[2023-03-18 21:15:29,382] [INFO] DFAST_QC pipeline started.
[2023-03-18 21:15:29,384] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 21:15:29,384] [INFO] DQC Reference Directory: /var/lib/cwl/stge6a63dbd-276d-466c-a7f1-02619a4f2c1d/dqc_reference
[2023-03-18 21:15:31,044] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 21:15:31,045] [INFO] Task started: Prodigal
[2023-03-18 21:15:31,045] [INFO] Running command: cat /var/lib/cwl/stgcb341c2e-87ec-4711-80e3-049be6969b37/OceanDNA-b33325.fa | prodigal -d OceanDNA-b33325/cds.fna -a OceanDNA-b33325/protein.faa -g 11 -q > /dev/null
[2023-03-18 21:15:52,556] [INFO] Task succeeded: Prodigal
[2023-03-18 21:15:52,556] [INFO] Task started: HMMsearch
[2023-03-18 21:15:52,556] [INFO] Running command: hmmsearch --tblout OceanDNA-b33325/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge6a63dbd-276d-466c-a7f1-02619a4f2c1d/dqc_reference/reference_markers.hmm OceanDNA-b33325/protein.faa > /dev/null
[2023-03-18 21:15:52,773] [INFO] Task succeeded: HMMsearch
[2023-03-18 21:15:52,774] [INFO] Found 6/6 markers.
[2023-03-18 21:15:52,806] [INFO] Query marker FASTA was written to OceanDNA-b33325/markers.fasta
[2023-03-18 21:15:52,806] [INFO] Task started: Blastn
[2023-03-18 21:15:52,806] [INFO] Running command: blastn -query OceanDNA-b33325/markers.fasta -db /var/lib/cwl/stge6a63dbd-276d-466c-a7f1-02619a4f2c1d/dqc_reference/reference_markers.fasta -out OceanDNA-b33325/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:15:53,422] [INFO] Task succeeded: Blastn
[2023-03-18 21:15:53,425] [INFO] Selected 27 target genomes.
[2023-03-18 21:15:53,425] [INFO] Target genome list was writen to OceanDNA-b33325/target_genomes.txt
[2023-03-18 21:15:53,442] [INFO] Task started: fastANI
[2023-03-18 21:15:53,442] [INFO] Running command: fastANI --query /var/lib/cwl/stgcb341c2e-87ec-4711-80e3-049be6969b37/OceanDNA-b33325.fa --refList OceanDNA-b33325/target_genomes.txt --output OceanDNA-b33325/fastani_result.tsv --threads 1
[2023-03-18 21:16:12,448] [INFO] Task succeeded: fastANI
[2023-03-18 21:16:12,448] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge6a63dbd-276d-466c-a7f1-02619a4f2c1d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 21:16:12,449] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge6a63dbd-276d-466c-a7f1-02619a4f2c1d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 21:16:12,455] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 21:16:12,455] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 21:16:12,456] [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
Limnobacter alexandrii	strain=LZ-4	GCA_005871185.1	2570352	2570352	type	True	82.9646	736	1047	95	below_threshold
Limnobacter humi	strain=NBRC 111650	GCA_024518835.1	1778671	1778671	type	True	78.5925	366	1047	95	below_threshold
Comamonas fluminis	strain=CJ34	GCA_019186805.1	2796366	2796366	type	True	76.3021	58	1047	95	below_threshold
Cupriavidus oxalaticus	strain=Ox1	GCA_016894385.1	96344	96344	type	True	76.275	60	1047	95	below_threshold
Achromobacter xylosoxidans	strain=PartM-Axylosoxidans-RM8376	GCA_022870085.1	85698	85698	type	True	76.176	50	1047	95	below_threshold
Duganella aceris	strain=SAP-35	GCA_011090165.1	2703883	2703883	type	True	76.036	50	1047	95	below_threshold
Acidovorax delafieldii	strain=DSM 64	GCA_007993815.1	47920	47920	type	True	75.6879	53	1047	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 21:16:12,457] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33325/tc_result.tsv
[2023-03-18 21:16:12,458] [INFO] ===== Taxonomy check completed =====
[2023-03-18 21:16:12,458] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 21:16:12,458] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge6a63dbd-276d-466c-a7f1-02619a4f2c1d/dqc_reference/checkm_data
[2023-03-18 21:16:12,459] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 21:16:12,465] [INFO] Task started: CheckM
[2023-03-18 21:16:12,465] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33325/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33325/checkm_input OceanDNA-b33325/checkm_result
[2023-03-18 21:17:08,459] [INFO] Task succeeded: CheckM
[2023-03-18 21:17:08,460] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 21:17:08,475] [INFO] ===== Completeness check finished =====
[2023-03-18 21:17:08,475] [INFO] ===== Start GTDB Search =====
[2023-03-18 21:17:08,476] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33325/markers.fasta)
[2023-03-18 21:17:08,476] [INFO] Task started: Blastn
[2023-03-18 21:17:08,477] [INFO] Running command: blastn -query OceanDNA-b33325/markers.fasta -db /var/lib/cwl/stge6a63dbd-276d-466c-a7f1-02619a4f2c1d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33325/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:17:09,346] [INFO] Task succeeded: Blastn
[2023-03-18 21:17:09,351] [INFO] Selected 8 target genomes.
[2023-03-18 21:17:09,351] [INFO] Target genome list was writen to OceanDNA-b33325/target_genomes_gtdb.txt
[2023-03-18 21:17:09,361] [INFO] Task started: fastANI
[2023-03-18 21:17:09,361] [INFO] Running command: fastANI --query /var/lib/cwl/stgcb341c2e-87ec-4711-80e3-049be6969b37/OceanDNA-b33325.fa --refList OceanDNA-b33325/target_genomes_gtdb.txt --output OceanDNA-b33325/fastani_result_gtdb.tsv --threads 1
[2023-03-18 21:17:15,150] [INFO] Task succeeded: fastANI
[2023-03-18 21:17:15,156] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 21:17:15,156] [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_018815245.1	s__Limnobacter sp018815245	99.9725	1023	1047	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnobacter	95.0	99.98	99.93	0.99	0.98	9	conclusive
GCF_902506325.1	s__Limnobacter sp902506325	83.1932	741	1047	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005871185.1	s__Limnobacter alexandrii	82.971	736	1047	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013004065.1	s__Limnobacter sp002954425	82.9359	732	1047	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnobacter	95.0	97.67	96.02	0.92	0.87	19	-
GCF_000170915.1	s__Limnobacter sp000170915	82.7356	710	1047	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnobacter	95.0	98.10	98.01	0.88	0.86	5	-
GCA_001601825.1	s__Limnobacter sp001601825	82.0133	666	1047	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018812945.1	s__Limnobacter sp018812945	81.8136	626	1047	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004291335.1	s__Limnobacter thiooxidans	81.5553	623	1047	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 21:17:15,159] [INFO] GTDB search result was written to OceanDNA-b33325/result_gtdb.tsv
[2023-03-18 21:17:15,161] [INFO] ===== GTDB Search completed =====
[2023-03-18 21:17:15,163] [INFO] DFAST_QC result json was written to OceanDNA-b33325/dqc_result.json
[2023-03-18 21:17:15,164] [INFO] DFAST_QC completed!
[2023-03-18 21:17:15,164] [INFO] Total running time: 0h1m46s