[2024-01-24 10:47:06,588] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:06,597] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:06,597] [INFO] DQC Reference Directory: /var/lib/cwl/stg6dfc162e-b49b-4365-ba29-8b8ff3bd6053/dqc_reference
[2024-01-24 10:47:12,679] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:12,816] [INFO] Task started: Prodigal
[2024-01-24 10:47:12,817] [INFO] Running command: gunzip -c /var/lib/cwl/stga024e9bb-ca52-4e03-a051-6cb974ac5d38/GCF_002155305.1_ASM215530v1_genomic.fna.gz | prodigal -d GCF_002155305.1_ASM215530v1_genomic.fna/cds.fna -a GCF_002155305.1_ASM215530v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:22,193] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:22,193] [INFO] Task started: HMMsearch
[2024-01-24 10:47:22,193] [INFO] Running command: hmmsearch --tblout GCF_002155305.1_ASM215530v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6dfc162e-b49b-4365-ba29-8b8ff3bd6053/dqc_reference/reference_markers.hmm GCF_002155305.1_ASM215530v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:22,458] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:22,459] [INFO] Found 6/6 markers.
[2024-01-24 10:47:22,500] [INFO] Query marker FASTA was written to GCF_002155305.1_ASM215530v1_genomic.fna/markers.fasta
[2024-01-24 10:47:22,500] [INFO] Task started: Blastn
[2024-01-24 10:47:22,501] [INFO] Running command: blastn -query GCF_002155305.1_ASM215530v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6dfc162e-b49b-4365-ba29-8b8ff3bd6053/dqc_reference/reference_markers.fasta -out GCF_002155305.1_ASM215530v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:23,351] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:23,356] [INFO] Selected 12 target genomes.
[2024-01-24 10:47:23,356] [INFO] Target genome list was writen to GCF_002155305.1_ASM215530v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:23,789] [INFO] Task started: fastANI
[2024-01-24 10:47:23,790] [INFO] Running command: fastANI --query /var/lib/cwl/stga024e9bb-ca52-4e03-a051-6cb974ac5d38/GCF_002155305.1_ASM215530v1_genomic.fna.gz --refList GCF_002155305.1_ASM215530v1_genomic.fna/target_genomes.txt --output GCF_002155305.1_ASM215530v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:32,631] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:32,632] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6dfc162e-b49b-4365-ba29-8b8ff3bd6053/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:32,632] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6dfc162e-b49b-4365-ba29-8b8ff3bd6053/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:32,642] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 10:47:32,642] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:47:32,642] [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	100.0	995	995	95	conclusive
Erythrobacter dokdonensis	strain=DSW-74	GCA_001677335.1	328225	328225	type	True	99.9908	989	995	95	conclusive
Erythrobacter sanguineus	strain=JCM 20691	GCA_002155655.1	198312	198312	type	True	83.9677	765	995	95	below_threshold
Erythrobacter sanguineus	strain=DSM 11032	GCA_900143235.1	198312	198312	type	True	83.8492	781	995	95	below_threshold
Erythrobacter tepidarius	strain=DSM 10594	GCA_002155695.1	60454	60454	type	True	83.7622	760	995	95	below_threshold
Erythrobacter colymbi	strain=JCM 18338	GCA_002155685.1	1161202	1161202	type	True	83.7256	749	995	95	below_threshold
Erythrobacter donghaensis	strain=DSM 16220	GCA_002155425.1	267135	267135	suspected-type	True	83.5648	764	995	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	79.1255	392	995	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	79.1121	341	995	95	below_threshold
Qipengyuania xiamenensis	strain=1XM1-15A	GCA_019711495.1	2867237	2867237	type	True	79.0392	407	995	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	78.9908	394	995	95	below_threshold
Qipengyuania huizhouensis	strain=YG19	GCA_019711635.1	2867245	2867245	type	True	78.7301	297	995	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:32,650] [INFO] DFAST Taxonomy check result was written to GCF_002155305.1_ASM215530v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:32,651] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:32,652] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:32,652] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6dfc162e-b49b-4365-ba29-8b8ff3bd6053/dqc_reference/checkm_data
[2024-01-24 10:47:32,654] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:32,689] [INFO] Task started: CheckM
[2024-01-24 10:47:32,689] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002155305.1_ASM215530v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002155305.1_ASM215530v1_genomic.fna/checkm_input GCF_002155305.1_ASM215530v1_genomic.fna/checkm_result
[2024-01-24 10:48:05,829] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:05,831] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:05,852] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:05,852] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:05,853] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002155305.1_ASM215530v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:05,854] [INFO] Task started: Blastn
[2024-01-24 10:48:05,854] [INFO] Running command: blastn -query GCF_002155305.1_ASM215530v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6dfc162e-b49b-4365-ba29-8b8ff3bd6053/dqc_reference/reference_markers_gtdb.fasta -out GCF_002155305.1_ASM215530v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:07,179] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:07,186] [INFO] Selected 13 target genomes.
[2024-01-24 10:48:07,186] [INFO] Target genome list was writen to GCF_002155305.1_ASM215530v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:07,277] [INFO] Task started: fastANI
[2024-01-24 10:48:07,277] [INFO] Running command: fastANI --query /var/lib/cwl/stga024e9bb-ca52-4e03-a051-6cb974ac5d38/GCF_002155305.1_ASM215530v1_genomic.fna.gz --refList GCF_002155305.1_ASM215530v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002155305.1_ASM215530v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:18,029] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:18,040] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:48:18,040] [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	99.9908	989	995	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_016125555.1	s__Erythrobacter sp016125555	84.6544	746	995	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	84.5992	583	995	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	84.2935	742	995	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	83.9339	791	995	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	83.9114	760	995	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	83.862	775	995	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	83.8539	780	995	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002155695.1	s__Erythrobacter tepidarius	83.7664	760	995	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	83.7561	763	995	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001720465.1	s__Erythrobacter sp001720465	83.5851	709	995	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	83.3749	715	995	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	83.258	684	995	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	99.84	99.84	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2024-01-24 10:48:18,042] [INFO] GTDB search result was written to GCF_002155305.1_ASM215530v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:18,043] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:18,049] [INFO] DFAST_QC result json was written to GCF_002155305.1_ASM215530v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:18,049] [INFO] DFAST_QC completed!
[2024-01-24 10:48:18,049] [INFO] Total running time: 0h1m11s