[2023-03-19 01:13:44,392] [INFO] DFAST_QC pipeline started.
[2023-03-19 01:13:44,392] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 01:13:44,392] [INFO] DQC Reference Directory: /var/lib/cwl/stg51ec5e66-6568-4248-9408-cfbe845d772b/dqc_reference
[2023-03-19 01:13:45,529] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 01:13:45,529] [INFO] Task started: Prodigal
[2023-03-19 01:13:45,529] [INFO] Running command: cat /var/lib/cwl/stg492ff9e7-75fd-49f8-8cfd-4317bd81b885/OceanDNA-b23124.fa | prodigal -d OceanDNA-b23124/cds.fna -a OceanDNA-b23124/protein.faa -g 11 -q > /dev/null
[2023-03-19 01:13:52,015] [INFO] Task succeeded: Prodigal
[2023-03-19 01:13:52,016] [INFO] Task started: HMMsearch
[2023-03-19 01:13:52,016] [INFO] Running command: hmmsearch --tblout OceanDNA-b23124/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg51ec5e66-6568-4248-9408-cfbe845d772b/dqc_reference/reference_markers.hmm OceanDNA-b23124/protein.faa > /dev/null
[2023-03-19 01:13:52,186] [INFO] Task succeeded: HMMsearch
[2023-03-19 01:13:52,187] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg492ff9e7-75fd-49f8-8cfd-4317bd81b885/OceanDNA-b23124.fa]
[2023-03-19 01:13:52,201] [INFO] Query marker FASTA was written to OceanDNA-b23124/markers.fasta
[2023-03-19 01:13:52,201] [INFO] Task started: Blastn
[2023-03-19 01:13:52,201] [INFO] Running command: blastn -query OceanDNA-b23124/markers.fasta -db /var/lib/cwl/stg51ec5e66-6568-4248-9408-cfbe845d772b/dqc_reference/reference_markers.fasta -out OceanDNA-b23124/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:13:52,720] [INFO] Task succeeded: Blastn
[2023-03-19 01:13:52,721] [INFO] Selected 10 target genomes.
[2023-03-19 01:13:52,721] [INFO] Target genome list was writen to OceanDNA-b23124/target_genomes.txt
[2023-03-19 01:13:52,728] [INFO] Task started: fastANI
[2023-03-19 01:13:52,728] [INFO] Running command: fastANI --query /var/lib/cwl/stg492ff9e7-75fd-49f8-8cfd-4317bd81b885/OceanDNA-b23124.fa --refList OceanDNA-b23124/target_genomes.txt --output OceanDNA-b23124/fastani_result.tsv --threads 1
[2023-03-19 01:13:59,372] [INFO] Task succeeded: fastANI
[2023-03-19 01:13:59,373] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg51ec5e66-6568-4248-9408-cfbe845d772b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 01:13:59,373] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg51ec5e66-6568-4248-9408-cfbe845d772b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 01:13:59,373] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 01:13:59,373] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 01:13:59,373] [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
--------------------------------------------------------------------------------
[2023-03-19 01:13:59,374] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23124/tc_result.tsv
[2023-03-19 01:13:59,374] [INFO] ===== Taxonomy check completed =====
[2023-03-19 01:13:59,374] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 01:13:59,374] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg51ec5e66-6568-4248-9408-cfbe845d772b/dqc_reference/checkm_data
[2023-03-19 01:13:59,377] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 01:13:59,531] [INFO] Task started: CheckM
[2023-03-19 01:13:59,531] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23124/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23124/checkm_input OceanDNA-b23124/checkm_result
[2023-03-19 01:14:21,995] [INFO] Task succeeded: CheckM
[2023-03-19 01:14:21,996] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.37%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 01:14:21,998] [INFO] ===== Completeness check finished =====
[2023-03-19 01:14:21,998] [INFO] ===== Start GTDB Search =====
[2023-03-19 01:14:21,998] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23124/markers.fasta)
[2023-03-19 01:14:21,999] [INFO] Task started: Blastn
[2023-03-19 01:14:21,999] [INFO] Running command: blastn -query OceanDNA-b23124/markers.fasta -db /var/lib/cwl/stg51ec5e66-6568-4248-9408-cfbe845d772b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23124/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:14:22,677] [INFO] Task succeeded: Blastn
[2023-03-19 01:14:22,678] [INFO] Selected 15 target genomes.
[2023-03-19 01:14:22,678] [INFO] Target genome list was writen to OceanDNA-b23124/target_genomes_gtdb.txt
[2023-03-19 01:14:22,749] [INFO] Task started: fastANI
[2023-03-19 01:14:22,749] [INFO] Running command: fastANI --query /var/lib/cwl/stg492ff9e7-75fd-49f8-8cfd-4317bd81b885/OceanDNA-b23124.fa --refList OceanDNA-b23124/target_genomes_gtdb.txt --output OceanDNA-b23124/fastani_result_gtdb.tsv --threads 1
[2023-03-19 01:14:29,368] [INFO] Task succeeded: fastANI
[2023-03-19 01:14:29,371] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 01:14:29,371] [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_002311345.1	s__UBA1146 sp002311345	99.4266	185	186	d__Bacteria;p__Planctomycetota;c__UBA8108;o__UBA1146;f__UBA1146;g__UBA1146	95.0	98.95	98.95	0.91	0.91	2	conclusive
GCA_002711105.1	s__UBA1146 sp002711105	80.0359	117	186	d__Bacteria;p__Planctomycetota;c__UBA8108;o__UBA1146;f__UBA1146;g__UBA1146	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 01:14:29,371] [INFO] GTDB search result was written to OceanDNA-b23124/result_gtdb.tsv
[2023-03-19 01:14:29,371] [INFO] ===== GTDB Search completed =====
[2023-03-19 01:14:29,372] [INFO] DFAST_QC result json was written to OceanDNA-b23124/dqc_result.json
[2023-03-19 01:14:29,372] [INFO] DFAST_QC completed!
[2023-03-19 01:14:29,372] [INFO] Total running time: 0h0m45s