[2023-03-15 10:56:32,987] [INFO] DFAST_QC pipeline started.
[2023-03-15 10:56:32,987] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 10:56:32,988] [INFO] DQC Reference Directory: /var/lib/cwl/stg9a593f05-aa67-4dee-bdbf-22d2c377dfa4/dqc_reference
[2023-03-15 10:56:34,087] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 10:56:34,087] [INFO] Task started: Prodigal
[2023-03-15 10:56:34,087] [INFO] Running command: cat /var/lib/cwl/stg299f384c-16e9-426d-bad5-343657bb9852/OceanDNA-b17388.fa | prodigal -d OceanDNA-b17388/cds.fna -a OceanDNA-b17388/protein.faa -g 11 -q > /dev/null
[2023-03-15 10:56:42,506] [INFO] Task succeeded: Prodigal
[2023-03-15 10:56:42,506] [INFO] Task started: HMMsearch
[2023-03-15 10:56:42,506] [INFO] Running command: hmmsearch --tblout OceanDNA-b17388/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9a593f05-aa67-4dee-bdbf-22d2c377dfa4/dqc_reference/reference_markers.hmm OceanDNA-b17388/protein.faa > /dev/null
[2023-03-15 10:56:42,678] [INFO] Task succeeded: HMMsearch
[2023-03-15 10:56:42,679] [INFO] Found 6/6 markers.
[2023-03-15 10:56:42,688] [INFO] Query marker FASTA was written to OceanDNA-b17388/markers.fasta
[2023-03-15 10:56:42,688] [INFO] Task started: Blastn
[2023-03-15 10:56:42,688] [INFO] Running command: blastn -query OceanDNA-b17388/markers.fasta -db /var/lib/cwl/stg9a593f05-aa67-4dee-bdbf-22d2c377dfa4/dqc_reference/reference_markers.fasta -out OceanDNA-b17388/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:56:43,180] [INFO] Task succeeded: Blastn
[2023-03-15 10:56:43,181] [INFO] Selected 14 target genomes.
[2023-03-15 10:56:43,181] [INFO] Target genome list was writen to OceanDNA-b17388/target_genomes.txt
[2023-03-15 10:56:43,188] [INFO] Task started: fastANI
[2023-03-15 10:56:43,188] [INFO] Running command: fastANI --query /var/lib/cwl/stg299f384c-16e9-426d-bad5-343657bb9852/OceanDNA-b17388.fa --refList OceanDNA-b17388/target_genomes.txt --output OceanDNA-b17388/fastani_result.tsv --threads 1
[2023-03-15 10:56:50,207] [INFO] Task succeeded: fastANI
[2023-03-15 10:56:50,207] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9a593f05-aa67-4dee-bdbf-22d2c377dfa4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 10:56:50,207] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9a593f05-aa67-4dee-bdbf-22d2c377dfa4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 10:56:50,207] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 10:56:50,207] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 10:56:50,208] [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 10:56:50,208] [INFO] DFAST Taxonomy check result was written to OceanDNA-b17388/tc_result.tsv
[2023-03-15 10:56:50,208] [INFO] ===== Taxonomy check completed =====
[2023-03-15 10:56:50,208] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 10:56:50,208] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9a593f05-aa67-4dee-bdbf-22d2c377dfa4/dqc_reference/checkm_data
[2023-03-15 10:56:50,210] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 10:56:50,214] [INFO] Task started: CheckM
[2023-03-15 10:56:50,214] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b17388/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b17388/checkm_input OceanDNA-b17388/checkm_result
[2023-03-15 10:57:15,908] [INFO] Task succeeded: CheckM
[2023-03-15 10:57:15,908] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 10:57:15,909] [INFO] ===== Completeness check finished =====
[2023-03-15 10:57:15,910] [INFO] ===== Start GTDB Search =====
[2023-03-15 10:57:15,910] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b17388/markers.fasta)
[2023-03-15 10:57:15,910] [INFO] Task started: Blastn
[2023-03-15 10:57:15,910] [INFO] Running command: blastn -query OceanDNA-b17388/markers.fasta -db /var/lib/cwl/stg9a593f05-aa67-4dee-bdbf-22d2c377dfa4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b17388/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:57:16,598] [INFO] Task succeeded: Blastn
[2023-03-15 10:57:16,599] [INFO] Selected 21 target genomes.
[2023-03-15 10:57:16,599] [INFO] Target genome list was writen to OceanDNA-b17388/target_genomes_gtdb.txt
[2023-03-15 10:57:16,617] [INFO] Task started: fastANI
[2023-03-15 10:57:16,617] [INFO] Running command: fastANI --query /var/lib/cwl/stg299f384c-16e9-426d-bad5-343657bb9852/OceanDNA-b17388.fa --refList OceanDNA-b17388/target_genomes_gtdb.txt --output OceanDNA-b17388/fastani_result_gtdb.tsv --threads 1
[2023-03-15 10:57:25,283] [INFO] Task succeeded: fastANI
[2023-03-15 10:57:25,285] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 10:57:25,285] [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_002346625.1	s__UBA6934 sp002346625	99.8822	251	501	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__UBA6934	95.0	99.94	99.94	0.79	0.79	2	conclusive
--------------------------------------------------------------------------------
[2023-03-15 10:57:25,285] [INFO] GTDB search result was written to OceanDNA-b17388/result_gtdb.tsv
[2023-03-15 10:57:25,286] [INFO] ===== GTDB Search completed =====
[2023-03-15 10:57:25,286] [INFO] DFAST_QC result json was written to OceanDNA-b17388/dqc_result.json
[2023-03-15 10:57:25,286] [INFO] DFAST_QC completed!
[2023-03-15 10:57:25,286] [INFO] Total running time: 0h0m52s