[2024-01-24 13:19:25,891] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:19:25,893] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:19:25,893] [INFO] DQC Reference Directory: /var/lib/cwl/stgfeb7a253-68b6-484e-8d10-bc1dff70b680/dqc_reference
[2024-01-24 13:19:27,139] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:19:27,140] [INFO] Task started: Prodigal
[2024-01-24 13:19:27,141] [INFO] Running command: gunzip -c /var/lib/cwl/stg17202630-8cc7-4deb-9396-8e4d483e3cdd/GCF_000422985.1_ASM42298v1_genomic.fna.gz | prodigal -d GCF_000422985.1_ASM42298v1_genomic.fna/cds.fna -a GCF_000422985.1_ASM42298v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:19:36,350] [INFO] Task succeeded: Prodigal
[2024-01-24 13:19:36,351] [INFO] Task started: HMMsearch
[2024-01-24 13:19:36,351] [INFO] Running command: hmmsearch --tblout GCF_000422985.1_ASM42298v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfeb7a253-68b6-484e-8d10-bc1dff70b680/dqc_reference/reference_markers.hmm GCF_000422985.1_ASM42298v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:36,583] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:36,584] [INFO] Found 6/6 markers.
[2024-01-24 13:19:36,636] [INFO] Query marker FASTA was written to GCF_000422985.1_ASM42298v1_genomic.fna/markers.fasta
[2024-01-24 13:19:36,636] [INFO] Task started: Blastn
[2024-01-24 13:19:36,637] [INFO] Running command: blastn -query GCF_000422985.1_ASM42298v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfeb7a253-68b6-484e-8d10-bc1dff70b680/dqc_reference/reference_markers.fasta -out GCF_000422985.1_ASM42298v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:37,549] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:37,553] [INFO] Selected 15 target genomes.
[2024-01-24 13:19:37,553] [INFO] Target genome list was writen to GCF_000422985.1_ASM42298v1_genomic.fna/target_genomes.txt
[2024-01-24 13:19:37,564] [INFO] Task started: fastANI
[2024-01-24 13:19:37,564] [INFO] Running command: fastANI --query /var/lib/cwl/stg17202630-8cc7-4deb-9396-8e4d483e3cdd/GCF_000422985.1_ASM42298v1_genomic.fna.gz --refList GCF_000422985.1_ASM42298v1_genomic.fna/target_genomes.txt --output GCF_000422985.1_ASM42298v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:47,546] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:47,547] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfeb7a253-68b6-484e-8d10-bc1dff70b680/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:47,547] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfeb7a253-68b6-484e-8d10-bc1dff70b680/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:47,559] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:19:47,560] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:19:47,560] [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 cryptus	strain=DSM 12079	GCA_000422985.1	196588	196588	type	True	99.9989	965	967	95	conclusive
Erythrobacter tepidarius	strain=DSM 10594	GCA_002155695.1	60454	60454	type	True	83.2801	780	967	95	below_threshold
Erythrobacter colymbi	strain=JCM 18338	GCA_002155685.1	1161202	1161202	type	True	82.8964	774	967	95	below_threshold
Erythrobacter donghaensis	strain=DSM 16220	GCA_002155425.1	267135	267135	suspected-type	True	82.5399	773	967	95	below_threshold
Erythrobacter dokdonensis	strain=DSM 17193	GCA_002155305.1	328225	328225	type	True	82.141	688	967	95	below_threshold
Erythrobacter dokdonensis	strain=DSW-74	GCA_001677335.1	328225	328225	type	True	82.0974	698	967	95	below_threshold
Erythrobacter neustonensis	strain=DSM 9434	GCA_001663175.1	1112	1112	type	True	81.4616	689	967	95	below_threshold
Erythrobacter ramosus	strain=DSM 8510	GCA_014195675.1	35811	35811	type	True	81.2808	714	967	95	below_threshold
Erythrobacter ramosus	strain=JCM 10282	GCA_009828055.1	35811	35811	type	True	81.2333	721	967	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	78.6768	395	967	95	below_threshold
Qipengyuania gelatinilytica	strain=1NDH1	GCA_019711315.1	2867231	2867231	type	True	78.3325	350	967	95	below_threshold
Qipengyuania xiapuensis	strain=1NDW9	GCA_019711395.1	2867236	2867236	type	True	78.2029	357	967	95	below_threshold
Alteriqipengyuania abyssalis	strain=NZ-12B	GCA_019857185.1	2860200	2860200	type	True	78.1463	421	967	95	below_threshold
Aurantiacibacter arachoides	strain=CGMCC 1.15507	GCA_014643415.1	1850444	1850444	type	True	77.9994	345	967	95	below_threshold
Croceicoccus hydrothermalis	strain=JLT1	GCA_022378335.1	2867964	2867964	type	True	77.2911	247	967	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:47,562] [INFO] DFAST Taxonomy check result was written to GCF_000422985.1_ASM42298v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:47,562] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:47,562] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:47,563] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfeb7a253-68b6-484e-8d10-bc1dff70b680/dqc_reference/checkm_data
[2024-01-24 13:19:47,564] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:47,599] [INFO] Task started: CheckM
[2024-01-24 13:19:47,600] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000422985.1_ASM42298v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000422985.1_ASM42298v1_genomic.fna/checkm_input GCF_000422985.1_ASM42298v1_genomic.fna/checkm_result
[2024-01-24 13:20:20,400] [INFO] Task succeeded: CheckM
[2024-01-24 13:20:20,402] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:20:20,422] [INFO] ===== Completeness check finished =====
[2024-01-24 13:20:20,422] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:20:20,423] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000422985.1_ASM42298v1_genomic.fna/markers.fasta)
[2024-01-24 13:20:20,423] [INFO] Task started: Blastn
[2024-01-24 13:20:20,424] [INFO] Running command: blastn -query GCF_000422985.1_ASM42298v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfeb7a253-68b6-484e-8d10-bc1dff70b680/dqc_reference/reference_markers_gtdb.fasta -out GCF_000422985.1_ASM42298v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:20:22,109] [INFO] Task succeeded: Blastn
[2024-01-24 13:20:22,113] [INFO] Selected 16 target genomes.
[2024-01-24 13:20:22,114] [INFO] Target genome list was writen to GCF_000422985.1_ASM42298v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:20:22,195] [INFO] Task started: fastANI
[2024-01-24 13:20:22,195] [INFO] Running command: fastANI --query /var/lib/cwl/stg17202630-8cc7-4deb-9396-8e4d483e3cdd/GCF_000422985.1_ASM42298v1_genomic.fna.gz --refList GCF_000422985.1_ASM42298v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000422985.1_ASM42298v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:20:33,186] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:33,199] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:20:33,199] [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_000422985.1	s__Erythrobacter cryptus	99.9989	965	967	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_011054555.1	s__Erythrobacter sp011054555	83.5779	556	967	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	83.3054	778	967	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	83.1965	680	967	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	99.70	99.64	0.86	0.85	7	-
GCA_016125555.1	s__Erythrobacter sp016125555	83.1532	706	967	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	83.0527	702	967	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	82.9338	771	967	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	82.783	692	967	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	99.84	99.84	0.90	0.90	2	-
GCF_006542605.1	s__Erythrobacter sp006542605	82.7828	760	967	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	82.5221	480	967	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	82.3223	720	967	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	82.1606	672	967	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	82.1004	698	967	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_004292705.1	s__Erythrobacter sp004292705	81.5951	509	967	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011765465.1	s__Erythrobacter sp011765465	80.2176	647	967	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	80.1922	445	967	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 13:20:33,201] [INFO] GTDB search result was written to GCF_000422985.1_ASM42298v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:20:33,201] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:20:33,205] [INFO] DFAST_QC result json was written to GCF_000422985.1_ASM42298v1_genomic.fna/dqc_result.json
[2024-01-24 13:20:33,205] [INFO] DFAST_QC completed!
[2024-01-24 13:20:33,205] [INFO] Total running time: 0h1m7s