[2023-03-15 22:48:49,180] [INFO] DFAST_QC pipeline started.
[2023-03-15 22:48:49,180] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 22:48:49,180] [INFO] DQC Reference Directory: /var/lib/cwl/stg85c7f00d-b9be-4f64-bb23-3cb3e51dd3ad/dqc_reference
[2023-03-15 22:48:50,294] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 22:48:50,295] [INFO] Task started: Prodigal
[2023-03-15 22:48:50,295] [INFO] Running command: cat /var/lib/cwl/stg67cdf513-77c9-4d90-8e24-283cca5fb2a8/OceanDNA-b26683.fa | prodigal -d OceanDNA-b26683/cds.fna -a OceanDNA-b26683/protein.faa -g 11 -q > /dev/null
[2023-03-15 22:49:15,402] [INFO] Task succeeded: Prodigal
[2023-03-15 22:49:15,402] [INFO] Task started: HMMsearch
[2023-03-15 22:49:15,402] [INFO] Running command: hmmsearch --tblout OceanDNA-b26683/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg85c7f00d-b9be-4f64-bb23-3cb3e51dd3ad/dqc_reference/reference_markers.hmm OceanDNA-b26683/protein.faa > /dev/null
[2023-03-15 22:49:15,621] [INFO] Task succeeded: HMMsearch
[2023-03-15 22:49:15,621] [INFO] Found 6/6 markers.
[2023-03-15 22:49:15,645] [INFO] Query marker FASTA was written to OceanDNA-b26683/markers.fasta
[2023-03-15 22:49:15,646] [INFO] Task started: Blastn
[2023-03-15 22:49:15,646] [INFO] Running command: blastn -query OceanDNA-b26683/markers.fasta -db /var/lib/cwl/stg85c7f00d-b9be-4f64-bb23-3cb3e51dd3ad/dqc_reference/reference_markers.fasta -out OceanDNA-b26683/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 22:49:16,321] [INFO] Task succeeded: Blastn
[2023-03-15 22:49:16,322] [INFO] Selected 16 target genomes.
[2023-03-15 22:49:16,322] [INFO] Target genome list was writen to OceanDNA-b26683/target_genomes.txt
[2023-03-15 22:49:16,334] [INFO] Task started: fastANI
[2023-03-15 22:49:16,334] [INFO] Running command: fastANI --query /var/lib/cwl/stg67cdf513-77c9-4d90-8e24-283cca5fb2a8/OceanDNA-b26683.fa --refList OceanDNA-b26683/target_genomes.txt --output OceanDNA-b26683/fastani_result.tsv --threads 1
[2023-03-15 22:49:29,917] [INFO] Task succeeded: fastANI
[2023-03-15 22:49:29,917] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg85c7f00d-b9be-4f64-bb23-3cb3e51dd3ad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 22:49:29,918] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg85c7f00d-b9be-4f64-bb23-3cb3e51dd3ad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 22:49:29,928] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 22:49:29,928] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 22:49:29,928] [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
Devosia beringensis	strain=S02	GCA_014926585.1	2657486	2657486	type	True	84.2082	880	1306	95	below_threshold
Devosia ginsengisoli	strain=Gsoil 520	GCA_007859655.1	400770	400770	type	True	81.2469	742	1306	95	below_threshold
Devosia oryziradicis	strain=G19	GCA_016698645.1	2801335	2801335	type	True	80.7019	679	1306	95	below_threshold
Devosia limi	strain=DSM 17137	GCA_000970435.1	288995	288995	type	True	80.4118	647	1306	95	below_threshold
Devosia limi	strain=DSM 17137	GCA_900128975.1	288995	288995	type	True	80.4098	658	1306	95	below_threshold
Devosia psychrophila	strain=CGMCC 1.10210	GCA_900112505.1	728005	728005	type	True	80.4005	658	1306	95	below_threshold
Devosia psychrophila	strain=Cr7-05	GCA_000971275.1	728005	728005	type	True	80.3407	648	1306	95	below_threshold
Devosia naphthalenivorans	strain=CM5-1	GCA_003056355.1	2082392	2082392	type	True	80.1525	608	1306	95	below_threshold
Devosia epidermidihirudinis	strain=E84	GCA_000971295.1	1293439	1293439	type	True	80.008	623	1306	95	below_threshold
Devosia elaeis	strain=S37	GCA_001650025.1	1770058	1770058	type	True	80.0066	615	1306	95	below_threshold
Devosia salina	strain=SCS-3	GCA_019504385.1	2860336	2860336	type	True	79.7946	647	1306	95	below_threshold
Devosia sediminis	strain=MSA67	GCA_016411825.1	2798801	2798801	type	True	79.6681	573	1306	95	below_threshold
Devosia chinhatensis	strain=IPL18	GCA_000969445.1	429727	429727	type	True	79.2935	551	1306	95	below_threshold
Devosia rhizoryzae	strain=LEGU1	GCA_016698665.1	2774137	2774137	type	True	79.1345	480	1306	95	below_threshold
Devosia soli	strain=GH2-10	GCA_000970455.1	361041	361041	type	True	78.4141	508	1306	95	below_threshold
Pelagibacterium sediminicola	strain=IMCC34151	GCA_003390885.1	2248761	2248761	type	True	77.0756	244	1306	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 22:49:29,928] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26683/tc_result.tsv
[2023-03-15 22:49:29,928] [INFO] ===== Taxonomy check completed =====
[2023-03-15 22:49:29,928] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 22:49:29,928] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg85c7f00d-b9be-4f64-bb23-3cb3e51dd3ad/dqc_reference/checkm_data
[2023-03-15 22:49:29,929] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 22:49:29,935] [INFO] Task started: CheckM
[2023-03-15 22:49:29,935] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26683/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26683/checkm_input OceanDNA-b26683/checkm_result
[2023-03-15 22:50:32,441] [INFO] Task succeeded: CheckM
[2023-03-15 22:50:32,441] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 22:50:32,478] [INFO] ===== Completeness check finished =====
[2023-03-15 22:50:32,478] [INFO] ===== Start GTDB Search =====
[2023-03-15 22:50:32,479] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26683/markers.fasta)
[2023-03-15 22:50:32,480] [INFO] Task started: Blastn
[2023-03-15 22:50:32,480] [INFO] Running command: blastn -query OceanDNA-b26683/markers.fasta -db /var/lib/cwl/stg85c7f00d-b9be-4f64-bb23-3cb3e51dd3ad/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26683/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 22:50:33,619] [INFO] Task succeeded: Blastn
[2023-03-15 22:50:33,625] [INFO] Selected 14 target genomes.
[2023-03-15 22:50:33,625] [INFO] Target genome list was writen to OceanDNA-b26683/target_genomes_gtdb.txt
[2023-03-15 22:50:33,957] [INFO] Task started: fastANI
[2023-03-15 22:50:33,957] [INFO] Running command: fastANI --query /var/lib/cwl/stg67cdf513-77c9-4d90-8e24-283cca5fb2a8/OceanDNA-b26683.fa --refList OceanDNA-b26683/target_genomes_gtdb.txt --output OceanDNA-b26683/fastani_result_gtdb.tsv --threads 1
[2023-03-15 22:50:45,599] [INFO] Task succeeded: fastANI
[2023-03-15 22:50:45,608] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 22:50:45,608] [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_014926585.1	s__Devosia sp014926585	84.2082	880	1306	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018334155.1	s__Devosia sp018334155	82.8705	803	1306	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005222805.1	s__Devosia sp005222805	82.6858	799	1306	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018820005.1	s__Devosia sp018820005	81.7484	468	1306	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018828145.1	s__Devosia sp018828145	81.7203	752	1306	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	99.99	99.98	0.99	0.98	4	-
GCA_014860165.1	s__Devosia sp014860165	81.3831	732	1306	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001427605.1	s__Devosia sp001427605	81.3017	696	1306	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001426345.1	s__Devosia sp001426345	81.2733	708	1306	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859655.1	s__Devosia ginsengisoli	81.227	746	1306	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900470445.1	s__Devosia sp900470445	80.8587	710	1306	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	95.41	95.41	0.81	0.81	2	-
GCF_016698645.1	s__Devosia sp016698645	80.7151	678	1306	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003056355.1	s__Devosia naphthalenivorans	80.1591	608	1306	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000971295.1	s__Devosia epidermidihirudinis	79.9904	625	1306	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 22:50:45,610] [INFO] GTDB search result was written to OceanDNA-b26683/result_gtdb.tsv
[2023-03-15 22:50:45,610] [INFO] ===== GTDB Search completed =====
[2023-03-15 22:50:45,612] [INFO] DFAST_QC result json was written to OceanDNA-b26683/dqc_result.json
[2023-03-15 22:50:45,612] [INFO] DFAST_QC completed!
[2023-03-15 22:50:45,612] [INFO] Total running time: 0h1m56s