[2023-03-15 23:58:55,535] [INFO] DFAST_QC pipeline started.
[2023-03-15 23:58:55,535] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 23:58:55,535] [INFO] DQC Reference Directory: /var/lib/cwl/stg1d9ce848-17d1-4fd1-a3fa-03fab5fc1bfb/dqc_reference
[2023-03-15 23:59:00,250] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 23:59:00,251] [INFO] Task started: Prodigal
[2023-03-15 23:59:00,251] [INFO] Running command: cat /var/lib/cwl/stgd4874490-f825-4700-bbd2-8f0c1a9c1972/OceanDNA-b22787.fa | prodigal -d OceanDNA-b22787/cds.fna -a OceanDNA-b22787/protein.faa -g 11 -q > /dev/null
[2023-03-15 23:59:17,141] [INFO] Task succeeded: Prodigal
[2023-03-15 23:59:17,141] [INFO] Task started: HMMsearch
[2023-03-15 23:59:17,141] [INFO] Running command: hmmsearch --tblout OceanDNA-b22787/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1d9ce848-17d1-4fd1-a3fa-03fab5fc1bfb/dqc_reference/reference_markers.hmm OceanDNA-b22787/protein.faa > /dev/null
[2023-03-15 23:59:17,425] [INFO] Task succeeded: HMMsearch
[2023-03-15 23:59:17,426] [INFO] Found 6/6 markers.
[2023-03-15 23:59:17,457] [INFO] Query marker FASTA was written to OceanDNA-b22787/markers.fasta
[2023-03-15 23:59:17,459] [INFO] Task started: Blastn
[2023-03-15 23:59:17,459] [INFO] Running command: blastn -query OceanDNA-b22787/markers.fasta -db /var/lib/cwl/stg1d9ce848-17d1-4fd1-a3fa-03fab5fc1bfb/dqc_reference/reference_markers.fasta -out OceanDNA-b22787/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:59:20,906] [INFO] Task succeeded: Blastn
[2023-03-15 23:59:20,912] [INFO] Selected 11 target genomes.
[2023-03-15 23:59:20,912] [INFO] Target genome list was writen to OceanDNA-b22787/target_genomes.txt
[2023-03-15 23:59:20,918] [INFO] Task started: fastANI
[2023-03-15 23:59:20,918] [INFO] Running command: fastANI --query /var/lib/cwl/stgd4874490-f825-4700-bbd2-8f0c1a9c1972/OceanDNA-b22787.fa --refList OceanDNA-b22787/target_genomes.txt --output OceanDNA-b22787/fastani_result.tsv --threads 1
[2023-03-15 23:59:27,000] [INFO] Task succeeded: fastANI
[2023-03-15 23:59:27,000] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1d9ce848-17d1-4fd1-a3fa-03fab5fc1bfb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 23:59:27,001] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1d9ce848-17d1-4fd1-a3fa-03fab5fc1bfb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 23:59:27,001] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 23:59:27,001] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 23:59:27,001] [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
--------------------------------------------------------------------------------
[2023-03-15 23:59:27,003] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22787/tc_result.tsv
[2023-03-15 23:59:27,006] [INFO] ===== Taxonomy check completed =====
[2023-03-15 23:59:27,006] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 23:59:27,007] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1d9ce848-17d1-4fd1-a3fa-03fab5fc1bfb/dqc_reference/checkm_data
[2023-03-15 23:59:27,010] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 23:59:27,017] [INFO] Task started: CheckM
[2023-03-15 23:59:27,017] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22787/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22787/checkm_input OceanDNA-b22787/checkm_result
[2023-03-16 00:00:13,074] [INFO] Task succeeded: CheckM
[2023-03-16 00:00:13,074] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 00:00:13,131] [INFO] ===== Completeness check finished =====
[2023-03-16 00:00:13,131] [INFO] ===== Start GTDB Search =====
[2023-03-16 00:00:13,131] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22787/markers.fasta)
[2023-03-16 00:00:13,132] [INFO] Task started: Blastn
[2023-03-16 00:00:13,132] [INFO] Running command: blastn -query OceanDNA-b22787/markers.fasta -db /var/lib/cwl/stg1d9ce848-17d1-4fd1-a3fa-03fab5fc1bfb/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22787/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 00:00:13,959] [INFO] Task succeeded: Blastn
[2023-03-16 00:00:13,964] [INFO] Selected 21 target genomes.
[2023-03-16 00:00:13,964] [INFO] Target genome list was writen to OceanDNA-b22787/target_genomes_gtdb.txt
[2023-03-16 00:00:14,180] [INFO] Task started: fastANI
[2023-03-16 00:00:14,180] [INFO] Running command: fastANI --query /var/lib/cwl/stgd4874490-f825-4700-bbd2-8f0c1a9c1972/OceanDNA-b22787.fa --refList OceanDNA-b22787/target_genomes_gtdb.txt --output OceanDNA-b22787/fastani_result_gtdb.tsv --threads 1
[2023-03-16 00:00:24,462] [INFO] Task succeeded: fastANI
[2023-03-16 00:00:24,464] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 00:00:24,465] [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_002168195.1	s__UBA7805 sp002168195	99.5402	875	904	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA7805;g__UBA7805	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902630355.1	s__UBA7805 sp902630355	77.461	127	904	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA7805;g__UBA7805	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002480485.1	s__UBA7805 sp002480485	77.2354	267	904	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA7805;g__UBA7805	95.0	99.65	99.63	0.90	0.89	3	-
--------------------------------------------------------------------------------
[2023-03-16 00:00:24,476] [INFO] GTDB search result was written to OceanDNA-b22787/result_gtdb.tsv
[2023-03-16 00:00:24,493] [INFO] ===== GTDB Search completed =====
[2023-03-16 00:00:24,503] [INFO] DFAST_QC result json was written to OceanDNA-b22787/dqc_result.json
[2023-03-16 00:00:24,503] [INFO] DFAST_QC completed!
[2023-03-16 00:00:24,503] [INFO] Total running time: 0h1m29s