[2023-03-15 04:45:50,550] [INFO] DFAST_QC pipeline started.
[2023-03-15 04:45:50,552] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 04:45:50,552] [INFO] DQC Reference Directory: /var/lib/cwl/stgc903e126-2c46-4ff9-954d-cc055853185c/dqc_reference
[2023-03-15 04:45:51,618] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 04:45:51,618] [INFO] Task started: Prodigal
[2023-03-15 04:45:51,618] [INFO] Running command: cat /var/lib/cwl/stgc532e27c-d0ca-4a09-a626-70494e9cd345/OceanDNA-b12871.fa | prodigal -d OceanDNA-b12871/cds.fna -a OceanDNA-b12871/protein.faa -g 11 -q > /dev/null
[2023-03-15 04:45:59,650] [INFO] Task succeeded: Prodigal
[2023-03-15 04:45:59,650] [INFO] Task started: HMMsearch
[2023-03-15 04:45:59,650] [INFO] Running command: hmmsearch --tblout OceanDNA-b12871/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc903e126-2c46-4ff9-954d-cc055853185c/dqc_reference/reference_markers.hmm OceanDNA-b12871/protein.faa > /dev/null
[2023-03-15 04:45:59,834] [INFO] Task succeeded: HMMsearch
[2023-03-15 04:45:59,835] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgc532e27c-d0ca-4a09-a626-70494e9cd345/OceanDNA-b12871.fa]
[2023-03-15 04:45:59,869] [INFO] Query marker FASTA was written to OceanDNA-b12871/markers.fasta
[2023-03-15 04:45:59,870] [INFO] Task started: Blastn
[2023-03-15 04:45:59,870] [INFO] Running command: blastn -query OceanDNA-b12871/markers.fasta -db /var/lib/cwl/stgc903e126-2c46-4ff9-954d-cc055853185c/dqc_reference/reference_markers.fasta -out OceanDNA-b12871/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 04:46:00,324] [INFO] Task succeeded: Blastn
[2023-03-15 04:46:00,328] [INFO] Selected 17 target genomes.
[2023-03-15 04:46:00,328] [INFO] Target genome list was writen to OceanDNA-b12871/target_genomes.txt
[2023-03-15 04:46:00,340] [INFO] Task started: fastANI
[2023-03-15 04:46:00,340] [INFO] Running command: fastANI --query /var/lib/cwl/stgc532e27c-d0ca-4a09-a626-70494e9cd345/OceanDNA-b12871.fa --refList OceanDNA-b12871/target_genomes.txt --output OceanDNA-b12871/fastani_result.tsv --threads 1
[2023-03-15 04:46:13,917] [INFO] Task succeeded: fastANI
[2023-03-15 04:46:13,918] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc903e126-2c46-4ff9-954d-cc055853185c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 04:46:13,918] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc903e126-2c46-4ff9-954d-cc055853185c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 04:46:13,921] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 04:46:13,921] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 04:46:13,921] [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
Daejeonella rubra	strain=DSM 24536	GCA_900103545.1	990371	990371	type	True	85.3605	202	219	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 04:46:13,923] [INFO] DFAST Taxonomy check result was written to OceanDNA-b12871/tc_result.tsv
[2023-03-15 04:46:13,926] [INFO] ===== Taxonomy check completed =====
[2023-03-15 04:46:13,926] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 04:46:13,926] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc903e126-2c46-4ff9-954d-cc055853185c/dqc_reference/checkm_data
[2023-03-15 04:46:13,927] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 04:46:13,933] [INFO] Task started: CheckM
[2023-03-15 04:46:13,933] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b12871/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b12871/checkm_input OceanDNA-b12871/checkm_result
[2023-03-15 04:46:40,782] [INFO] Task succeeded: CheckM
[2023-03-15 04:46:40,783] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.62%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 04:46:40,793] [INFO] ===== Completeness check finished =====
[2023-03-15 04:46:40,793] [INFO] ===== Start GTDB Search =====
[2023-03-15 04:46:40,793] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b12871/markers.fasta)
[2023-03-15 04:46:40,794] [INFO] Task started: Blastn
[2023-03-15 04:46:40,794] [INFO] Running command: blastn -query OceanDNA-b12871/markers.fasta -db /var/lib/cwl/stgc903e126-2c46-4ff9-954d-cc055853185c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b12871/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 04:46:41,262] [INFO] Task succeeded: Blastn
[2023-03-15 04:46:41,267] [INFO] Selected 13 target genomes.
[2023-03-15 04:46:41,267] [INFO] Target genome list was writen to OceanDNA-b12871/target_genomes_gtdb.txt
[2023-03-15 04:46:41,283] [INFO] Task started: fastANI
[2023-03-15 04:46:41,284] [INFO] Running command: fastANI --query /var/lib/cwl/stgc532e27c-d0ca-4a09-a626-70494e9cd345/OceanDNA-b12871.fa --refList OceanDNA-b12871/target_genomes_gtdb.txt --output OceanDNA-b12871/fastani_result_gtdb.tsv --threads 1
[2023-03-15 04:46:49,610] [INFO] Task succeeded: fastANI
[2023-03-15 04:46:49,614] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 04:46:49,614] [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_903821625.1	s__Daejeonella sp903821625	90.3507	179	219	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Daejeonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103545.1	s__Daejeonella rubra	85.3605	202	219	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Daejeonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002257025.1	s__Daejeonella sp002257025	79.2399	101	219	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Daejeonella	95.0	99.99	99.99	1.00	1.00	2	-
GCA_017495225.1	s__Daejeonella sp017495225	78.7209	93	219	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Daejeonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016868395.1	s__Daejeonella sp016868395	77.1912	61	219	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Daejeonella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 04:46:49,618] [INFO] GTDB search result was written to OceanDNA-b12871/result_gtdb.tsv
[2023-03-15 04:46:49,622] [INFO] ===== GTDB Search completed =====
[2023-03-15 04:46:49,626] [INFO] DFAST_QC result json was written to OceanDNA-b12871/dqc_result.json
[2023-03-15 04:46:49,627] [INFO] DFAST_QC completed!
[2023-03-15 04:46:49,627] [INFO] Total running time: 0h0m59s