[2023-03-16 08:59:43,908] [INFO] DFAST_QC pipeline started.
[2023-03-16 08:59:43,908] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 08:59:43,908] [INFO] DQC Reference Directory: /var/lib/cwl/stg04383799-9a65-4c58-8ca1-24bda4adf75d/dqc_reference
[2023-03-16 08:59:45,386] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 08:59:45,387] [INFO] Task started: Prodigal
[2023-03-16 08:59:45,387] [INFO] Running command: cat /var/lib/cwl/stg28b1df9f-da75-4a64-ba11-2a47af32b75e/OceanDNA-b258.fa | prodigal -d OceanDNA-b258/cds.fna -a OceanDNA-b258/protein.faa -g 11 -q > /dev/null
[2023-03-16 08:59:56,235] [INFO] Task succeeded: Prodigal
[2023-03-16 08:59:56,235] [INFO] Task started: HMMsearch
[2023-03-16 08:59:56,235] [INFO] Running command: hmmsearch --tblout OceanDNA-b258/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg04383799-9a65-4c58-8ca1-24bda4adf75d/dqc_reference/reference_markers.hmm OceanDNA-b258/protein.faa > /dev/null
[2023-03-16 08:59:56,394] [INFO] Task succeeded: HMMsearch
[2023-03-16 08:59:56,395] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg28b1df9f-da75-4a64-ba11-2a47af32b75e/OceanDNA-b258.fa]
[2023-03-16 08:59:56,408] [INFO] Query marker FASTA was written to OceanDNA-b258/markers.fasta
[2023-03-16 08:59:56,408] [INFO] Task started: Blastn
[2023-03-16 08:59:56,408] [INFO] Running command: blastn -query OceanDNA-b258/markers.fasta -db /var/lib/cwl/stg04383799-9a65-4c58-8ca1-24bda4adf75d/dqc_reference/reference_markers.fasta -out OceanDNA-b258/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:59:57,027] [INFO] Task succeeded: Blastn
[2023-03-16 08:59:57,028] [INFO] Selected 24 target genomes.
[2023-03-16 08:59:57,029] [INFO] Target genome list was writen to OceanDNA-b258/target_genomes.txt
[2023-03-16 08:59:57,042] [INFO] Task started: fastANI
[2023-03-16 08:59:57,042] [INFO] Running command: fastANI --query /var/lib/cwl/stg28b1df9f-da75-4a64-ba11-2a47af32b75e/OceanDNA-b258.fa --refList OceanDNA-b258/target_genomes.txt --output OceanDNA-b258/fastani_result.tsv --threads 1
[2023-03-16 09:00:11,651] [INFO] Task succeeded: fastANI
[2023-03-16 09:00:11,651] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg04383799-9a65-4c58-8ca1-24bda4adf75d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 09:00:11,651] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg04383799-9a65-4c58-8ca1-24bda4adf75d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 09:00:11,651] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 09:00:11,651] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 09:00:11,651] [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
--------------------------------------------------------------------------------
[2023-03-16 09:00:11,652] [INFO] DFAST Taxonomy check result was written to OceanDNA-b258/tc_result.tsv
[2023-03-16 09:00:11,652] [INFO] ===== Taxonomy check completed =====
[2023-03-16 09:00:11,652] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 09:00:11,652] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg04383799-9a65-4c58-8ca1-24bda4adf75d/dqc_reference/checkm_data
[2023-03-16 09:00:11,655] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 09:00:11,660] [INFO] Task started: CheckM
[2023-03-16 09:00:11,660] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b258/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b258/checkm_input OceanDNA-b258/checkm_result
[2023-03-16 09:00:42,994] [INFO] Task succeeded: CheckM
[2023-03-16 09:00:42,994] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.62%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 09:00:43,051] [INFO] ===== Completeness check finished =====
[2023-03-16 09:00:43,051] [INFO] ===== Start GTDB Search =====
[2023-03-16 09:00:43,052] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b258/markers.fasta)
[2023-03-16 09:00:43,053] [INFO] Task started: Blastn
[2023-03-16 09:00:43,053] [INFO] Running command: blastn -query OceanDNA-b258/markers.fasta -db /var/lib/cwl/stg04383799-9a65-4c58-8ca1-24bda4adf75d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b258/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:00:43,948] [INFO] Task succeeded: Blastn
[2023-03-16 09:00:43,954] [INFO] Selected 24 target genomes.
[2023-03-16 09:00:43,954] [INFO] Target genome list was writen to OceanDNA-b258/target_genomes_gtdb.txt
[2023-03-16 09:00:43,976] [INFO] Task started: fastANI
[2023-03-16 09:00:43,976] [INFO] Running command: fastANI --query /var/lib/cwl/stg28b1df9f-da75-4a64-ba11-2a47af32b75e/OceanDNA-b258.fa --refList OceanDNA-b258/target_genomes_gtdb.txt --output OceanDNA-b258/fastani_result_gtdb.tsv --threads 1
[2023-03-16 09:00:58,701] [INFO] Task succeeded: fastANI
[2023-03-16 09:00:58,704] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 09:00:58,704] [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_009861545.1	s__WTFV01 sp009861545	76.1807	76	605	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__WTFV01	95.0	96.15	96.15	0.82	0.82	2	-
GCA_012271165.1	s__JAAXGX01 sp012271165	75.5231	55	605	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__JAAXGX01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 09:00:58,704] [INFO] GTDB search result was written to OceanDNA-b258/result_gtdb.tsv
[2023-03-16 09:00:58,704] [INFO] ===== GTDB Search completed =====
[2023-03-16 09:00:58,705] [INFO] DFAST_QC result json was written to OceanDNA-b258/dqc_result.json
[2023-03-16 09:00:58,705] [INFO] DFAST_QC completed!
[2023-03-16 09:00:58,705] [INFO] Total running time: 0h1m15s