[2023-03-16 23:23:11,940] [INFO] DFAST_QC pipeline started.
[2023-03-16 23:23:11,940] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 23:23:11,940] [INFO] DQC Reference Directory: /var/lib/cwl/stg7b7d6b91-c963-4c7b-b8ec-ea8965cebf07/dqc_reference
[2023-03-16 23:23:13,105] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 23:23:13,106] [INFO] Task started: Prodigal
[2023-03-16 23:23:13,106] [INFO] Running command: cat /var/lib/cwl/stg1abcf00b-b3cb-4718-b0d8-f43520382baf/OceanDNA-b29.fa | prodigal -d OceanDNA-b29/cds.fna -a OceanDNA-b29/protein.faa -g 11 -q > /dev/null
[2023-03-16 23:23:55,504] [INFO] Task succeeded: Prodigal
[2023-03-16 23:23:55,504] [INFO] Task started: HMMsearch
[2023-03-16 23:23:55,505] [INFO] Running command: hmmsearch --tblout OceanDNA-b29/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7b7d6b91-c963-4c7b-b8ec-ea8965cebf07/dqc_reference/reference_markers.hmm OceanDNA-b29/protein.faa > /dev/null
[2023-03-16 23:23:55,770] [INFO] Task succeeded: HMMsearch
[2023-03-16 23:23:55,770] [INFO] Found 6/6 markers.
[2023-03-16 23:23:55,811] [INFO] Query marker FASTA was written to OceanDNA-b29/markers.fasta
[2023-03-16 23:23:55,813] [INFO] Task started: Blastn
[2023-03-16 23:23:55,813] [INFO] Running command: blastn -query OceanDNA-b29/markers.fasta -db /var/lib/cwl/stg7b7d6b91-c963-4c7b-b8ec-ea8965cebf07/dqc_reference/reference_markers.fasta -out OceanDNA-b29/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 23:23:56,338] [INFO] Task succeeded: Blastn
[2023-03-16 23:23:56,339] [INFO] Selected 24 target genomes.
[2023-03-16 23:23:56,339] [INFO] Target genome list was writen to OceanDNA-b29/target_genomes.txt
[2023-03-16 23:23:56,352] [INFO] Task started: fastANI
[2023-03-16 23:23:56,352] [INFO] Running command: fastANI --query /var/lib/cwl/stg1abcf00b-b3cb-4718-b0d8-f43520382baf/OceanDNA-b29.fa --refList OceanDNA-b29/target_genomes.txt --output OceanDNA-b29/fastani_result.tsv --threads 1
[2023-03-16 23:24:11,413] [INFO] Task succeeded: fastANI
[2023-03-16 23:24:11,413] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7b7d6b91-c963-4c7b-b8ec-ea8965cebf07/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 23:24:11,413] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7b7d6b91-c963-4c7b-b8ec-ea8965cebf07/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 23:24:11,417] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 23:24:11,417] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 23:24:11,417] [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
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	74.904	59	2353	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 23:24:11,417] [INFO] DFAST Taxonomy check result was written to OceanDNA-b29/tc_result.tsv
[2023-03-16 23:24:11,417] [INFO] ===== Taxonomy check completed =====
[2023-03-16 23:24:11,417] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 23:24:11,417] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7b7d6b91-c963-4c7b-b8ec-ea8965cebf07/dqc_reference/checkm_data
[2023-03-16 23:24:11,418] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 23:24:11,426] [INFO] Task started: CheckM
[2023-03-16 23:24:11,427] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b29/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b29/checkm_input OceanDNA-b29/checkm_result
[2023-03-16 23:25:49,413] [INFO] Task succeeded: CheckM
[2023-03-16 23:25:49,414] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 23:25:49,417] [INFO] ===== Completeness check finished =====
[2023-03-16 23:25:49,418] [INFO] ===== Start GTDB Search =====
[2023-03-16 23:25:49,418] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b29/markers.fasta)
[2023-03-16 23:25:49,419] [INFO] Task started: Blastn
[2023-03-16 23:25:49,419] [INFO] Running command: blastn -query OceanDNA-b29/markers.fasta -db /var/lib/cwl/stg7b7d6b91-c963-4c7b-b8ec-ea8965cebf07/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b29/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 23:25:50,189] [INFO] Task succeeded: Blastn
[2023-03-16 23:25:50,190] [INFO] Selected 30 target genomes.
[2023-03-16 23:25:50,190] [INFO] Target genome list was writen to OceanDNA-b29/target_genomes_gtdb.txt
[2023-03-16 23:25:51,479] [INFO] Task started: fastANI
[2023-03-16 23:25:51,479] [INFO] Running command: fastANI --query /var/lib/cwl/stg1abcf00b-b3cb-4718-b0d8-f43520382baf/OceanDNA-b29.fa --refList OceanDNA-b29/target_genomes_gtdb.txt --output OceanDNA-b29/fastani_result_gtdb.tsv --threads 1
[2023-03-16 23:26:14,732] [INFO] Task succeeded: fastANI
[2023-03-16 23:26:14,737] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 23:26:14,737] [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_016125275.1	s__RI-231 sp016125275	75.5866	195	2353	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__UBA6623;g__RI-231	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009841225.1	s__VXMF01 sp009841225	75.52	111	2353	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__UBA6623;g__VXMF01	95.0	97.84	97.84	0.95	0.95	2	-
GCA_009838515.1	s__VXMF01 sp009838515	75.4722	126	2353	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__UBA6623;g__VXMF01	95.0	99.95	99.93	0.99	0.98	3	-
GCA_903907865.1	s__BOG-234 sp903907865	75.2935	69	2353	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__BOG-234	95.0	99.99	99.99	0.99	0.98	3	-
GCF_014652915.1	s__Thalassobaculum_A fulvum	74.904	59	2353	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Thalassobaculum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016871155.1	s__Ga0077553 sp016871155	74.7873	62	2353	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__Ga0077553	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 23:26:14,737] [INFO] GTDB search result was written to OceanDNA-b29/result_gtdb.tsv
[2023-03-16 23:26:14,737] [INFO] ===== GTDB Search completed =====
[2023-03-16 23:26:14,738] [INFO] DFAST_QC result json was written to OceanDNA-b29/dqc_result.json
[2023-03-16 23:26:14,738] [INFO] DFAST_QC completed!
[2023-03-16 23:26:14,738] [INFO] Total running time: 0h3m3s