[2023-03-18 09:27:55,576] [INFO] DFAST_QC pipeline started.
[2023-03-18 09:27:55,576] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 09:27:55,576] [INFO] DQC Reference Directory: /var/lib/cwl/stg0bc8bc34-22ef-4ecb-86aa-a43877b2dff2/dqc_reference
[2023-03-18 09:27:56,657] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 09:27:56,658] [INFO] Task started: Prodigal
[2023-03-18 09:27:56,659] [INFO] Running command: cat /var/lib/cwl/stg05d62b3d-d703-4c79-ac85-b7e747b85dcc/OceanDNA-b22992.fa | prodigal -d OceanDNA-b22992/cds.fna -a OceanDNA-b22992/protein.faa -g 11 -q > /dev/null
[2023-03-18 09:28:08,364] [INFO] Task succeeded: Prodigal
[2023-03-18 09:28:08,365] [INFO] Task started: HMMsearch
[2023-03-18 09:28:08,365] [INFO] Running command: hmmsearch --tblout OceanDNA-b22992/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0bc8bc34-22ef-4ecb-86aa-a43877b2dff2/dqc_reference/reference_markers.hmm OceanDNA-b22992/protein.faa > /dev/null
[2023-03-18 09:28:08,564] [INFO] Task succeeded: HMMsearch
[2023-03-18 09:28:08,564] [INFO] Found 6/6 markers.
[2023-03-18 09:28:08,585] [INFO] Query marker FASTA was written to OceanDNA-b22992/markers.fasta
[2023-03-18 09:28:08,586] [INFO] Task started: Blastn
[2023-03-18 09:28:08,586] [INFO] Running command: blastn -query OceanDNA-b22992/markers.fasta -db /var/lib/cwl/stg0bc8bc34-22ef-4ecb-86aa-a43877b2dff2/dqc_reference/reference_markers.fasta -out OceanDNA-b22992/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:28:09,150] [INFO] Task succeeded: Blastn
[2023-03-18 09:28:09,151] [INFO] Selected 29 target genomes.
[2023-03-18 09:28:09,151] [INFO] Target genome list was writen to OceanDNA-b22992/target_genomes.txt
[2023-03-18 09:28:09,169] [INFO] Task started: fastANI
[2023-03-18 09:28:09,169] [INFO] Running command: fastANI --query /var/lib/cwl/stg05d62b3d-d703-4c79-ac85-b7e747b85dcc/OceanDNA-b22992.fa --refList OceanDNA-b22992/target_genomes.txt --output OceanDNA-b22992/fastani_result.tsv --threads 1
[2023-03-18 09:28:34,556] [INFO] Task succeeded: fastANI
[2023-03-18 09:28:34,556] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0bc8bc34-22ef-4ecb-86aa-a43877b2dff2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 09:28:34,556] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0bc8bc34-22ef-4ecb-86aa-a43877b2dff2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 09:28:34,562] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 09:28:34,562] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 09:28:34,562] [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
Aquisphaera giovannonii	strain=OJF2	GCA_008087625.1	406548	406548	type	True	74.9806	63	593	95	below_threshold
Salinarimonas ramus	strain=CGMCC 1.9161	GCA_014645695.1	690164	690164	type	True	74.7824	64	593	95	below_threshold
Cellulomonas shaoxiangyii	strain=Z28	GCA_004798685.1	2566013	2566013	type	True	74.7452	51	593	95	below_threshold
Nonomuraea montanisoli	strain=SMC 257	GCA_013363975.1	2741721	2741721	type	True	74.7053	68	593	95	below_threshold
Burkholderia glumae	strain=LMG 2196	GCA_902832765.1	337	337	type	True	74.6924	51	593	95	below_threshold
Pseudorhodoferax soli	strain=DSM 21634	GCA_003337555.1	545864	545864	type	True	74.6818	59	593	95	below_threshold
Roseiarcus fermentans	strain=DSM 24875	GCA_003315135.1	1473586	1473586	type	True	74.6715	54	593	95	below_threshold
Cellulomonas telluris	strain=CPCC 204705	GCA_004886325.1	2306636	2306636	type	True	74.6273	57	593	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 09:28:34,562] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22992/tc_result.tsv
[2023-03-18 09:28:34,563] [INFO] ===== Taxonomy check completed =====
[2023-03-18 09:28:34,563] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 09:28:34,563] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0bc8bc34-22ef-4ecb-86aa-a43877b2dff2/dqc_reference/checkm_data
[2023-03-18 09:28:34,563] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 09:28:34,568] [INFO] Task started: CheckM
[2023-03-18 09:28:34,568] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22992/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22992/checkm_input OceanDNA-b22992/checkm_result
[2023-03-18 09:29:07,214] [INFO] Task succeeded: CheckM
[2023-03-18 09:29:07,214] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.88%
Contamintation: 8.33%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-18 09:29:07,216] [INFO] ===== Completeness check finished =====
[2023-03-18 09:29:07,217] [INFO] ===== Start GTDB Search =====
[2023-03-18 09:29:07,217] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22992/markers.fasta)
[2023-03-18 09:29:07,218] [INFO] Task started: Blastn
[2023-03-18 09:29:07,218] [INFO] Running command: blastn -query OceanDNA-b22992/markers.fasta -db /var/lib/cwl/stg0bc8bc34-22ef-4ecb-86aa-a43877b2dff2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22992/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:29:08,103] [INFO] Task succeeded: Blastn
[2023-03-18 09:29:08,103] [INFO] Selected 33 target genomes.
[2023-03-18 09:29:08,104] [INFO] Target genome list was writen to OceanDNA-b22992/target_genomes_gtdb.txt
[2023-03-18 09:29:08,332] [INFO] Task started: fastANI
[2023-03-18 09:29:08,332] [INFO] Running command: fastANI --query /var/lib/cwl/stg05d62b3d-d703-4c79-ac85-b7e747b85dcc/OceanDNA-b22992.fa --refList OceanDNA-b22992/target_genomes_gtdb.txt --output OceanDNA-b22992/fastani_result_gtdb.tsv --threads 1
[2023-03-18 09:29:33,789] [INFO] Task succeeded: fastANI
[2023-03-18 09:29:33,795] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 09:29:33,795] [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_016795345.1	s__JAEUHO01 sp016795345	75.9202	117	593	d__Bacteria;p__Planctomycetota;c__PLA2;o__PLA2;f__JAEUHO01;g__JAEUHO01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008087625.1	s__Aquisphaera giovannonii	74.9806	63	593	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Isosphaerales;f__Isosphaeraceae;g__Aquisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016872715.1	s__F1-120-MAGs118 sp016872715	74.9411	52	593	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__F1-120-MAGs118	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013340205.1	s__R267 sp013340205	74.9247	60	593	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Anaeromyxobacteraceae;g__R267	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793245.1	s__JADKAF01 sp016793245	74.8906	83	593	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__JADKAF01;g__JADKAF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903893335.1	s__CAITLX01 sp903893335	74.8818	83	593	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__CAITLX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016709145.1	s__JADJEK01 sp016709145	74.8263	61	593	d__Bacteria;p__Planctomycetota;c__B15-G4;o__B15-G4;f__JADJEK01;g__JADJEK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016719295.1	s__JADKAF01 sp016719295	74.8078	90	593	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__JADKAF01;g__JADKAF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016707895.1	s__UBA2376 sp016707895	74.7759	113	593	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__UBA2376	95.0	99.64	99.63	0.96	0.96	3	-
GCF_004798685.1	s__Cellulomonas shaoxiangyii	74.7417	53	593	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2023-03-18 09:29:33,796] [INFO] GTDB search result was written to OceanDNA-b22992/result_gtdb.tsv
[2023-03-18 09:29:33,796] [INFO] ===== GTDB Search completed =====
[2023-03-18 09:29:33,797] [INFO] DFAST_QC result json was written to OceanDNA-b22992/dqc_result.json
[2023-03-18 09:29:33,797] [INFO] DFAST_QC completed!
[2023-03-18 09:29:33,797] [INFO] Total running time: 0h1m38s