[2023-03-14 13:52:17,738] [INFO] DFAST_QC pipeline started.
[2023-03-14 13:52:17,738] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 13:52:17,738] [INFO] DQC Reference Directory: /var/lib/cwl/stgcd176ec2-1562-4fbe-b62d-74ab225719c0/dqc_reference
[2023-03-14 13:52:19,162] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 13:52:19,163] [INFO] Task started: Prodigal
[2023-03-14 13:52:19,163] [INFO] Running command: cat /var/lib/cwl/stg385b807e-6eff-4bf7-a4d6-56c644eeda14/OceanDNA-b15272.fa | prodigal -d OceanDNA-b15272/cds.fna -a OceanDNA-b15272/protein.faa -g 11 -q > /dev/null
[2023-03-14 13:52:26,356] [INFO] Task succeeded: Prodigal
[2023-03-14 13:52:26,356] [INFO] Task started: HMMsearch
[2023-03-14 13:52:26,356] [INFO] Running command: hmmsearch --tblout OceanDNA-b15272/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcd176ec2-1562-4fbe-b62d-74ab225719c0/dqc_reference/reference_markers.hmm OceanDNA-b15272/protein.faa > /dev/null
[2023-03-14 13:52:26,531] [INFO] Task succeeded: HMMsearch
[2023-03-14 13:52:26,531] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg385b807e-6eff-4bf7-a4d6-56c644eeda14/OceanDNA-b15272.fa]
[2023-03-14 13:52:26,542] [INFO] Query marker FASTA was written to OceanDNA-b15272/markers.fasta
[2023-03-14 13:52:26,543] [INFO] Task started: Blastn
[2023-03-14 13:52:26,543] [INFO] Running command: blastn -query OceanDNA-b15272/markers.fasta -db /var/lib/cwl/stgcd176ec2-1562-4fbe-b62d-74ab225719c0/dqc_reference/reference_markers.fasta -out OceanDNA-b15272/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:52:27,092] [INFO] Task succeeded: Blastn
[2023-03-14 13:52:27,093] [INFO] Selected 14 target genomes.
[2023-03-14 13:52:27,093] [INFO] Target genome list was writen to OceanDNA-b15272/target_genomes.txt
[2023-03-14 13:52:27,101] [INFO] Task started: fastANI
[2023-03-14 13:52:27,101] [INFO] Running command: fastANI --query /var/lib/cwl/stg385b807e-6eff-4bf7-a4d6-56c644eeda14/OceanDNA-b15272.fa --refList OceanDNA-b15272/target_genomes.txt --output OceanDNA-b15272/fastani_result.tsv --threads 1
[2023-03-14 13:52:34,579] [INFO] Task succeeded: fastANI
[2023-03-14 13:52:34,580] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcd176ec2-1562-4fbe-b62d-74ab225719c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 13:52:34,580] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcd176ec2-1562-4fbe-b62d-74ab225719c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 13:52:34,580] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 13:52:34,580] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 13:52:34,580] [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
--------------------------------------------------------------------------------
[2023-03-14 13:52:34,581] [INFO] DFAST Taxonomy check result was written to OceanDNA-b15272/tc_result.tsv
[2023-03-14 13:52:34,581] [INFO] ===== Taxonomy check completed =====
[2023-03-14 13:52:34,581] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 13:52:34,581] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcd176ec2-1562-4fbe-b62d-74ab225719c0/dqc_reference/checkm_data
[2023-03-14 13:52:34,584] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 13:52:34,588] [INFO] Task started: CheckM
[2023-03-14 13:52:34,588] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b15272/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b15272/checkm_input OceanDNA-b15272/checkm_result
[2023-03-14 13:52:57,298] [INFO] Task succeeded: CheckM
[2023-03-14 13:52:57,299] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 13:52:57,302] [INFO] ===== Completeness check finished =====
[2023-03-14 13:52:57,302] [INFO] ===== Start GTDB Search =====
[2023-03-14 13:52:57,302] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b15272/markers.fasta)
[2023-03-14 13:52:57,304] [INFO] Task started: Blastn
[2023-03-14 13:52:57,304] [INFO] Running command: blastn -query OceanDNA-b15272/markers.fasta -db /var/lib/cwl/stgcd176ec2-1562-4fbe-b62d-74ab225719c0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b15272/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:52:58,164] [INFO] Task succeeded: Blastn
[2023-03-14 13:52:58,166] [INFO] Selected 15 target genomes.
[2023-03-14 13:52:58,166] [INFO] Target genome list was writen to OceanDNA-b15272/target_genomes_gtdb.txt
[2023-03-14 13:52:58,182] [INFO] Task started: fastANI
[2023-03-14 13:52:58,183] [INFO] Running command: fastANI --query /var/lib/cwl/stg385b807e-6eff-4bf7-a4d6-56c644eeda14/OceanDNA-b15272.fa --refList OceanDNA-b15272/target_genomes_gtdb.txt --output OceanDNA-b15272/fastani_result_gtdb.tsv --threads 1
[2023-03-14 13:53:04,086] [INFO] Task succeeded: fastANI
[2023-03-14 13:53:04,088] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 13:53:04,089] [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_009391535.1	s__VFHP01 sp009391535	99.6607	292	406	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA2985;f__UBA2985;g__VFHP01	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2023-03-14 13:53:04,089] [INFO] GTDB search result was written to OceanDNA-b15272/result_gtdb.tsv
[2023-03-14 13:53:04,090] [INFO] ===== GTDB Search completed =====
[2023-03-14 13:53:04,091] [INFO] DFAST_QC result json was written to OceanDNA-b15272/dqc_result.json
[2023-03-14 13:53:04,091] [INFO] DFAST_QC completed!
[2023-03-14 13:53:04,091] [INFO] Total running time: 0h0m46s