[2023-03-18 01:24:39,915] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:24:39,915] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:24:39,915] [INFO] DQC Reference Directory: /var/lib/cwl/stgaa6aefe6-7116-4d11-ae1d-7bb5da3db2a8/dqc_reference
[2023-03-18 01:24:41,192] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:24:41,193] [INFO] Task started: Prodigal
[2023-03-18 01:24:41,193] [INFO] Running command: cat /var/lib/cwl/stg77a42e1a-72cd-4656-93c4-a7dec6586f71/OceanDNA-b32038.fa | prodigal -d OceanDNA-b32038/cds.fna -a OceanDNA-b32038/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:24:59,533] [INFO] Task succeeded: Prodigal
[2023-03-18 01:24:59,533] [INFO] Task started: HMMsearch
[2023-03-18 01:24:59,534] [INFO] Running command: hmmsearch --tblout OceanDNA-b32038/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaa6aefe6-7116-4d11-ae1d-7bb5da3db2a8/dqc_reference/reference_markers.hmm OceanDNA-b32038/protein.faa > /dev/null
[2023-03-18 01:24:59,717] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:24:59,718] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg77a42e1a-72cd-4656-93c4-a7dec6586f71/OceanDNA-b32038.fa]
[2023-03-18 01:24:59,736] [INFO] Query marker FASTA was written to OceanDNA-b32038/markers.fasta
[2023-03-18 01:24:59,737] [INFO] Task started: Blastn
[2023-03-18 01:24:59,737] [INFO] Running command: blastn -query OceanDNA-b32038/markers.fasta -db /var/lib/cwl/stgaa6aefe6-7116-4d11-ae1d-7bb5da3db2a8/dqc_reference/reference_markers.fasta -out OceanDNA-b32038/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:25:00,438] [INFO] Task succeeded: Blastn
[2023-03-18 01:25:00,439] [INFO] Selected 14 target genomes.
[2023-03-18 01:25:00,439] [INFO] Target genome list was writen to OceanDNA-b32038/target_genomes.txt
[2023-03-18 01:25:00,446] [INFO] Task started: fastANI
[2023-03-18 01:25:00,446] [INFO] Running command: fastANI --query /var/lib/cwl/stg77a42e1a-72cd-4656-93c4-a7dec6586f71/OceanDNA-b32038.fa --refList OceanDNA-b32038/target_genomes.txt --output OceanDNA-b32038/fastani_result.tsv --threads 1
[2023-03-18 01:25:08,290] [INFO] Task succeeded: fastANI
[2023-03-18 01:25:08,290] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaa6aefe6-7116-4d11-ae1d-7bb5da3db2a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 01:25:08,290] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaa6aefe6-7116-4d11-ae1d-7bb5da3db2a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 01:25:08,299] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 01:25:08,300] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 01:25:08,300] [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=DSM 11032	GCA_900143235.1	198312	198312	type	True	80.5859	530	923	95	below_threshold
Erythrobacter sanguineus	strain=JCM 20691	GCA_002155655.1	198312	198312	type	True	80.5745	528	923	95	below_threshold
Erythrobacter dokdonensis	strain=DSM 17193	GCA_002155305.1	328225	328225	type	True	80.1915	504	923	95	below_threshold
Erythrobacter dokdonensis	strain=DSW-74	GCA_001677335.1	328225	328225	type	True	80.1743	506	923	95	below_threshold
Erythrobacter donghaensis	strain=DSM 16220	GCA_002155425.1	267135	267135	suspected-type	True	79.9511	529	923	95	below_threshold
Erythrobacter ramosus	strain=JCM 10282	GCA_009828055.1	35811	35811	type	True	79.8374	501	923	95	below_threshold
Erythrobacter ramosus	strain=DSM 8510	GCA_014195675.1	35811	35811	type	True	79.7743	505	923	95	below_threshold
Erythrobacter tepidarius	strain=DSM 10594	GCA_002155695.1	60454	60454	type	True	79.7361	527	923	95	below_threshold
Erythrobacter colymbi	strain=JCM 18338	GCA_002155685.1	1161202	1161202	type	True	79.6876	511	923	95	below_threshold
Qipengyuania aurantiaca	strain=1NDH13	GCA_019711375.1	2867233	2867233	type	True	77.791	253	923	95	below_threshold
Qipengyuania huizhouensis	strain=YG19	GCA_019711635.1	2867245	2867245	type	True	77.6926	191	923	95	below_threshold
Qipengyuania xiapuensis	strain=1NDW9	GCA_019711395.1	2867236	2867236	type	True	77.5446	226	923	95	below_threshold
Qipengyuania flava	strain=DSM 16421	GCA_011762005.1	192812	192812	type	True	77.4842	245	923	95	below_threshold
Erythrobacter rubeus	strain=KMU-140	GCA_014705715.1	2760803	2760803	type	True	77.4591	288	923	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 01:25:08,300] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32038/tc_result.tsv
[2023-03-18 01:25:08,300] [INFO] ===== Taxonomy check completed =====
[2023-03-18 01:25:08,300] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 01:25:08,300] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaa6aefe6-7116-4d11-ae1d-7bb5da3db2a8/dqc_reference/checkm_data
[2023-03-18 01:25:08,301] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 01:25:08,352] [INFO] Task started: CheckM
[2023-03-18 01:25:08,352] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32038/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32038/checkm_input OceanDNA-b32038/checkm_result
[2023-03-18 01:25:55,449] [INFO] Task succeeded: CheckM
[2023-03-18 01:25:55,449] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 01:25:55,451] [INFO] ===== Completeness check finished =====
[2023-03-18 01:25:55,451] [INFO] ===== Start GTDB Search =====
[2023-03-18 01:25:55,451] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32038/markers.fasta)
[2023-03-18 01:25:55,452] [INFO] Task started: Blastn
[2023-03-18 01:25:55,453] [INFO] Running command: blastn -query OceanDNA-b32038/markers.fasta -db /var/lib/cwl/stgaa6aefe6-7116-4d11-ae1d-7bb5da3db2a8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32038/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:25:56,745] [INFO] Task succeeded: Blastn
[2023-03-18 01:25:56,746] [INFO] Selected 16 target genomes.
[2023-03-18 01:25:56,746] [INFO] Target genome list was writen to OceanDNA-b32038/target_genomes_gtdb.txt
[2023-03-18 01:25:56,823] [INFO] Task started: fastANI
[2023-03-18 01:25:56,823] [INFO] Running command: fastANI --query /var/lib/cwl/stg77a42e1a-72cd-4656-93c4-a7dec6586f71/OceanDNA-b32038.fa --refList OceanDNA-b32038/target_genomes_gtdb.txt --output OceanDNA-b32038/fastani_result_gtdb.tsv --threads 1
[2023-03-18 01:26:06,533] [INFO] Task succeeded: fastANI
[2023-03-18 01:26:06,543] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 01:26:06,543] [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_001724215.1	s__Erythrobacter sp001724215	97.3369	713	923	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_900143235.1	s__Erythrobacter sanguineus	80.5886	529	923	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCA_903934325.1	s__Erythrobacter sp903934325	80.5352	512	923	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000744895.1	s__Erythrobacter sp000744895	80.3414	549	923	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	80.2655	544	923	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	80.2052	484	923	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	95.33	95.33	0.91	0.91	2	-
GCF_001677335.1	s__Erythrobacter dokdonensis	80.1744	506	923	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002855495.1	s__Erythrobacter sp002855495	80.158	500	923	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	80.1531	513	923	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	80.1479	510	923	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	80.0527	361	923	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	80.0031	399	923	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001464915.1	s__Erythrobacter sp001464915	79.9762	472	923	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	79.7557	498	923	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002155695.1	s__Erythrobacter tepidarius	79.7267	528	923	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	79.6571	515	923	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 01:26:06,543] [INFO] GTDB search result was written to OceanDNA-b32038/result_gtdb.tsv
[2023-03-18 01:26:06,543] [INFO] ===== GTDB Search completed =====
[2023-03-18 01:26:06,545] [INFO] DFAST_QC result json was written to OceanDNA-b32038/dqc_result.json
[2023-03-18 01:26:06,545] [INFO] DFAST_QC completed!
[2023-03-18 01:26:06,545] [INFO] Total running time: 0h1m27s