[2024-01-24 13:41:26,239] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:41:26,241] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:41:26,241] [INFO] DQC Reference Directory: /var/lib/cwl/stg45a2e464-db8e-425f-83c3-841866f72f86/dqc_reference
[2024-01-24 13:41:27,539] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:41:27,540] [INFO] Task started: Prodigal
[2024-01-24 13:41:27,540] [INFO] Running command: gunzip -c /var/lib/cwl/stg60b2cb3d-a619-49d4-92cc-4d5b109a7630/GCF_001663175.1_ASM166317v1_genomic.fna.gz | prodigal -d GCF_001663175.1_ASM166317v1_genomic.fna/cds.fna -a GCF_001663175.1_ASM166317v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:37,936] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:37,936] [INFO] Task started: HMMsearch
[2024-01-24 13:41:37,936] [INFO] Running command: hmmsearch --tblout GCF_001663175.1_ASM166317v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg45a2e464-db8e-425f-83c3-841866f72f86/dqc_reference/reference_markers.hmm GCF_001663175.1_ASM166317v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:38,204] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:38,205] [INFO] Found 6/6 markers.
[2024-01-24 13:41:38,233] [INFO] Query marker FASTA was written to GCF_001663175.1_ASM166317v1_genomic.fna/markers.fasta
[2024-01-24 13:41:38,234] [INFO] Task started: Blastn
[2024-01-24 13:41:38,234] [INFO] Running command: blastn -query GCF_001663175.1_ASM166317v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg45a2e464-db8e-425f-83c3-841866f72f86/dqc_reference/reference_markers.fasta -out GCF_001663175.1_ASM166317v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:39,170] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:39,173] [INFO] Selected 12 target genomes.
[2024-01-24 13:41:39,174] [INFO] Target genome list was writen to GCF_001663175.1_ASM166317v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:39,178] [INFO] Task started: fastANI
[2024-01-24 13:41:39,178] [INFO] Running command: fastANI --query /var/lib/cwl/stg60b2cb3d-a619-49d4-92cc-4d5b109a7630/GCF_001663175.1_ASM166317v1_genomic.fna.gz --refList GCF_001663175.1_ASM166317v1_genomic.fna/target_genomes.txt --output GCF_001663175.1_ASM166317v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:47,844] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:47,845] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg45a2e464-db8e-425f-83c3-841866f72f86/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:47,845] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg45a2e464-db8e-425f-83c3-841866f72f86/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:47,855] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:47,855] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:47,855] [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 neustonensis	strain=DSM 9434	GCA_001663175.1	1112	1112	type	True	100.0	1030	1030	95	conclusive
Erythrobacter colymbi	strain=JCM 18338	GCA_002155685.1	1161202	1161202	type	True	84.7513	803	1030	95	below_threshold
Erythrobacter donghaensis	strain=DSM 16220	GCA_002155425.1	267135	267135	suspected-type	True	84.2674	782	1030	95	below_threshold
Erythrobacter ramosus	strain=JCM 10282	GCA_009828055.1	35811	35811	type	True	82.973	753	1030	95	below_threshold
Erythrobacter ramosus	strain=DSM 8510	GCA_014195675.1	35811	35811	type	True	82.95	762	1030	95	below_threshold
Erythrobacter sanguineus	strain=DSM 11032	GCA_900143235.1	198312	198312	type	True	82.2456	670	1030	95	below_threshold
Erythrobacter sanguineus	strain=JCM 20691	GCA_002155655.1	198312	198312	type	True	82.0924	693	1030	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	79.5343	441	1030	95	below_threshold
Qipengyuania pelagi	strain=JCM 17468	GCA_009827295.1	994320	994320	type	True	79.3315	418	1030	95	below_threshold
Qipengyuania sphaerica	strain=GH29	GCA_019711595.1	2867243	2867243	type	True	79.0378	387	1030	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	79.0068	388	1030	95	below_threshold
Qipengyuania huizhouensis	strain=YG19	GCA_019711635.1	2867245	2867245	type	True	78.7779	296	1030	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:47,857] [INFO] DFAST Taxonomy check result was written to GCF_001663175.1_ASM166317v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:47,857] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:47,857] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:47,858] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg45a2e464-db8e-425f-83c3-841866f72f86/dqc_reference/checkm_data
[2024-01-24 13:41:47,858] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:47,894] [INFO] Task started: CheckM
[2024-01-24 13:41:47,894] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001663175.1_ASM166317v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001663175.1_ASM166317v1_genomic.fna/checkm_input GCF_001663175.1_ASM166317v1_genomic.fna/checkm_result
[2024-01-24 13:42:21,930] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:21,932] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:21,951] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:21,952] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:21,952] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001663175.1_ASM166317v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:21,952] [INFO] Task started: Blastn
[2024-01-24 13:42:21,953] [INFO] Running command: blastn -query GCF_001663175.1_ASM166317v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg45a2e464-db8e-425f-83c3-841866f72f86/dqc_reference/reference_markers_gtdb.fasta -out GCF_001663175.1_ASM166317v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:23,314] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:23,318] [INFO] Selected 16 target genomes.
[2024-01-24 13:42:23,318] [INFO] Target genome list was writen to GCF_001663175.1_ASM166317v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:23,333] [INFO] Task started: fastANI
[2024-01-24 13:42:23,333] [INFO] Running command: fastANI --query /var/lib/cwl/stg60b2cb3d-a619-49d4-92cc-4d5b109a7630/GCF_001663175.1_ASM166317v1_genomic.fna.gz --refList GCF_001663175.1_ASM166317v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001663175.1_ASM166317v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:34,792] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:34,812] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:34,812] [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_001663175.1	s__Erythrobacter neustonensis	100.0	1030	1030	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002155685.1	s__Erythrobacter colymbi	84.7435	804	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	84.3689	785	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_000331285.1	s__Erythrobacter sp000331285	84.2685	731	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	84.2674	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_001557325.1	s__Erythrobacter donghaensis_B	84.1012	699	1030	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	99.70	99.64	0.86	0.85	7	-
GCA_013911835.1	s__Erythrobacter sp013911835	83.9536	502	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_013822695.1	s__Erythrobacter sp013822695	83.9132	717	1030	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	99.78	99.78	0.82	0.82	2	-
GCF_001557115.1	s__Erythrobacter sp001557115	83.9129	717	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_002215495.1	s__Erythrobacter sp002215495	83.7374	780	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_003724185.1	s__Erythrobacter sp003724185	83.5549	757	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_018991295.1	s__Erythrobacter sp018991295	83.5399	507	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	83.5318	692	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_009905735.1	s__Erythrobacter sp009905735	83.455	733	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_002855495.1	s__Erythrobacter sp002855495	83.1618	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	-
GCA_016125555.1	s__Erythrobacter sp016125555	82.9516	687	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 13:42:34,814] [INFO] GTDB search result was written to GCF_001663175.1_ASM166317v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:34,815] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:34,819] [INFO] DFAST_QC result json was written to GCF_001663175.1_ASM166317v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:34,820] [INFO] DFAST_QC completed!
[2024-01-24 13:42:34,820] [INFO] Total running time: 0h1m9s