[2024-01-24 14:22:16,810] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:16,812] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:16,812] [INFO] DQC Reference Directory: /var/lib/cwl/stg30fc1904-0dfb-4c52-ba46-c1d90034ea9b/dqc_reference
[2024-01-24 14:22:18,088] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:18,089] [INFO] Task started: Prodigal
[2024-01-24 14:22:18,089] [INFO] Running command: gunzip -c /var/lib/cwl/stg0f620069-2144-43e5-9075-c0ff90e6fe2f/GCF_028595285.1_ASM2859528v1_genomic.fna.gz | prodigal -d GCF_028595285.1_ASM2859528v1_genomic.fna/cds.fna -a GCF_028595285.1_ASM2859528v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:27,504] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:27,505] [INFO] Task started: HMMsearch
[2024-01-24 14:22:27,505] [INFO] Running command: hmmsearch --tblout GCF_028595285.1_ASM2859528v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg30fc1904-0dfb-4c52-ba46-c1d90034ea9b/dqc_reference/reference_markers.hmm GCF_028595285.1_ASM2859528v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:27,751] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:27,753] [INFO] Found 6/6 markers.
[2024-01-24 14:22:27,787] [INFO] Query marker FASTA was written to GCF_028595285.1_ASM2859528v1_genomic.fna/markers.fasta
[2024-01-24 14:22:27,787] [INFO] Task started: Blastn
[2024-01-24 14:22:27,787] [INFO] Running command: blastn -query GCF_028595285.1_ASM2859528v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg30fc1904-0dfb-4c52-ba46-c1d90034ea9b/dqc_reference/reference_markers.fasta -out GCF_028595285.1_ASM2859528v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:28,700] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:28,704] [INFO] Selected 14 target genomes.
[2024-01-24 14:22:28,705] [INFO] Target genome list was writen to GCF_028595285.1_ASM2859528v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:28,718] [INFO] Task started: fastANI
[2024-01-24 14:22:28,718] [INFO] Running command: fastANI --query /var/lib/cwl/stg0f620069-2144-43e5-9075-c0ff90e6fe2f/GCF_028595285.1_ASM2859528v1_genomic.fna.gz --refList GCF_028595285.1_ASM2859528v1_genomic.fna/target_genomes.txt --output GCF_028595285.1_ASM2859528v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:22:37,959] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:37,959] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg30fc1904-0dfb-4c52-ba46-c1d90034ea9b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:22:37,960] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg30fc1904-0dfb-4c52-ba46-c1d90034ea9b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:22:37,971] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:22:37,971] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:22:37,972] [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 dokdonensis	strain=DSM 17193	GCA_002155305.1	328225	328225	type	True	85.0795	806	1030	95	below_threshold
Erythrobacter dokdonensis	strain=DSW-74	GCA_001677335.1	328225	328225	type	True	85.0468	811	1030	95	below_threshold
Erythrobacter sanguineus	strain=JCM 20691	GCA_002155655.1	198312	198312	type	True	84.1183	799	1030	95	below_threshold
Erythrobacter sanguineus	strain=DSM 11032	GCA_900143235.1	198312	198312	type	True	84.107	789	1030	95	below_threshold
Erythrobacter tepidarius	strain=DSM 10594	GCA_002155695.1	60454	60454	type	True	83.899	765	1030	95	below_threshold
Erythrobacter donghaensis	strain=DSM 16220	GCA_002155425.1	267135	267135	suspected-type	True	83.7971	786	1030	95	below_threshold
Erythrobacter colymbi	strain=JCM 18338	GCA_002155685.1	1161202	1161202	type	True	83.5196	784	1030	95	below_threshold
Erythrobacter ramosus	strain=JCM 10282	GCA_009828055.1	35811	35811	type	True	82.8719	756	1030	95	below_threshold
Erythrobacter ramosus	strain=DSM 8510	GCA_014195675.1	35811	35811	type	True	82.8243	770	1030	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	79.445	471	1030	95	below_threshold
Qipengyuania aurantiaca	strain=1NDH13	GCA_019711375.1	2867233	2867233	type	True	79.1556	443	1030	95	below_threshold
Qipengyuania gelatinilytica	strain=1NDH1	GCA_019711315.1	2867231	2867231	type	True	79.052	396	1030	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	78.8605	412	1030	95	below_threshold
Qipengyuania huizhouensis	strain=YG19	GCA_019711635.1	2867245	2867245	type	True	78.7544	326	1030	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:22:37,973] [INFO] DFAST Taxonomy check result was written to GCF_028595285.1_ASM2859528v1_genomic.fna/tc_result.tsv
[2024-01-24 14:22:37,974] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:22:37,974] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:22:37,974] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg30fc1904-0dfb-4c52-ba46-c1d90034ea9b/dqc_reference/checkm_data
[2024-01-24 14:22:37,975] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:22:38,012] [INFO] Task started: CheckM
[2024-01-24 14:22:38,012] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_028595285.1_ASM2859528v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_028595285.1_ASM2859528v1_genomic.fna/checkm_input GCF_028595285.1_ASM2859528v1_genomic.fna/checkm_result
[2024-01-24 14:23:09,371] [INFO] Task succeeded: CheckM
[2024-01-24 14:23:09,373] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:23:09,399] [INFO] ===== Completeness check finished =====
[2024-01-24 14:23:09,399] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:23:09,399] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_028595285.1_ASM2859528v1_genomic.fna/markers.fasta)
[2024-01-24 14:23:09,400] [INFO] Task started: Blastn
[2024-01-24 14:23:09,400] [INFO] Running command: blastn -query GCF_028595285.1_ASM2859528v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg30fc1904-0dfb-4c52-ba46-c1d90034ea9b/dqc_reference/reference_markers_gtdb.fasta -out GCF_028595285.1_ASM2859528v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:10,998] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:11,001] [INFO] Selected 15 target genomes.
[2024-01-24 14:23:11,002] [INFO] Target genome list was writen to GCF_028595285.1_ASM2859528v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:23:11,014] [INFO] Task started: fastANI
[2024-01-24 14:23:11,014] [INFO] Running command: fastANI --query /var/lib/cwl/stg0f620069-2144-43e5-9075-c0ff90e6fe2f/GCF_028595285.1_ASM2859528v1_genomic.fna.gz --refList GCF_028595285.1_ASM2859528v1_genomic.fna/target_genomes_gtdb.txt --output GCF_028595285.1_ASM2859528v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:23:22,549] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:22,567] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:23:22,567] [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_001677335.1	s__Erythrobacter dokdonensis	85.0596	810	1030	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_011054555.1	s__Erythrobacter sp011054555	84.8233	568	1030	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016125555.1	s__Erythrobacter sp016125555	84.619	773	1030	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903934325.1	s__Erythrobacter sp903934325	84.5044	745	1030	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000744895.1	s__Erythrobacter sp000744895	84.2849	782	1030	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900143235.1	s__Erythrobacter sanguineus	84.107	789	1030	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001720465.1	s__Erythrobacter sp001720465	83.9775	746	1030	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	83.899	765	1030	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	83.8501	783	1030	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	83.8157	784	1030	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	83.626	735	1030	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	83.5313	783	1030	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	83.522	789	1030	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	83.1974	680	1030	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	83.1524	723	1030	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 14:23:22,569] [INFO] GTDB search result was written to GCF_028595285.1_ASM2859528v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:23:22,569] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:23:22,579] [INFO] DFAST_QC result json was written to GCF_028595285.1_ASM2859528v1_genomic.fna/dqc_result.json
[2024-01-24 14:23:22,579] [INFO] DFAST_QC completed!
[2024-01-24 14:23:22,579] [INFO] Total running time: 0h1m6s