[2023-03-15 13:39:34,878] [INFO] DFAST_QC pipeline started.
[2023-03-15 13:39:34,879] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 13:39:34,879] [INFO] DQC Reference Directory: /var/lib/cwl/stg09ea1ac3-2ac0-4cf1-9628-b595197a5f85/dqc_reference
[2023-03-15 13:39:37,045] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 13:39:37,047] [INFO] Task started: Prodigal
[2023-03-15 13:39:37,047] [INFO] Running command: cat /var/lib/cwl/stg4adc5242-dd1c-472a-9320-9f54e46728a5/OceanDNA-b42843.fa | prodigal -d OceanDNA-b42843/cds.fna -a OceanDNA-b42843/protein.faa -g 11 -q > /dev/null
[2023-03-15 13:39:40,033] [INFO] Task succeeded: Prodigal
[2023-03-15 13:39:40,033] [INFO] Task started: HMMsearch
[2023-03-15 13:39:40,033] [INFO] Running command: hmmsearch --tblout OceanDNA-b42843/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg09ea1ac3-2ac0-4cf1-9628-b595197a5f85/dqc_reference/reference_markers.hmm OceanDNA-b42843/protein.faa > /dev/null
[2023-03-15 13:39:40,262] [INFO] Task succeeded: HMMsearch
[2023-03-15 13:39:40,263] [INFO] Found 6/6 markers.
[2023-03-15 13:39:40,279] [INFO] Query marker FASTA was written to OceanDNA-b42843/markers.fasta
[2023-03-15 13:39:40,281] [INFO] Task started: Blastn
[2023-03-15 13:39:40,281] [INFO] Running command: blastn -query OceanDNA-b42843/markers.fasta -db /var/lib/cwl/stg09ea1ac3-2ac0-4cf1-9628-b595197a5f85/dqc_reference/reference_markers.fasta -out OceanDNA-b42843/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:39:43,705] [INFO] Task succeeded: Blastn
[2023-03-15 13:39:43,708] [INFO] Selected 10 target genomes.
[2023-03-15 13:39:43,708] [INFO] Target genome list was writen to OceanDNA-b42843/target_genomes.txt
[2023-03-15 13:39:43,749] [INFO] Task started: fastANI
[2023-03-15 13:39:43,749] [INFO] Running command: fastANI --query /var/lib/cwl/stg4adc5242-dd1c-472a-9320-9f54e46728a5/OceanDNA-b42843.fa --refList OceanDNA-b42843/target_genomes.txt --output OceanDNA-b42843/fastani_result.tsv --threads 1
[2023-03-15 13:39:48,879] [INFO] Task succeeded: fastANI
[2023-03-15 13:39:48,880] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg09ea1ac3-2ac0-4cf1-9628-b595197a5f85/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 13:39:48,880] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg09ea1ac3-2ac0-4cf1-9628-b595197a5f85/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 13:39:48,880] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 13:39:48,880] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 13:39:48,880] [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 13:39:48,881] [INFO] DFAST Taxonomy check result was written to OceanDNA-b42843/tc_result.tsv
[2023-03-15 13:39:48,883] [INFO] ===== Taxonomy check completed =====
[2023-03-15 13:39:48,883] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 13:39:48,884] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg09ea1ac3-2ac0-4cf1-9628-b595197a5f85/dqc_reference/checkm_data
[2023-03-15 13:39:48,933] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 13:39:48,948] [INFO] Task started: CheckM
[2023-03-15 13:39:48,948] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b42843/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b42843/checkm_input OceanDNA-b42843/checkm_result
[2023-03-15 13:40:07,486] [INFO] Task succeeded: CheckM
[2023-03-15 13:40:07,487] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 69.91%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 13:40:07,781] [INFO] ===== Completeness check finished =====
[2023-03-15 13:40:07,782] [INFO] ===== Start GTDB Search =====
[2023-03-15 13:40:07,782] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b42843/markers.fasta)
[2023-03-15 13:40:07,783] [INFO] Task started: Blastn
[2023-03-15 13:40:07,783] [INFO] Running command: blastn -query OceanDNA-b42843/markers.fasta -db /var/lib/cwl/stg09ea1ac3-2ac0-4cf1-9628-b595197a5f85/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b42843/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:40:08,784] [INFO] Task succeeded: Blastn
[2023-03-15 13:40:08,788] [INFO] Selected 26 target genomes.
[2023-03-15 13:40:08,788] [INFO] Target genome list was writen to OceanDNA-b42843/target_genomes_gtdb.txt
[2023-03-15 13:40:08,856] [INFO] Task started: fastANI
[2023-03-15 13:40:08,856] [INFO] Running command: fastANI --query /var/lib/cwl/stg4adc5242-dd1c-472a-9320-9f54e46728a5/OceanDNA-b42843.fa --refList OceanDNA-b42843/target_genomes_gtdb.txt --output OceanDNA-b42843/fastani_result_gtdb.tsv --threads 1
[2023-03-15 13:40:16,450] [INFO] Task succeeded: fastANI
[2023-03-15 13:40:16,452] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 13:40:16,452] [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_000372785.1	s__Pseudothioglobus sp000372785	77.4524	56	178	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	95.69	95.69	0.64	0.64	2	-
--------------------------------------------------------------------------------
[2023-03-15 13:40:16,454] [INFO] GTDB search result was written to OceanDNA-b42843/result_gtdb.tsv
[2023-03-15 13:40:16,456] [INFO] ===== GTDB Search completed =====
[2023-03-15 13:40:16,459] [INFO] DFAST_QC result json was written to OceanDNA-b42843/dqc_result.json
[2023-03-15 13:40:16,459] [INFO] DFAST_QC completed!
[2023-03-15 13:40:16,459] [INFO] Total running time: 0h0m42s