[2023-03-16 08:10:35,181] [INFO] DFAST_QC pipeline started.
[2023-03-16 08:10:35,183] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 08:10:35,183] [INFO] DQC Reference Directory: /var/lib/cwl/stg0bbff418-952b-4021-bb97-1fba504c75c2/dqc_reference
[2023-03-16 08:10:36,312] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 08:10:36,312] [INFO] Task started: Prodigal
[2023-03-16 08:10:36,313] [INFO] Running command: cat /var/lib/cwl/stgfa6ba153-5266-454f-810a-2336e4b4e330/OceanDNA-b21535.fa | prodigal -d OceanDNA-b21535/cds.fna -a OceanDNA-b21535/protein.faa -g 11 -q > /dev/null
[2023-03-16 08:10:42,706] [INFO] Task succeeded: Prodigal
[2023-03-16 08:10:42,706] [INFO] Task started: HMMsearch
[2023-03-16 08:10:42,706] [INFO] Running command: hmmsearch --tblout OceanDNA-b21535/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0bbff418-952b-4021-bb97-1fba504c75c2/dqc_reference/reference_markers.hmm OceanDNA-b21535/protein.faa > /dev/null
[2023-03-16 08:10:42,899] [INFO] Task succeeded: HMMsearch
[2023-03-16 08:10:42,900] [INFO] Found 6/6 markers.
[2023-03-16 08:10:42,945] [INFO] Query marker FASTA was written to OceanDNA-b21535/markers.fasta
[2023-03-16 08:10:42,947] [INFO] Task started: Blastn
[2023-03-16 08:10:42,947] [INFO] Running command: blastn -query OceanDNA-b21535/markers.fasta -db /var/lib/cwl/stg0bbff418-952b-4021-bb97-1fba504c75c2/dqc_reference/reference_markers.fasta -out OceanDNA-b21535/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:10:43,654] [INFO] Task succeeded: Blastn
[2023-03-16 08:10:43,665] [INFO] Selected 10 target genomes.
[2023-03-16 08:10:43,665] [INFO] Target genome list was writen to OceanDNA-b21535/target_genomes.txt
[2023-03-16 08:10:43,671] [INFO] Task started: fastANI
[2023-03-16 08:10:43,671] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa6ba153-5266-454f-810a-2336e4b4e330/OceanDNA-b21535.fa --refList OceanDNA-b21535/target_genomes.txt --output OceanDNA-b21535/fastani_result.tsv --threads 1
[2023-03-16 08:10:46,906] [INFO] Task succeeded: fastANI
[2023-03-16 08:10:46,906] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0bbff418-952b-4021-bb97-1fba504c75c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 08:10:46,906] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0bbff418-952b-4021-bb97-1fba504c75c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 08:10:46,907] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 08:10:46,907] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 08:10:46,907] [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 08:10:46,912] [INFO] DFAST Taxonomy check result was written to OceanDNA-b21535/tc_result.tsv
[2023-03-16 08:10:46,920] [INFO] ===== Taxonomy check completed =====
[2023-03-16 08:10:46,920] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 08:10:46,920] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0bbff418-952b-4021-bb97-1fba504c75c2/dqc_reference/checkm_data
[2023-03-16 08:10:46,971] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 08:10:46,979] [INFO] Task started: CheckM
[2023-03-16 08:10:46,979] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b21535/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b21535/checkm_input OceanDNA-b21535/checkm_result
[2023-03-16 08:11:13,153] [INFO] Task succeeded: CheckM
[2023-03-16 08:11:13,153] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 08:11:13,234] [INFO] ===== Completeness check finished =====
[2023-03-16 08:11:13,235] [INFO] ===== Start GTDB Search =====
[2023-03-16 08:11:13,235] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b21535/markers.fasta)
[2023-03-16 08:11:13,236] [INFO] Task started: Blastn
[2023-03-16 08:11:13,236] [INFO] Running command: blastn -query OceanDNA-b21535/markers.fasta -db /var/lib/cwl/stg0bbff418-952b-4021-bb97-1fba504c75c2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b21535/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:11:14,347] [INFO] Task succeeded: Blastn
[2023-03-16 08:11:14,358] [INFO] Selected 17 target genomes.
[2023-03-16 08:11:14,359] [INFO] Target genome list was writen to OceanDNA-b21535/target_genomes_gtdb.txt
[2023-03-16 08:11:14,466] [INFO] Task started: fastANI
[2023-03-16 08:11:14,466] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa6ba153-5266-454f-810a-2336e4b4e330/OceanDNA-b21535.fa --refList OceanDNA-b21535/target_genomes_gtdb.txt --output OceanDNA-b21535/fastani_result_gtdb.tsv --threads 1
[2023-03-16 08:11:19,195] [INFO] Task succeeded: fastANI
[2023-03-16 08:11:19,197] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 08:11:19,197] [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_018652265.1	s__JABICL01 sp018652265	99.9382	287	310	d__Bacteria;p__Patescibacteria;c__Gracilibacteria;o__Peribacterales;f__JABICL01;g__JABICL01	95.0	99.93	99.91	0.96	0.94	4	conclusive
--------------------------------------------------------------------------------
[2023-03-16 08:11:19,203] [INFO] GTDB search result was written to OceanDNA-b21535/result_gtdb.tsv
[2023-03-16 08:11:19,211] [INFO] ===== GTDB Search completed =====
[2023-03-16 08:11:19,217] [INFO] DFAST_QC result json was written to OceanDNA-b21535/dqc_result.json
[2023-03-16 08:11:19,217] [INFO] DFAST_QC completed!
[2023-03-16 08:11:19,217] [INFO] Total running time: 0h0m44s