[2023-03-14 11:13:58,995] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:13:58,995] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:13:58,995] [INFO] DQC Reference Directory: /var/lib/cwl/stgb041700b-cf49-4154-b653-7aaa51b92104/dqc_reference
[2023-03-14 11:14:00,598] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:14:00,598] [INFO] Task started: Prodigal
[2023-03-14 11:14:00,598] [INFO] Running command: cat /var/lib/cwl/stg8ec5342e-3b35-40aa-807d-9991380cd899/OceanDNA-b23180.fa | prodigal -d OceanDNA-b23180/cds.fna -a OceanDNA-b23180/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:14:18,663] [INFO] Task succeeded: Prodigal
[2023-03-14 11:14:18,664] [INFO] Task started: HMMsearch
[2023-03-14 11:14:18,664] [INFO] Running command: hmmsearch --tblout OceanDNA-b23180/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb041700b-cf49-4154-b653-7aaa51b92104/dqc_reference/reference_markers.hmm OceanDNA-b23180/protein.faa > /dev/null
[2023-03-14 11:14:18,868] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:14:18,869] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg8ec5342e-3b35-40aa-807d-9991380cd899/OceanDNA-b23180.fa]
[2023-03-14 11:14:18,898] [INFO] Query marker FASTA was written to OceanDNA-b23180/markers.fasta
[2023-03-14 11:14:18,900] [INFO] Task started: Blastn
[2023-03-14 11:14:18,900] [INFO] Running command: blastn -query OceanDNA-b23180/markers.fasta -db /var/lib/cwl/stgb041700b-cf49-4154-b653-7aaa51b92104/dqc_reference/reference_markers.fasta -out OceanDNA-b23180/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:14:19,354] [INFO] Task succeeded: Blastn
[2023-03-14 11:14:19,355] [INFO] Selected 20 target genomes.
[2023-03-14 11:14:19,355] [INFO] Target genome list was writen to OceanDNA-b23180/target_genomes.txt
[2023-03-14 11:14:19,370] [INFO] Task started: fastANI
[2023-03-14 11:14:19,370] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ec5342e-3b35-40aa-807d-9991380cd899/OceanDNA-b23180.fa --refList OceanDNA-b23180/target_genomes.txt --output OceanDNA-b23180/fastani_result.tsv --threads 1
[2023-03-14 11:14:33,109] [INFO] Task succeeded: fastANI
[2023-03-14 11:14:33,109] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb041700b-cf49-4154-b653-7aaa51b92104/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 11:14:33,110] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb041700b-cf49-4154-b653-7aaa51b92104/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 11:14:33,110] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 11:14:33,110] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 11:14:33,110] [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
--------------------------------------------------------------------------------
[2023-03-14 11:14:33,110] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23180/tc_result.tsv
[2023-03-14 11:14:33,110] [INFO] ===== Taxonomy check completed =====
[2023-03-14 11:14:33,110] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:14:33,110] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb041700b-cf49-4154-b653-7aaa51b92104/dqc_reference/checkm_data
[2023-03-14 11:14:33,114] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:14:33,119] [INFO] Task started: CheckM
[2023-03-14 11:14:33,119] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23180/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23180/checkm_input OceanDNA-b23180/checkm_result
[2023-03-14 11:15:19,308] [INFO] Task succeeded: CheckM
[2023-03-14 11:15:19,309] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 11:15:19,340] [INFO] ===== Completeness check finished =====
[2023-03-14 11:15:19,340] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:15:19,341] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23180/markers.fasta)
[2023-03-14 11:15:19,342] [INFO] Task started: Blastn
[2023-03-14 11:15:19,342] [INFO] Running command: blastn -query OceanDNA-b23180/markers.fasta -db /var/lib/cwl/stgb041700b-cf49-4154-b653-7aaa51b92104/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23180/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:15:19,816] [INFO] Task succeeded: Blastn
[2023-03-14 11:15:19,817] [INFO] Selected 15 target genomes.
[2023-03-14 11:15:19,817] [INFO] Target genome list was writen to OceanDNA-b23180/target_genomes_gtdb.txt
[2023-03-14 11:15:19,834] [INFO] Task started: fastANI
[2023-03-14 11:15:19,834] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ec5342e-3b35-40aa-807d-9991380cd899/OceanDNA-b23180.fa --refList OceanDNA-b23180/target_genomes_gtdb.txt --output OceanDNA-b23180/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:15:30,013] [INFO] Task succeeded: fastANI
[2023-03-14 11:15:30,016] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 11:15:30,016] [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_018644665.1	s__GCA-2687025 sp018644665	99.8514	761	778	d__Bacteria;p__Poribacteria;c__WGA-4E;o__GCA-2687025;f__GCA-2687025;g__GCA-2687025	95.0	99.94	99.91	0.97	0.97	3	conclusive
GCA_002687025.1	s__GCA-2687025 sp002687025	83.5642	497	778	d__Bacteria;p__Poribacteria;c__WGA-4E;o__GCA-2687025;f__GCA-2687025;g__GCA-2687025	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016866785.1	s__VGLH01 sp016866785	76.1346	75	778	d__Bacteria;p__Poribacteria;c__WGA-4E;o__GCA-2687025;f__GCA-2687025;g__VGLH01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 11:15:30,016] [INFO] GTDB search result was written to OceanDNA-b23180/result_gtdb.tsv
[2023-03-14 11:15:30,017] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:15:30,017] [INFO] DFAST_QC result json was written to OceanDNA-b23180/dqc_result.json
[2023-03-14 11:15:30,017] [INFO] DFAST_QC completed!
[2023-03-14 11:15:30,017] [INFO] Total running time: 0h1m31s