[2023-03-16 08:10:35,269] [INFO] DFAST_QC pipeline started.
[2023-03-16 08:10:35,269] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 08:10:35,269] [INFO] DQC Reference Directory: /var/lib/cwl/stgfa94cd70-0fab-4794-add2-fae9561a17d7/dqc_reference
[2023-03-16 08:10:36,354] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 08:10:36,354] [INFO] Task started: Prodigal
[2023-03-16 08:10:36,354] [INFO] Running command: cat /var/lib/cwl/stgb3f17abb-339f-4135-b255-02a72691ee3c/OceanDNA-b32031.fa | prodigal -d OceanDNA-b32031/cds.fna -a OceanDNA-b32031/protein.faa -g 11 -q > /dev/null
[2023-03-16 08:10:46,332] [INFO] Task succeeded: Prodigal
[2023-03-16 08:10:46,333] [INFO] Task started: HMMsearch
[2023-03-16 08:10:46,333] [INFO] Running command: hmmsearch --tblout OceanDNA-b32031/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfa94cd70-0fab-4794-add2-fae9561a17d7/dqc_reference/reference_markers.hmm OceanDNA-b32031/protein.faa > /dev/null
[2023-03-16 08:10:46,491] [INFO] Task succeeded: HMMsearch
[2023-03-16 08:10:46,492] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgb3f17abb-339f-4135-b255-02a72691ee3c/OceanDNA-b32031.fa]
[2023-03-16 08:10:46,583] [INFO] Query marker FASTA was written to OceanDNA-b32031/markers.fasta
[2023-03-16 08:10:46,584] [INFO] Task started: Blastn
[2023-03-16 08:10:46,584] [INFO] Running command: blastn -query OceanDNA-b32031/markers.fasta -db /var/lib/cwl/stgfa94cd70-0fab-4794-add2-fae9561a17d7/dqc_reference/reference_markers.fasta -out OceanDNA-b32031/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:10:47,092] [INFO] Task succeeded: Blastn
[2023-03-16 08:10:47,110] [INFO] Selected 12 target genomes.
[2023-03-16 08:10:47,110] [INFO] Target genome list was writen to OceanDNA-b32031/target_genomes.txt
[2023-03-16 08:10:47,120] [INFO] Task started: fastANI
[2023-03-16 08:10:47,120] [INFO] Running command: fastANI --query /var/lib/cwl/stgb3f17abb-339f-4135-b255-02a72691ee3c/OceanDNA-b32031.fa --refList OceanDNA-b32031/target_genomes.txt --output OceanDNA-b32031/fastani_result.tsv --threads 1
[2023-03-16 08:10:54,111] [INFO] Task succeeded: fastANI
[2023-03-16 08:10:54,111] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfa94cd70-0fab-4794-add2-fae9561a17d7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 08:10:54,111] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfa94cd70-0fab-4794-add2-fae9561a17d7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 08:10:54,120] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 08:10:54,120] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 08:10:54,120] [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	81.9302	325	470	95	below_threshold
Erythrobacter ramosus	strain=DSM 8510	GCA_014195675.1	35811	35811	type	True	81.5205	313	470	95	below_threshold
Erythrobacter ramosus	strain=JCM 10282	GCA_009828055.1	35811	35811	type	True	81.466	312	470	95	below_threshold
Erythrobacter donghaensis	strain=DSM 16220	GCA_002155425.1	267135	267135	suspected-type	True	81.3273	309	470	95	below_threshold
Erythrobacter dokdonensis	strain=DSW-74	GCA_001677335.1	328225	328225	type	True	80.8828	302	470	95	below_threshold
Erythrobacter colymbi	strain=JCM 18338	GCA_002155685.1	1161202	1161202	type	True	80.7128	305	470	95	below_threshold
Erythrobacter neustonensis	strain=DSM 9434	GCA_001663175.1	1112	1112	type	True	80.5704	280	470	95	below_threshold
Qipengyuania pelagi	strain=JCM 17468	GCA_009827295.1	994320	994320	type	True	77.4372	119	470	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	77.3394	89	470	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	76.8542	109	470	95	below_threshold
Novosphingobium aquimarinum	strain=M24A2M	GCA_009746585.1	2682494	2682494	type	True	76.8054	78	470	95	below_threshold
Novosphingobium percolationis	strain=c1	GCA_020179425.1	2871811	2871811	type	True	76.6969	121	470	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 08:10:54,128] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32031/tc_result.tsv
[2023-03-16 08:10:54,144] [INFO] ===== Taxonomy check completed =====
[2023-03-16 08:10:54,144] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 08:10:54,144] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfa94cd70-0fab-4794-add2-fae9561a17d7/dqc_reference/checkm_data
[2023-03-16 08:10:54,145] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 08:10:54,177] [INFO] Task started: CheckM
[2023-03-16 08:10:54,177] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32031/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32031/checkm_input OceanDNA-b32031/checkm_result
[2023-03-16 08:11:23,966] [INFO] Task succeeded: CheckM
[2023-03-16 08:11:23,966] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 55.21%
Contamintation: 1.39%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 08:11:24,058] [INFO] ===== Completeness check finished =====
[2023-03-16 08:11:24,058] [INFO] ===== Start GTDB Search =====
[2023-03-16 08:11:24,058] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32031/markers.fasta)
[2023-03-16 08:11:24,060] [INFO] Task started: Blastn
[2023-03-16 08:11:24,060] [INFO] Running command: blastn -query OceanDNA-b32031/markers.fasta -db /var/lib/cwl/stgfa94cd70-0fab-4794-add2-fae9561a17d7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32031/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:11:24,727] [INFO] Task succeeded: Blastn
[2023-03-16 08:11:24,740] [INFO] Selected 15 target genomes.
[2023-03-16 08:11:24,740] [INFO] Target genome list was writen to OceanDNA-b32031/target_genomes_gtdb.txt
[2023-03-16 08:11:24,818] [INFO] Task started: fastANI
[2023-03-16 08:11:24,818] [INFO] Running command: fastANI --query /var/lib/cwl/stgb3f17abb-339f-4135-b255-02a72691ee3c/OceanDNA-b32031.fa --refList OceanDNA-b32031/target_genomes_gtdb.txt --output OceanDNA-b32031/fastani_result_gtdb.tsv --threads 1
[2023-03-16 08:11:32,651] [INFO] Task succeeded: fastANI
[2023-03-16 08:11:32,660] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 08:11:32,660] [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_001464915.1	s__Erythrobacter sp001464915	82.964	315	470	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	82.6691	314	470	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	82.1949	338	470	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	82.0344	283	470	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	81.6874	239	470	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002842925.1	s__Erythrobacter sp002842925	81.4127	272	470	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	81.3765	296	470	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	81.3726	309	470	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	81.3131	310	470	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	81.3095	278	470	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	81.1485	244	470	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	80.7367	243	470	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	80.5515	318	470	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	80.4194	278	470	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	99.84	99.84	0.90	0.90	2	-
GCA_016125555.1	s__Erythrobacter sp016125555	80.3731	280	470	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 08:11:32,665] [INFO] GTDB search result was written to OceanDNA-b32031/result_gtdb.tsv
[2023-03-16 08:11:32,671] [INFO] ===== GTDB Search completed =====
[2023-03-16 08:11:32,678] [INFO] DFAST_QC result json was written to OceanDNA-b32031/dqc_result.json
[2023-03-16 08:11:32,678] [INFO] DFAST_QC completed!
[2023-03-16 08:11:32,678] [INFO] Total running time: 0h0m57s