[2023-03-18 21:53:45,257] [INFO] DFAST_QC pipeline started.
[2023-03-18 21:53:45,257] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 21:53:45,257] [INFO] DQC Reference Directory: /var/lib/cwl/stg13a447b6-60d2-497f-ae6e-2a8dcceb3afa/dqc_reference
[2023-03-18 21:53:47,071] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 21:53:47,072] [INFO] Task started: Prodigal
[2023-03-18 21:53:47,072] [INFO] Running command: cat /var/lib/cwl/stg927584dd-34a9-451c-a2a5-3ad2438cd023/OceanDNA-b32036.fa | prodigal -d OceanDNA-b32036/cds.fna -a OceanDNA-b32036/protein.faa -g 11 -q > /dev/null
[2023-03-18 21:54:07,506] [INFO] Task succeeded: Prodigal
[2023-03-18 21:54:07,506] [INFO] Task started: HMMsearch
[2023-03-18 21:54:07,506] [INFO] Running command: hmmsearch --tblout OceanDNA-b32036/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg13a447b6-60d2-497f-ae6e-2a8dcceb3afa/dqc_reference/reference_markers.hmm OceanDNA-b32036/protein.faa > /dev/null
[2023-03-18 21:54:07,708] [INFO] Task succeeded: HMMsearch
[2023-03-18 21:54:07,709] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg927584dd-34a9-451c-a2a5-3ad2438cd023/OceanDNA-b32036.fa]
[2023-03-18 21:54:07,732] [INFO] Query marker FASTA was written to OceanDNA-b32036/markers.fasta
[2023-03-18 21:54:07,734] [INFO] Task started: Blastn
[2023-03-18 21:54:07,734] [INFO] Running command: blastn -query OceanDNA-b32036/markers.fasta -db /var/lib/cwl/stg13a447b6-60d2-497f-ae6e-2a8dcceb3afa/dqc_reference/reference_markers.fasta -out OceanDNA-b32036/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:54:08,477] [INFO] Task succeeded: Blastn
[2023-03-18 21:54:08,480] [INFO] Selected 13 target genomes.
[2023-03-18 21:54:08,481] [INFO] Target genome list was writen to OceanDNA-b32036/target_genomes.txt
[2023-03-18 21:54:08,490] [INFO] Task started: fastANI
[2023-03-18 21:54:08,490] [INFO] Running command: fastANI --query /var/lib/cwl/stg927584dd-34a9-451c-a2a5-3ad2438cd023/OceanDNA-b32036.fa --refList OceanDNA-b32036/target_genomes.txt --output OceanDNA-b32036/fastani_result.tsv --threads 1
[2023-03-18 21:54:17,681] [INFO] Task succeeded: fastANI
[2023-03-18 21:54:17,682] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg13a447b6-60d2-497f-ae6e-2a8dcceb3afa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 21:54:17,682] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg13a447b6-60d2-497f-ae6e-2a8dcceb3afa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 21:54:17,690] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 21:54:17,690] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 21:54:17,690] [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 donghaensis	strain=DSM 16220	GCA_002155425.1	267135	267135	suspected-type	True	85.4487	786	1076	95	below_threshold
Erythrobacter colymbi	strain=JCM 18338	GCA_002155685.1	1161202	1161202	type	True	84.2366	804	1076	95	below_threshold
Erythrobacter ramosus	strain=DSM 8510	GCA_014195675.1	35811	35811	type	True	84.0723	761	1076	95	below_threshold
Erythrobacter ramosus	strain=JCM 10282	GCA_009828055.1	35811	35811	type	True	84.0712	759	1076	95	below_threshold
Erythrobacter neustonensis	strain=DSM 9434	GCA_001663175.1	1112	1112	type	True	83.4046	697	1076	95	below_threshold
Erythrobacter dokdonensis	strain=DSW-74	GCA_001677335.1	328225	328225	type	True	82.9103	676	1076	95	below_threshold
Erythrobacter tepidarius	strain=DSM 10594	GCA_002155695.1	60454	60454	type	True	82.7668	688	1076	95	below_threshold
Erythrobacter sanguineus	strain=JCM 20691	GCA_002155655.1	198312	198312	type	True	82.7414	673	1076	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	78.9357	411	1076	95	below_threshold
Alteriqipengyuania abyssalis	strain=NZ-12B	GCA_019857185.1	2860200	2860200	type	True	78.8008	390	1076	95	below_threshold
Qipengyuania xiamenensis	strain=1XM1-15A	GCA_019711495.1	2867237	2867237	type	True	78.3134	362	1076	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	78.2977	382	1076	95	below_threshold
Qipengyuania huizhouensis	strain=YG19	GCA_019711635.1	2867245	2867245	type	True	78.1734	271	1076	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 21:54:17,692] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32036/tc_result.tsv
[2023-03-18 21:54:17,693] [INFO] ===== Taxonomy check completed =====
[2023-03-18 21:54:17,693] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 21:54:17,693] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg13a447b6-60d2-497f-ae6e-2a8dcceb3afa/dqc_reference/checkm_data
[2023-03-18 21:54:17,694] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 21:54:17,703] [INFO] Task started: CheckM
[2023-03-18 21:54:17,703] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32036/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32036/checkm_input OceanDNA-b32036/checkm_result
[2023-03-18 21:55:11,355] [INFO] Task succeeded: CheckM
[2023-03-18 21:55:11,356] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 21:55:11,461] [INFO] ===== Completeness check finished =====
[2023-03-18 21:55:11,462] [INFO] ===== Start GTDB Search =====
[2023-03-18 21:55:11,462] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32036/markers.fasta)
[2023-03-18 21:55:11,463] [INFO] Task started: Blastn
[2023-03-18 21:55:11,463] [INFO] Running command: blastn -query OceanDNA-b32036/markers.fasta -db /var/lib/cwl/stg13a447b6-60d2-497f-ae6e-2a8dcceb3afa/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32036/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:55:12,828] [INFO] Task succeeded: Blastn
[2023-03-18 21:55:12,844] [INFO] Selected 16 target genomes.
[2023-03-18 21:55:12,844] [INFO] Target genome list was writen to OceanDNA-b32036/target_genomes_gtdb.txt
[2023-03-18 21:55:12,858] [INFO] Task started: fastANI
[2023-03-18 21:55:12,858] [INFO] Running command: fastANI --query /var/lib/cwl/stg927584dd-34a9-451c-a2a5-3ad2438cd023/OceanDNA-b32036.fa --refList OceanDNA-b32036/target_genomes_gtdb.txt --output OceanDNA-b32036/fastani_result_gtdb.tsv --threads 1
[2023-03-18 21:55:24,311] [INFO] Task succeeded: fastANI
[2023-03-18 21:55:24,321] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 21:55:24,321] [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_002155425.1	s__Erythrobacter donghaensis	85.4622	785	1076	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	85.2366	799	1076	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	85.0839	794	1076	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	84.2721	762	1076	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	84.261	802	1076	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	84.1968	722	1076	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009828055.1	s__Erythrobacter ramosus	84.0834	758	1076	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001557115.1	s__Erythrobacter sp001557115	83.9505	735	1076	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	83.9269	688	1076	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	83.8959	486	1076	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	83.816	702	1076	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002482865.1	s__Erythrobacter sp002482865	83.8052	538	1076	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	83.7997	710	1076	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	99.78	99.78	0.82	0.82	2	-
GCF_002855495.1	s__Erythrobacter sp002855495	83.6442	730	1076	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	83.4651	502	1076	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009995225.1	s__Erythrobacter sp009995225	82.854	672	1076	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	99.97	99.95	0.97	0.95	3	-
--------------------------------------------------------------------------------
[2023-03-18 21:55:24,321] [INFO] GTDB search result was written to OceanDNA-b32036/result_gtdb.tsv
[2023-03-18 21:55:24,321] [INFO] ===== GTDB Search completed =====
[2023-03-18 21:55:24,323] [INFO] DFAST_QC result json was written to OceanDNA-b32036/dqc_result.json
[2023-03-18 21:55:24,323] [INFO] DFAST_QC completed!
[2023-03-18 21:55:24,323] [INFO] Total running time: 0h1m39s