[2023-03-18 23:11:06,976] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:11:06,976] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:11:06,977] [INFO] DQC Reference Directory: /var/lib/cwl/stga26cef85-a7b1-496e-a264-644083d6cab1/dqc_reference
[2023-03-18 23:11:08,238] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:11:08,239] [INFO] Task started: Prodigal
[2023-03-18 23:11:08,239] [INFO] Running command: cat /var/lib/cwl/stge95c0b5b-ce5b-4bf4-bbf3-9764f92e2887/OceanDNA-b44576.fa | prodigal -d OceanDNA-b44576/cds.fna -a OceanDNA-b44576/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:11:12,759] [INFO] Task succeeded: Prodigal
[2023-03-18 23:11:12,759] [INFO] Task started: HMMsearch
[2023-03-18 23:11:12,759] [INFO] Running command: hmmsearch --tblout OceanDNA-b44576/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga26cef85-a7b1-496e-a264-644083d6cab1/dqc_reference/reference_markers.hmm OceanDNA-b44576/protein.faa > /dev/null
[2023-03-18 23:11:12,939] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:11:12,940] [INFO] Found 6/6 markers.
[2023-03-18 23:11:12,948] [INFO] Query marker FASTA was written to OceanDNA-b44576/markers.fasta
[2023-03-18 23:11:12,948] [INFO] Task started: Blastn
[2023-03-18 23:11:12,948] [INFO] Running command: blastn -query OceanDNA-b44576/markers.fasta -db /var/lib/cwl/stga26cef85-a7b1-496e-a264-644083d6cab1/dqc_reference/reference_markers.fasta -out OceanDNA-b44576/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:11:13,521] [INFO] Task succeeded: Blastn
[2023-03-18 23:11:13,522] [INFO] Selected 24 target genomes.
[2023-03-18 23:11:13,522] [INFO] Target genome list was writen to OceanDNA-b44576/target_genomes.txt
[2023-03-18 23:11:13,537] [INFO] Task started: fastANI
[2023-03-18 23:11:13,537] [INFO] Running command: fastANI --query /var/lib/cwl/stge95c0b5b-ce5b-4bf4-bbf3-9764f92e2887/OceanDNA-b44576.fa --refList OceanDNA-b44576/target_genomes.txt --output OceanDNA-b44576/fastani_result.tsv --threads 1
[2023-03-18 23:11:25,855] [INFO] Task succeeded: fastANI
[2023-03-18 23:11:25,856] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga26cef85-a7b1-496e-a264-644083d6cab1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:11:25,856] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga26cef85-a7b1-496e-a264-644083d6cab1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:11:25,856] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:11:25,856] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 23:11:25,856] [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
--------------------------------------------------------------------------------
[2023-03-18 23:11:25,856] [INFO] DFAST Taxonomy check result was written to OceanDNA-b44576/tc_result.tsv
[2023-03-18 23:11:25,857] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:11:25,857] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:11:25,857] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga26cef85-a7b1-496e-a264-644083d6cab1/dqc_reference/checkm_data
[2023-03-18 23:11:25,859] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:11:25,862] [INFO] Task started: CheckM
[2023-03-18 23:11:25,862] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b44576/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b44576/checkm_input OceanDNA-b44576/checkm_result
[2023-03-18 23:11:42,941] [INFO] Task succeeded: CheckM
[2023-03-18 23:11:42,942] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 45.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 23:11:42,943] [INFO] ===== Completeness check finished =====
[2023-03-18 23:11:42,943] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:11:42,943] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b44576/markers.fasta)
[2023-03-18 23:11:42,944] [INFO] Task started: Blastn
[2023-03-18 23:11:42,944] [INFO] Running command: blastn -query OceanDNA-b44576/markers.fasta -db /var/lib/cwl/stga26cef85-a7b1-496e-a264-644083d6cab1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b44576/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:11:43,873] [INFO] Task succeeded: Blastn
[2023-03-18 23:11:43,874] [INFO] Selected 25 target genomes.
[2023-03-18 23:11:43,874] [INFO] Target genome list was writen to OceanDNA-b44576/target_genomes_gtdb.txt
[2023-03-18 23:11:43,897] [INFO] Task started: fastANI
[2023-03-18 23:11:43,897] [INFO] Running command: fastANI --query /var/lib/cwl/stge95c0b5b-ce5b-4bf4-bbf3-9764f92e2887/OceanDNA-b44576.fa --refList OceanDNA-b44576/target_genomes_gtdb.txt --output OceanDNA-b44576/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:11:53,455] [INFO] Task succeeded: fastANI
[2023-03-18 23:11:53,457] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 23:11:53,457] [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_002717685.1	s__PBBK01 sp002717685	98.0089	121	269	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__PBBK01	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2023-03-18 23:11:53,457] [INFO] GTDB search result was written to OceanDNA-b44576/result_gtdb.tsv
[2023-03-18 23:11:53,457] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:11:53,458] [INFO] DFAST_QC result json was written to OceanDNA-b44576/dqc_result.json
[2023-03-18 23:11:53,458] [INFO] DFAST_QC completed!
[2023-03-18 23:11:53,458] [INFO] Total running time: 0h0m46s