[2023-06-19 04:44:37,917] [INFO] DFAST_QC pipeline started.
[2023-06-19 04:44:37,920] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 04:44:37,920] [INFO] DQC Reference Directory: /var/lib/cwl/stg0ae1857c-33f0-4d21-a1ea-b81cbbc77286/dqc_reference
[2023-06-19 04:44:39,276] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 04:44:39,277] [INFO] Task started: Prodigal
[2023-06-19 04:44:39,278] [INFO] Running command: gunzip -c /var/lib/cwl/stg48341717-d75c-448b-afbc-149b460cb49b/GCA_937867455.1_SRR7468254_bin.46_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_937867455.1_SRR7468254_bin.46_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_937867455.1_SRR7468254_bin.46_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 04:44:43,834] [INFO] Task succeeded: Prodigal
[2023-06-19 04:44:43,835] [INFO] Task started: HMMsearch
[2023-06-19 04:44:43,835] [INFO] Running command: hmmsearch --tblout GCA_937867455.1_SRR7468254_bin.46_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0ae1857c-33f0-4d21-a1ea-b81cbbc77286/dqc_reference/reference_markers.hmm GCA_937867455.1_SRR7468254_bin.46_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-19 04:44:44,046] [INFO] Task succeeded: HMMsearch
[2023-06-19 04:44:44,048] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg48341717-d75c-448b-afbc-149b460cb49b/GCA_937867455.1_SRR7468254_bin.46_CONCOCT_v1.1_MAG_genomic.fna.gz]
[2023-06-19 04:44:44,074] [INFO] Query marker FASTA was written to GCA_937867455.1_SRR7468254_bin.46_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-19 04:44:44,074] [INFO] Task started: Blastn
[2023-06-19 04:44:44,075] [INFO] Running command: blastn -query GCA_937867455.1_SRR7468254_bin.46_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ae1857c-33f0-4d21-a1ea-b81cbbc77286/dqc_reference/reference_markers.fasta -out GCA_937867455.1_SRR7468254_bin.46_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 04:44:44,756] [INFO] Task succeeded: Blastn
[2023-06-19 04:44:44,761] [INFO] Selected 12 target genomes.
[2023-06-19 04:44:44,761] [INFO] Target genome list was writen to GCA_937867455.1_SRR7468254_bin.46_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-19 04:44:44,763] [INFO] Task started: fastANI
[2023-06-19 04:44:44,763] [INFO] Running command: fastANI --query /var/lib/cwl/stg48341717-d75c-448b-afbc-149b460cb49b/GCA_937867455.1_SRR7468254_bin.46_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937867455.1_SRR7468254_bin.46_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_937867455.1_SRR7468254_bin.46_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 04:44:50,953] [INFO] Task succeeded: fastANI
[2023-06-19 04:44:50,954] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0ae1857c-33f0-4d21-a1ea-b81cbbc77286/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 04:44:50,954] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0ae1857c-33f0-4d21-a1ea-b81cbbc77286/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 04:44:50,974] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 04:44:50,974] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 04:44:50,974] [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 ramosus	strain=DSM 8510	GCA_014195675.1	35811	35811	type	True	83.1167	110	141	95	below_threshold
Erythrobacter ramosus	strain=JCM 10282	GCA_009828055.1	35811	35811	type	True	83.1167	110	141	95	below_threshold
Erythrobacter donghaensis	strain=DSM 16220	GCA_002155425.1	267135	267135	suspected-type	True	82.8857	114	141	95	below_threshold
Erythrobacter colymbi	strain=JCM 18338	GCA_002155685.1	1161202	1161202	type	True	82.4208	114	141	95	below_threshold
Erythrobacter neustonensis	strain=DSM 9434	GCA_001663175.1	1112	1112	type	True	82.0766	107	141	95	below_threshold
Erythrobacter sanguineus	strain=JCM 20691	GCA_002155655.1	198312	198312	type	True	81.693	108	141	95	below_threshold
Erythrobacter sanguineus	strain=DSM 11032	GCA_900143235.1	198312	198312	type	True	81.6908	109	141	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	78.0579	63	141	95	below_threshold
Qipengyuania aurantiaca	strain=1NDH13	GCA_019711375.1	2867233	2867233	type	True	77.7964	57	141	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 04:44:50,977] [INFO] DFAST Taxonomy check result was written to GCA_937867455.1_SRR7468254_bin.46_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-19 04:44:50,978] [INFO] ===== Taxonomy check completed =====
[2023-06-19 04:44:50,978] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 04:44:50,978] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0ae1857c-33f0-4d21-a1ea-b81cbbc77286/dqc_reference/checkm_data
[2023-06-19 04:44:50,980] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 04:44:51,005] [INFO] Task started: CheckM
[2023-06-19 04:44:51,005] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_937867455.1_SRR7468254_bin.46_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_937867455.1_SRR7468254_bin.46_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_937867455.1_SRR7468254_bin.46_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-19 04:45:11,148] [INFO] Task succeeded: CheckM
[2023-06-19 04:45:11,150] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.37%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 04:45:11,173] [INFO] ===== Completeness check finished =====
[2023-06-19 04:45:11,174] [INFO] ===== Start GTDB Search =====
[2023-06-19 04:45:11,174] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_937867455.1_SRR7468254_bin.46_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-19 04:45:11,175] [INFO] Task started: Blastn
[2023-06-19 04:45:11,175] [INFO] Running command: blastn -query GCA_937867455.1_SRR7468254_bin.46_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ae1857c-33f0-4d21-a1ea-b81cbbc77286/dqc_reference/reference_markers_gtdb.fasta -out GCA_937867455.1_SRR7468254_bin.46_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 04:45:12,237] [INFO] Task succeeded: Blastn
[2023-06-19 04:45:12,241] [INFO] Selected 18 target genomes.
[2023-06-19 04:45:12,241] [INFO] Target genome list was writen to GCA_937867455.1_SRR7468254_bin.46_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 04:45:12,251] [INFO] Task started: fastANI
[2023-06-19 04:45:12,251] [INFO] Running command: fastANI --query /var/lib/cwl/stg48341717-d75c-448b-afbc-149b460cb49b/GCA_937867455.1_SRR7468254_bin.46_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937867455.1_SRR7468254_bin.46_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_937867455.1_SRR7468254_bin.46_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 04:45:20,409] [INFO] Task succeeded: fastANI
[2023-06-19 04:45:20,428] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-19 04:45:20,428] [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
GCA_003724185.1	s__Erythrobacter sp003724185	83.9844	115	141	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	83.6183	108	141	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	83.1205	109	141	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	83.1167	110	141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002155425.1	s__Erythrobacter donghaensis	82.8857	114	141	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	82.8609	113	141	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	82.5816	89	141	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	82.4514	112	141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002155685.1	s__Erythrobacter colymbi	82.4208	114	141	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	82.3721	80	141	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	82.3538	103	141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	99.78	99.78	0.82	0.82	2	-
GCF_002952215.1	s__Erythrobacter sp002952215	82.1671	109	141	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	81.7355	96	141	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	81.6367	107	141	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	81.6049	100	141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	99.97	99.95	0.97	0.95	3	-
GCA_004292705.1	s__Erythrobacter sp004292705	81.5659	101	141	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	81.554	95	141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	95.33	95.33	0.91	0.91	2	-
GCA_018830415.1	s__Erythrobacter sp018830415	80.6966	87	141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 04:45:20,430] [INFO] GTDB search result was written to GCA_937867455.1_SRR7468254_bin.46_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-19 04:45:20,431] [INFO] ===== GTDB Search completed =====
[2023-06-19 04:45:20,436] [INFO] DFAST_QC result json was written to GCA_937867455.1_SRR7468254_bin.46_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-19 04:45:20,437] [INFO] DFAST_QC completed!
[2023-06-19 04:45:20,437] [INFO] Total running time: 0h0m43s