[2023-03-18 04:04:53,886] [INFO] DFAST_QC pipeline started.
[2023-03-18 04:04:53,887] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 04:04:53,887] [INFO] DQC Reference Directory: /var/lib/cwl/stgb35d6ae4-0ea5-4a38-95e0-8459f8d4460b/dqc_reference
[2023-03-18 04:04:55,026] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 04:04:55,026] [INFO] Task started: Prodigal
[2023-03-18 04:04:55,026] [INFO] Running command: cat /var/lib/cwl/stg3a0cc772-19b7-4c8c-91a1-e8c8f9fa354e/OceanDNA-b32.fa | prodigal -d OceanDNA-b32/cds.fna -a OceanDNA-b32/protein.faa -g 11 -q > /dev/null
[2023-03-18 04:05:08,419] [INFO] Task succeeded: Prodigal
[2023-03-18 04:05:08,420] [INFO] Task started: HMMsearch
[2023-03-18 04:05:08,420] [INFO] Running command: hmmsearch --tblout OceanDNA-b32/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb35d6ae4-0ea5-4a38-95e0-8459f8d4460b/dqc_reference/reference_markers.hmm OceanDNA-b32/protein.faa > /dev/null
[2023-03-18 04:05:08,611] [INFO] Task succeeded: HMMsearch
[2023-03-18 04:05:08,611] [INFO] Found 6/6 markers.
[2023-03-18 04:05:08,625] [INFO] Query marker FASTA was written to OceanDNA-b32/markers.fasta
[2023-03-18 04:05:08,626] [INFO] Task started: Blastn
[2023-03-18 04:05:08,626] [INFO] Running command: blastn -query OceanDNA-b32/markers.fasta -db /var/lib/cwl/stgb35d6ae4-0ea5-4a38-95e0-8459f8d4460b/dqc_reference/reference_markers.fasta -out OceanDNA-b32/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:05:09,184] [INFO] Task succeeded: Blastn
[2023-03-18 04:05:09,184] [INFO] Selected 12 target genomes.
[2023-03-18 04:05:09,185] [INFO] Target genome list was writen to OceanDNA-b32/target_genomes.txt
[2023-03-18 04:05:09,243] [INFO] Task started: fastANI
[2023-03-18 04:05:09,243] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a0cc772-19b7-4c8c-91a1-e8c8f9fa354e/OceanDNA-b32.fa --refList OceanDNA-b32/target_genomes.txt --output OceanDNA-b32/fastani_result.tsv --threads 1
[2023-03-18 04:05:17,056] [INFO] Task succeeded: fastANI
[2023-03-18 04:05:17,056] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb35d6ae4-0ea5-4a38-95e0-8459f8d4460b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 04:05:17,056] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb35d6ae4-0ea5-4a38-95e0-8459f8d4460b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 04:05:17,057] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 04:05:17,057] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 04:05:17,057] [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 04:05:17,057] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32/tc_result.tsv
[2023-03-18 04:05:17,057] [INFO] ===== Taxonomy check completed =====
[2023-03-18 04:05:17,057] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 04:05:17,057] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb35d6ae4-0ea5-4a38-95e0-8459f8d4460b/dqc_reference/checkm_data
[2023-03-18 04:05:17,060] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 04:05:17,063] [INFO] Task started: CheckM
[2023-03-18 04:05:17,063] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32/checkm_input OceanDNA-b32/checkm_result
[2023-03-18 04:05:53,861] [INFO] Task succeeded: CheckM
[2023-03-18 04:05:53,861] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 04:05:53,903] [INFO] ===== Completeness check finished =====
[2023-03-18 04:05:53,903] [INFO] ===== Start GTDB Search =====
[2023-03-18 04:05:53,903] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32/markers.fasta)
[2023-03-18 04:05:53,904] [INFO] Task started: Blastn
[2023-03-18 04:05:53,904] [INFO] Running command: blastn -query OceanDNA-b32/markers.fasta -db /var/lib/cwl/stgb35d6ae4-0ea5-4a38-95e0-8459f8d4460b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:05:54,599] [INFO] Task succeeded: Blastn
[2023-03-18 04:05:54,600] [INFO] Selected 17 target genomes.
[2023-03-18 04:05:54,600] [INFO] Target genome list was writen to OceanDNA-b32/target_genomes_gtdb.txt
[2023-03-18 04:05:54,928] [INFO] Task started: fastANI
[2023-03-18 04:05:54,928] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a0cc772-19b7-4c8c-91a1-e8c8f9fa354e/OceanDNA-b32.fa --refList OceanDNA-b32/target_genomes_gtdb.txt --output OceanDNA-b32/fastani_result_gtdb.tsv --threads 1
[2023-03-18 04:06:03,054] [INFO] Task succeeded: fastANI
[2023-03-18 04:06:03,056] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 04:06:03,056] [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_002433055.1	s__UBA6623 sp002433055	99.9636	492	753	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__UBA6623;g__UBA6623	95.0	99.97	99.97	0.88	0.88	2	conclusive
--------------------------------------------------------------------------------
[2023-03-18 04:06:03,063] [INFO] GTDB search result was written to OceanDNA-b32/result_gtdb.tsv
[2023-03-18 04:06:03,064] [INFO] ===== GTDB Search completed =====
[2023-03-18 04:06:03,064] [INFO] DFAST_QC result json was written to OceanDNA-b32/dqc_result.json
[2023-03-18 04:06:03,065] [INFO] DFAST_QC completed!
[2023-03-18 04:06:03,065] [INFO] Total running time: 0h1m9s