] [INFO] Task started: Blastn
[2024-01-24 10:48:12,810] [INFO] Running command: blastn -query GCF_000714795.1_Ery_DSM_8509_v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4f622c2c-a69b-4ee1-b7a3-044fd9184610/dqc_reference/reference_markers.fasta -out GCF_000714795.1_Ery_DSM_8509_v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:13,648] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:13,652] [INFO] Selected 15 target genomes.
[2024-01-24 10:48:13,653] [INFO] Target genome list was writen to GCF_000714795.1_Ery_DSM_8509_v1_genomic.fna/target_genomes.txt
[2024-01-24 10:48:14,245] [INFO] Task started: fastANI
[2024-01-24 10:48:14,246] [INFO] Running command: fastANI --query /var/lib/cwl/stg44e52e42-5626-44df-bb4a-df100f8f9cee/GCF_000714795.1_Ery_DSM_8509_v1_genomic.fna.gz --refList GCF_000714795.1_Ery_DSM_8509_v1_genomic.fna/target_genomes.txt --output GCF_000714795.1_Ery_DSM_8509_v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:24,240] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:24,241] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4f622c2c-a69b-4ee1-b7a3-044fd9184610/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:24,241] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4f622c2c-a69b-4ee1-b7a3-044fd9184610/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:24,254] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 10:48:24,254] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:48:24,254] [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 litoralis	strain=DSM 8509	GCA_000714795.1	39960	39960	type	True	100.0	1059	1060	95	conclusive
Erythrobacter litoralis	strain=DSM 8509	GCA_001719165.1	39960	39960	type	True	99.9987	1059	1060	95	conclusive
Erythrobacter colymbi	strain=JCM 18338	GCA_002155685.1	1161202	1161202	type	True	80.725	641	1060	95	below_threshold
Erythrobacter donghaensis	strain=DSM 16220	GCA_002155425.1	267135	267135	suspected-type	True	80.6521	619	1060	95	below_threshold
Erythrobacter dokdonensis	strain=DSW-74	GCA_001677335.1	328225	328225	type	True	80.6431	625	1060	95	below_threshold
Erythrobacter dokdonensis	strain=DSM 17193	GCA_002155305.1	328225	328225	type	True	80.6058	632	1060	95	below_threshold
Erythrobacter sanguineus	strain=JCM 20691	GCA_002155655.1	198312	198312	type	True	80.3148	617	1060	95	below_threshold
Erythrobacter tepidarius	strain=DSM 10594	GCA_002155695.1	60454	60454	type	True	80.3068	608	1060	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	79.6596	476	1060	95	below_threshold
Qipengyuania pelagi	strain=JCM 17468	GCA_009827295.1	994320	994320	type	True	79.4848	456	1060	95	below_threshold
Alteriqipengyuania abyssalis	strain=NZ-12B	GCA_019857185.1	2860200	2860200	type	True	79.2595	455	1060	95	below_threshold
Qipengyuania sphaerica	strain=GH29	GCA_019711595.1	2867243	2867243	type	True	79.1376	416	1060	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	79.0699	435	1060	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	79.016	443	1060	95	below_threshold
Erythrobacter rubeus	strain=KMU-140	GCA_014705715.1	2760803	2760803	type	True	78.9643	479	1060	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:24,257] [INFO] DFAST Taxonomy check result was written to GCF_000714795.1_Ery_DSM_8509_v1_genomic.fna/tc_result.tsv
[2024-01-24 10:48:24,257] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:24,257] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:24,258] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4f622c2c-a69b-4ee1-b7a3-044fd9184610/dqc_reference/checkm_data
[2024-01-24 10:48:24,258] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:24,294] [INFO] Task started: CheckM
[2024-01-24 10:48:24,294] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000714795.1_Ery_DSM_8509_v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000714795.1_Ery_DSM_8509_v1_genomic.fna/checkm_input GCF_000714795.1_Ery_DSM_8509_v1_genomic.fna/checkm_result
[2024-01-24 10:48:54,788] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:54,790] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:54,808] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:54,808] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:54,809] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000714795.1_Ery_DSM_8509_v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:54,809] [INFO] Task started: Blastn
[2024-01-24 10:48:54,809] [INFO] Running command: blastn -query GCF_000714795.1_Ery_DSM_8509_v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4f622c2c-a69b-4ee1-b7a3-044fd9184610/dqc_reference/reference_markers_gtdb.fasta -out GCF_000714795.1_Ery_DSM_8509_v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:56,240] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:56,245] [INFO] Selected 13 target genomes.
[2024-01-24 10:48:56,245] [INFO] Target genome list was writen to GCF_000714795.1_Ery_DSM_8509_v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:56,272] [INFO] Task started: fastANI
[2024-01-24 10:48:56,272] [INFO] Running command: fastANI --query /var/lib/cwl/stg44e52e42-5626-44df-bb4a-df100f8f9cee/GCF_000714795.1_Ery_DSM_8509_v1_genomic.fna.gz --refList GCF_000714795.1_Ery_DSM_8509_v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000714795.1_Ery_DSM_8509_v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:49:05,710] [INFO] Task succeeded: fastANI
[2024-01-24 10:49:05,727] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:49:05,727] [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_001719165.1	s__Erythrobacter litoralis	99.9987	1059	1060	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCA_011765465.1	s__Erythrobacter sp011765465	86.7882	882	1060	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105095.1	s__Erythrobacter sp900105095	86.1824	829	1060	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCA_016125555.1	s__Erythrobacter sp016125555	81.4854	653	1060	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	81.1353	656	1060	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	81.0054	486	1060	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018205975.1	s__Erythrobacter sp018205975	80.9402	642	1060	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	80.7849	627	1060	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	80.7579	562	1060	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	99.84	99.84	0.90	0.90	2	-
GCF_002155685.1	s__Erythrobacter colymbi	80.7247	641	1060	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000331285.1	s__Erythrobacter sp000331285	80.6964	606	1060	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001677335.1	s__Erythrobacter dokdonensis	80.6238	627	1060	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_009993605.1	s__Qipengyuania sp009993605	79.3953	445	1060	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:49:05,731] [INFO] GTDB search result was written to GCF_000714795.1_Ery_DSM_8509_v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:49:05,732] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:49:05,736] [INFO] DFAST_QC result json was written to GCF_000714795.1_Ery_DSM_8509_v1_genomic.fna/dqc_result.json
[2024-01-24 10:49:05,737] [INFO] DFAST_QC completed!
[2024-01-24 10:49:05,737] [INFO] Total running time: 0h1m12s