[2023-03-17 11:36:53,884] [INFO] DFAST_QC pipeline started.
[2023-03-17 11:36:53,884] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 11:36:53,884] [INFO] DQC Reference Directory: /var/lib/cwl/stge8150071-edb6-40a5-9ac9-c76d780327ae/dqc_reference
[2023-03-17 11:36:55,024] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 11:36:55,025] [INFO] Task started: Prodigal
[2023-03-17 11:36:55,025] [INFO] Running command: cat /var/lib/cwl/stgb8225a7c-7b1e-4e1c-958f-792a9683ab03/OceanDNA-b33964.fa | prodigal -d OceanDNA-b33964/cds.fna -a OceanDNA-b33964/protein.faa -g 11 -q > /dev/null
[2023-03-17 11:36:58,377] [INFO] Task succeeded: Prodigal
[2023-03-17 11:36:58,377] [INFO] Task started: HMMsearch
[2023-03-17 11:36:58,377] [INFO] Running command: hmmsearch --tblout OceanDNA-b33964/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge8150071-edb6-40a5-9ac9-c76d780327ae/dqc_reference/reference_markers.hmm OceanDNA-b33964/protein.faa > /dev/null
[2023-03-17 11:36:58,532] [INFO] Task succeeded: HMMsearch
[2023-03-17 11:36:58,533] [INFO] Found 6/6 markers.
[2023-03-17 11:36:58,545] [INFO] Query marker FASTA was written to OceanDNA-b33964/markers.fasta
[2023-03-17 11:36:58,549] [INFO] Task started: Blastn
[2023-03-17 11:36:58,549] [INFO] Running command: blastn -query OceanDNA-b33964/markers.fasta -db /var/lib/cwl/stge8150071-edb6-40a5-9ac9-c76d780327ae/dqc_reference/reference_markers.fasta -out OceanDNA-b33964/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:36:59,235] [INFO] Task succeeded: Blastn
[2023-03-17 11:36:59,236] [INFO] Selected 27 target genomes.
[2023-03-17 11:36:59,236] [INFO] Target genome list was writen to OceanDNA-b33964/target_genomes.txt
[2023-03-17 11:36:59,254] [INFO] Task started: fastANI
[2023-03-17 11:36:59,254] [INFO] Running command: fastANI --query /var/lib/cwl/stgb8225a7c-7b1e-4e1c-958f-792a9683ab03/OceanDNA-b33964.fa --refList OceanDNA-b33964/target_genomes.txt --output OceanDNA-b33964/fastani_result.tsv --threads 1
[2023-03-17 11:37:13,628] [INFO] Task succeeded: fastANI
[2023-03-17 11:37:13,628] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge8150071-edb6-40a5-9ac9-c76d780327ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 11:37:13,629] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge8150071-edb6-40a5-9ac9-c76d780327ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 11:37:13,629] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 11:37:13,629] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 11:37:13,629] [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
--------------------------------------------------------------------------------
[2023-03-17 11:37:13,630] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33964/tc_result.tsv
[2023-03-17 11:37:13,630] [INFO] ===== Taxonomy check completed =====
[2023-03-17 11:37:13,630] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 11:37:13,630] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge8150071-edb6-40a5-9ac9-c76d780327ae/dqc_reference/checkm_data
[2023-03-17 11:37:13,633] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 11:37:13,637] [INFO] Task started: CheckM
[2023-03-17 11:37:13,637] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33964/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33964/checkm_input OceanDNA-b33964/checkm_result
[2023-03-17 11:37:29,277] [INFO] Task succeeded: CheckM
[2023-03-17 11:37:29,277] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.36%
Contamintation: 6.54%
Strain heterogeneity: 25.00%
--------------------------------------------------------------------------------
[2023-03-17 11:37:29,283] [INFO] ===== Completeness check finished =====
[2023-03-17 11:37:29,283] [INFO] ===== Start GTDB Search =====
[2023-03-17 11:37:29,283] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33964/markers.fasta)
[2023-03-17 11:37:29,285] [INFO] Task started: Blastn
[2023-03-17 11:37:29,285] [INFO] Running command: blastn -query OceanDNA-b33964/markers.fasta -db /var/lib/cwl/stge8150071-edb6-40a5-9ac9-c76d780327ae/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33964/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:37:30,051] [INFO] Task succeeded: Blastn
[2023-03-17 11:37:30,054] [INFO] Selected 42 target genomes.
[2023-03-17 11:37:30,055] [INFO] Target genome list was writen to OceanDNA-b33964/target_genomes_gtdb.txt
[2023-03-17 11:37:30,091] [INFO] Task started: fastANI
[2023-03-17 11:37:30,091] [INFO] Running command: fastANI --query /var/lib/cwl/stgb8225a7c-7b1e-4e1c-958f-792a9683ab03/OceanDNA-b33964.fa --refList OceanDNA-b33964/target_genomes_gtdb.txt --output OceanDNA-b33964/fastani_result_gtdb.tsv --threads 1
[2023-03-17 11:37:41,552] [INFO] Task succeeded: fastANI
[2023-03-17 11:37:41,554] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 11:37:41,554] [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_905618945.1	s__BACL14 sp905618945	79.1252	117	201	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__BACL14	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 11:37:41,557] [INFO] GTDB search result was written to OceanDNA-b33964/result_gtdb.tsv
[2023-03-17 11:37:41,559] [INFO] ===== GTDB Search completed =====
[2023-03-17 11:37:41,561] [INFO] DFAST_QC result json was written to OceanDNA-b33964/dqc_result.json
[2023-03-17 11:37:41,561] [INFO] DFAST_QC completed!
[2023-03-17 11:37:41,561] [INFO] Total running time: 0h0m48s