[2023-03-19 02:40:15,840] [INFO] DFAST_QC pipeline started.
[2023-03-19 02:40:15,840] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 02:40:15,840] [INFO] DQC Reference Directory: /var/lib/cwl/stg2a13e1f4-d0c2-465b-b82c-86502d27aaa9/dqc_reference
[2023-03-19 02:40:17,573] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 02:40:17,573] [INFO] Task started: Prodigal
[2023-03-19 02:40:17,573] [INFO] Running command: cat /var/lib/cwl/stg0e32f582-ba11-4758-9af4-74e69b58c8a6/OceanDNA-b26127.fa | prodigal -d OceanDNA-b26127/cds.fna -a OceanDNA-b26127/protein.faa -g 11 -q > /dev/null
[2023-03-19 02:40:28,364] [INFO] Task succeeded: Prodigal
[2023-03-19 02:40:28,364] [INFO] Task started: HMMsearch
[2023-03-19 02:40:28,364] [INFO] Running command: hmmsearch --tblout OceanDNA-b26127/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2a13e1f4-d0c2-465b-b82c-86502d27aaa9/dqc_reference/reference_markers.hmm OceanDNA-b26127/protein.faa > /dev/null
[2023-03-19 02:40:28,545] [INFO] Task succeeded: HMMsearch
[2023-03-19 02:40:28,545] [INFO] Found 6/6 markers.
[2023-03-19 02:40:28,562] [INFO] Query marker FASTA was written to OceanDNA-b26127/markers.fasta
[2023-03-19 02:40:28,563] [INFO] Task started: Blastn
[2023-03-19 02:40:28,563] [INFO] Running command: blastn -query OceanDNA-b26127/markers.fasta -db /var/lib/cwl/stg2a13e1f4-d0c2-465b-b82c-86502d27aaa9/dqc_reference/reference_markers.fasta -out OceanDNA-b26127/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:40:29,152] [INFO] Task succeeded: Blastn
[2023-03-19 02:40:29,153] [INFO] Selected 37 target genomes.
[2023-03-19 02:40:29,154] [INFO] Target genome list was writen to OceanDNA-b26127/target_genomes.txt
[2023-03-19 02:40:29,175] [INFO] Task started: fastANI
[2023-03-19 02:40:29,175] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e32f582-ba11-4758-9af4-74e69b58c8a6/OceanDNA-b26127.fa --refList OceanDNA-b26127/target_genomes.txt --output OceanDNA-b26127/fastani_result.tsv --threads 1
[2023-03-19 02:40:54,283] [INFO] Task succeeded: fastANI
[2023-03-19 02:40:54,284] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2a13e1f4-d0c2-465b-b82c-86502d27aaa9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 02:40:54,284] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2a13e1f4-d0c2-465b-b82c-86502d27aaa9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 02:40:54,284] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 02:40:54,284] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 02:40:54,284] [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
--------------------------------------------------------------------------------
[2023-03-19 02:40:54,285] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26127/tc_result.tsv
[2023-03-19 02:40:54,285] [INFO] ===== Taxonomy check completed =====
[2023-03-19 02:40:54,285] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 02:40:54,285] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2a13e1f4-d0c2-465b-b82c-86502d27aaa9/dqc_reference/checkm_data
[2023-03-19 02:40:54,288] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 02:40:54,395] [INFO] Task started: CheckM
[2023-03-19 02:40:54,395] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26127/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26127/checkm_input OceanDNA-b26127/checkm_result
[2023-03-19 02:41:26,714] [INFO] Task succeeded: CheckM
[2023-03-19 02:41:26,715] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.38%
Contamintation: 0.93%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-19 02:41:26,759] [INFO] ===== Completeness check finished =====
[2023-03-19 02:41:26,759] [INFO] ===== Start GTDB Search =====
[2023-03-19 02:41:26,759] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26127/markers.fasta)
[2023-03-19 02:41:26,760] [INFO] Task started: Blastn
[2023-03-19 02:41:26,761] [INFO] Running command: blastn -query OceanDNA-b26127/markers.fasta -db /var/lib/cwl/stg2a13e1f4-d0c2-465b-b82c-86502d27aaa9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26127/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:41:27,768] [INFO] Task succeeded: Blastn
[2023-03-19 02:41:27,769] [INFO] Selected 30 target genomes.
[2023-03-19 02:41:27,769] [INFO] Target genome list was writen to OceanDNA-b26127/target_genomes_gtdb.txt
[2023-03-19 02:41:27,801] [INFO] Task started: fastANI
[2023-03-19 02:41:27,801] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e32f582-ba11-4758-9af4-74e69b58c8a6/OceanDNA-b26127.fa --refList OceanDNA-b26127/target_genomes_gtdb.txt --output OceanDNA-b26127/fastani_result_gtdb.tsv --threads 1
[2023-03-19 02:41:40,688] [INFO] Task succeeded: fastANI
[2023-03-19 02:41:40,695] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 02:41:40,695] [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_009920665.1	s__UBA8309 sp009920665	77.9552	95	526	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902547925.1	s__MED-G116 sp902547925	77.2261	69	526	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__MED-G116	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004212735.1	s__MED-G116 sp004212735	77.0397	130	526	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__MED-G116	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002686685.1	s__UBA8309 sp002686685	77.0201	54	526	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	97.96	97.78	0.70	0.66	5	-
GCA_905182545.1	s__UBA3439 sp905182545	76.8277	55	526	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA3439	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902578815.1	s__MED-G116 sp902578815	76.7991	67	526	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__MED-G116	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016780765.1	s__UBA8309 sp016780765	76.6394	86	526	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	98.39	97.46	0.74	0.59	14	-
GCA_002378605.1	s__UBA3439 sp002378605	76.5406	53	526	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA3439	95.0	99.28	99.28	0.80	0.80	2	-
GCA_009919335.1	s__UBA3439 sp009919335	76.5048	50	526	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA3439	95.0	98.81	98.81	0.76	0.76	2	-
GCA_017859295.1	s__UBA3439 sp017859295	76.3983	56	526	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA3439	95.0	98.52	98.52	0.78	0.78	2	-
GCA_011524735.1	s__UBA8309 sp011524735	76.3348	67	526	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 02:41:40,696] [INFO] GTDB search result was written to OceanDNA-b26127/result_gtdb.tsv
[2023-03-19 02:41:40,696] [INFO] ===== GTDB Search completed =====
[2023-03-19 02:41:40,698] [INFO] DFAST_QC result json was written to OceanDNA-b26127/dqc_result.json
[2023-03-19 02:41:40,698] [INFO] DFAST_QC completed!
[2023-03-19 02:41:40,698] [INFO] Total running time: 0h1m25s