[2024-01-24 14:14:19,222] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:19,223] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:19,223] [INFO] DQC Reference Directory: /var/lib/cwl/stg5667286d-3b80-476c-8a62-aef250c86c80/dqc_reference
[2024-01-24 14:14:20,501] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:20,502] [INFO] Task started: Prodigal
[2024-01-24 14:14:20,502] [INFO] Running command: gunzip -c /var/lib/cwl/stg7ded27d9-8510-42ba-94f6-e42353dac0eb/GCF_002155655.1_ASM215565v1_genomic.fna.gz | prodigal -d GCF_002155655.1_ASM215565v1_genomic.fna/cds.fna -a GCF_002155655.1_ASM215565v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:14:29,986] [INFO] Task succeeded: Prodigal
[2024-01-24 14:14:29,986] [INFO] Task started: HMMsearch
[2024-01-24 14:14:29,986] [INFO] Running command: hmmsearch --tblout GCF_002155655.1_ASM215565v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5667286d-3b80-476c-8a62-aef250c86c80/dqc_reference/reference_markers.hmm GCF_002155655.1_ASM215565v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:14:30,274] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:14:30,275] [INFO] Found 6/6 markers.
[2024-01-24 14:14:30,303] [INFO] Query marker FASTA was written to GCF_002155655.1_ASM215565v1_genomic.fna/markers.fasta
[2024-01-24 14:14:30,304] [INFO] Task started: Blastn
[2024-01-24 14:14:30,304] [INFO] Running command: blastn -query GCF_002155655.1_ASM215565v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5667286d-3b80-476c-8a62-aef250c86c80/dqc_reference/reference_markers.fasta -out GCF_002155655.1_ASM215565v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:31,319] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:31,322] [INFO] Selected 14 target genomes.
[2024-01-24 14:14:31,323] [INFO] Target genome list was writen to GCF_002155655.1_ASM215565v1_genomic.fna/target_genomes.txt
[2024-01-24 14:14:31,330] [INFO] Task started: fastANI
[2024-01-24 14:14:31,330] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ded27d9-8510-42ba-94f6-e42353dac0eb/GCF_002155655.1_ASM215565v1_genomic.fna.gz --refList GCF_002155655.1_ASM215565v1_genomic.fna/target_genomes.txt --output GCF_002155655.1_ASM215565v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:14:42,388] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:42,389] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5667286d-3b80-476c-8a62-aef250c86c80/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:14:42,389] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5667286d-3b80-476c-8a62-aef250c86c80/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:14:42,401] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:14:42,401] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:14:42,401] [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 sanguineus	strain=JCM 20691	GCA_002155655.1	198312	198312	type	True	100.0	993	994	95	conclusive
Erythrobacter sanguineus	strain=DSM 11032	GCA_900143235.1	198312	198312	type	True	99.9913	971	994	95	conclusive
Erythrobacter dokdonensis	strain=DSM 17193	GCA_002155305.1	328225	328225	type	True	83.8804	774	994	95	below_threshold
Erythrobacter dokdonensis	strain=DSW-74	GCA_001677335.1	328225	328225	type	True	83.8759	778	994	95	below_threshold
Erythrobacter ramosus	strain=JCM 10282	GCA_009828055.1	35811	35811	type	True	83.0572	727	994	95	below_threshold
Erythrobacter donghaensis	strain=DSM 16220	GCA_002155425.1	267135	267135	suspected-type	True	83.0274	745	994	95	below_threshold
Erythrobacter ramosus	strain=DSM 8510	GCA_014195675.1	35811	35811	type	True	82.9762	734	994	95	below_threshold
Erythrobacter tepidarius	strain=DSM 10594	GCA_002155695.1	60454	60454	type	True	82.7717	742	994	95	below_threshold
Erythrobacter colymbi	strain=JCM 18338	GCA_002155685.1	1161202	1161202	type	True	82.3245	766	994	95	below_threshold
Qipengyuania aurantiaca	strain=1NDH13	GCA_019711375.1	2867233	2867233	type	True	78.8924	397	994	95	below_threshold
Qipengyuania sphaerica	strain=GH29	GCA_019711595.1	2867243	2867243	type	True	78.7624	390	994	95	below_threshold
Qipengyuania gelatinilytica	strain=1NDH1	GCA_019711315.1	2867231	2867231	type	True	78.5964	366	994	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	78.4464	362	994	95	below_threshold
Erythrobacter rubeus	strain=KMU-140	GCA_014705715.1	2760803	2760803	type	True	78.2981	439	994	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:14:42,403] [INFO] DFAST Taxonomy check result was written to GCF_002155655.1_ASM215565v1_genomic.fna/tc_result.tsv
[2024-01-24 14:14:42,403] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:14:42,403] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:14:42,403] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5667286d-3b80-476c-8a62-aef250c86c80/dqc_reference/checkm_data
[2024-01-24 14:14:42,404] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:14:42,446] [INFO] Task started: CheckM
[2024-01-24 14:14:42,446] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002155655.1_ASM215565v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002155655.1_ASM215565v1_genomic.fna/checkm_input GCF_002155655.1_ASM215565v1_genomic.fna/checkm_result
[2024-01-24 14:15:14,493] [INFO] Task succeeded: CheckM
[2024-01-24 14:15:14,495] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:15:14,513] [INFO] ===== Completeness check finished =====
[2024-01-24 14:15:14,513] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:15:14,514] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002155655.1_ASM215565v1_genomic.fna/markers.fasta)
[2024-01-24 14:15:14,514] [INFO] Task started: Blastn
[2024-01-24 14:15:14,514] [INFO] Running command: blastn -query GCF_002155655.1_ASM215565v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5667286d-3b80-476c-8a62-aef250c86c80/dqc_reference/reference_markers_gtdb.fasta -out GCF_002155655.1_ASM215565v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:16,083] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:16,087] [INFO] Selected 18 target genomes.
[2024-01-24 14:15:16,087] [INFO] Target genome list was writen to GCF_002155655.1_ASM215565v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:15:16,120] [INFO] Task started: fastANI
[2024-01-24 14:15:16,120] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ded27d9-8510-42ba-94f6-e42353dac0eb/GCF_002155655.1_ASM215565v1_genomic.fna.gz --refList GCF_002155655.1_ASM215565v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002155655.1_ASM215565v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:15:28,700] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:28,716] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:15:28,719] [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_900143235.1	s__Erythrobacter sanguineus	99.9786	972	994	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_000744895.1	s__Erythrobacter sp000744895	87.3517	840	994	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	83.9153	555	994	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	83.864	779	994	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_903934325.1	s__Erythrobacter sp903934325	83.6221	725	994	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	83.1661	732	994	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002842735.1	s__Erythrobacter sp002842735	83.0903	652	994	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	95.33	95.33	0.91	0.91	2	-
GCF_002952215.1	s__Erythrobacter sp002952215	83.062	742	994	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001296025.1	s__Erythrobacter sp001296025	83.0356	739	994	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	83.0147	747	994	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	83.0008	724	994	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018830415.1	s__Erythrobacter sp018830415	82.9154	479	994	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001556995.1	s__Erythrobacter sp001556995	82.8905	675	994	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	82.7924	740	994	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001464915.1	s__Erythrobacter sp001464915	82.6402	690	994	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013822695.1	s__Erythrobacter sp013822695	82.405	677	994	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	99.78	99.78	0.82	0.82	2	-
GCF_001663175.1	s__Erythrobacter neustonensis	82.3417	665	994	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013911835.1	s__Erythrobacter sp013911835	82.3374	471	994	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 14:15:28,722] [INFO] GTDB search result was written to GCF_002155655.1_ASM215565v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:15:28,722] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:15:28,727] [INFO] DFAST_QC result json was written to GCF_002155655.1_ASM215565v1_genomic.fna/dqc_result.json
[2024-01-24 14:15:28,727] [INFO] DFAST_QC completed!
[2024-01-24 14:15:28,728] [INFO] Total running time: 0h1m10s