[2023-03-15 22:15:27,733] [INFO] DFAST_QC pipeline started.
[2023-03-15 22:15:27,741] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 22:15:27,741] [INFO] DQC Reference Directory: /var/lib/cwl/stge1ed95a3-95b7-4560-8e7c-34fca43452d5/dqc_reference
[2023-03-15 22:15:29,360] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 22:15:29,361] [INFO] Task started: Prodigal
[2023-03-15 22:15:29,361] [INFO] Running command: cat /var/lib/cwl/stg09673f5d-abcc-485f-943a-6868b5611ce2/OceanDNA-b13521.fa | prodigal -d OceanDNA-b13521/cds.fna -a OceanDNA-b13521/protein.faa -g 11 -q > /dev/null
[2023-03-15 22:15:37,803] [INFO] Task succeeded: Prodigal
[2023-03-15 22:15:37,804] [INFO] Task started: HMMsearch
[2023-03-15 22:15:37,804] [INFO] Running command: hmmsearch --tblout OceanDNA-b13521/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge1ed95a3-95b7-4560-8e7c-34fca43452d5/dqc_reference/reference_markers.hmm OceanDNA-b13521/protein.faa > /dev/null
[2023-03-15 22:15:38,035] [INFO] Task succeeded: HMMsearch
[2023-03-15 22:15:38,036] [INFO] Found 6/6 markers.
[2023-03-15 22:15:38,094] [INFO] Query marker FASTA was written to OceanDNA-b13521/markers.fasta
[2023-03-15 22:15:38,096] [INFO] Task started: Blastn
[2023-03-15 22:15:38,096] [INFO] Running command: blastn -query OceanDNA-b13521/markers.fasta -db /var/lib/cwl/stge1ed95a3-95b7-4560-8e7c-34fca43452d5/dqc_reference/reference_markers.fasta -out OceanDNA-b13521/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 22:15:38,605] [INFO] Task succeeded: Blastn
[2023-03-15 22:15:38,620] [INFO] Selected 12 target genomes.
[2023-03-15 22:15:38,620] [INFO] Target genome list was writen to OceanDNA-b13521/target_genomes.txt
[2023-03-15 22:15:38,626] [INFO] Task started: fastANI
[2023-03-15 22:15:38,626] [INFO] Running command: fastANI --query /var/lib/cwl/stg09673f5d-abcc-485f-943a-6868b5611ce2/OceanDNA-b13521.fa --refList OceanDNA-b13521/target_genomes.txt --output OceanDNA-b13521/fastani_result.tsv --threads 1
[2023-03-15 22:15:45,624] [INFO] Task succeeded: fastANI
[2023-03-15 22:15:45,624] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge1ed95a3-95b7-4560-8e7c-34fca43452d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 22:15:45,625] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge1ed95a3-95b7-4560-8e7c-34fca43452d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 22:15:45,625] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 22:15:45,625] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 22:15:45,625] [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 22:15:45,627] [INFO] DFAST Taxonomy check result was written to OceanDNA-b13521/tc_result.tsv
[2023-03-15 22:15:45,628] [INFO] ===== Taxonomy check completed =====
[2023-03-15 22:15:45,628] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 22:15:45,629] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge1ed95a3-95b7-4560-8e7c-34fca43452d5/dqc_reference/checkm_data
[2023-03-15 22:15:45,632] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 22:15:45,639] [INFO] Task started: CheckM
[2023-03-15 22:15:45,640] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b13521/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b13521/checkm_input OceanDNA-b13521/checkm_result
[2023-03-15 22:16:11,579] [INFO] Task succeeded: CheckM
[2023-03-15 22:16:11,579] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.37%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 22:16:11,674] [INFO] ===== Completeness check finished =====
[2023-03-15 22:16:11,674] [INFO] ===== Start GTDB Search =====
[2023-03-15 22:16:11,674] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b13521/markers.fasta)
[2023-03-15 22:16:11,675] [INFO] Task started: Blastn
[2023-03-15 22:16:11,675] [INFO] Running command: blastn -query OceanDNA-b13521/markers.fasta -db /var/lib/cwl/stge1ed95a3-95b7-4560-8e7c-34fca43452d5/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b13521/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 22:16:12,332] [INFO] Task succeeded: Blastn
[2023-03-15 22:16:12,338] [INFO] Selected 15 target genomes.
[2023-03-15 22:16:12,338] [INFO] Target genome list was writen to OceanDNA-b13521/target_genomes_gtdb.txt
[2023-03-15 22:16:12,433] [INFO] Task started: fastANI
[2023-03-15 22:16:12,433] [INFO] Running command: fastANI --query /var/lib/cwl/stg09673f5d-abcc-485f-943a-6868b5611ce2/OceanDNA-b13521.fa --refList OceanDNA-b13521/target_genomes_gtdb.txt --output OceanDNA-b13521/fastani_result_gtdb.tsv --threads 1
[2023-03-15 22:16:19,066] [INFO] Task succeeded: fastANI
[2023-03-15 22:16:19,070] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 22:16:19,070] [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_002311455.1	s__UBA11657 sp002311455	90.4166	439	512	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__UBA11657;g__UBA11657	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002346435.1	s__UBA11657 sp002346435	81.0709	337	512	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__UBA11657;g__UBA11657	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002377585.1	s__UBA11657 sp002377585	80.7252	367	512	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__UBA11657;g__UBA11657	95.0	99.07	98.64	0.89	0.85	4	-
GCA_002296125.1	s__UBA11657 sp002296125	76.2495	60	512	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__UBA11657;g__UBA11657	95.0	99.33	99.25	0.80	0.79	3	-
--------------------------------------------------------------------------------
[2023-03-15 22:16:19,072] [INFO] GTDB search result was written to OceanDNA-b13521/result_gtdb.tsv
[2023-03-15 22:16:19,074] [INFO] ===== GTDB Search completed =====
[2023-03-15 22:16:19,077] [INFO] DFAST_QC result json was written to OceanDNA-b13521/dqc_result.json
[2023-03-15 22:16:19,077] [INFO] DFAST_QC completed!
[2023-03-15 22:16:19,077] [INFO] Total running time: 0h0m51s