[2023-03-17 23:54:10,802] [INFO] DFAST_QC pipeline started.
[2023-03-17 23:54:10,802] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 23:54:10,803] [INFO] DQC Reference Directory: /var/lib/cwl/stga2020ff5-6b07-4685-ac5e-ac8d26a583c6/dqc_reference
[2023-03-17 23:54:11,981] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 23:54:11,982] [INFO] Task started: Prodigal
[2023-03-17 23:54:11,982] [INFO] Running command: cat /var/lib/cwl/stgb561fab0-c6e8-40f0-b391-f69865eb088f/OceanDNA-b13496.fa | prodigal -d OceanDNA-b13496/cds.fna -a OceanDNA-b13496/protein.faa -g 11 -q > /dev/null
[2023-03-17 23:54:27,261] [INFO] Task succeeded: Prodigal
[2023-03-17 23:54:27,261] [INFO] Task started: HMMsearch
[2023-03-17 23:54:27,261] [INFO] Running command: hmmsearch --tblout OceanDNA-b13496/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga2020ff5-6b07-4685-ac5e-ac8d26a583c6/dqc_reference/reference_markers.hmm OceanDNA-b13496/protein.faa > /dev/null
[2023-03-17 23:54:27,456] [INFO] Task succeeded: HMMsearch
[2023-03-17 23:54:27,457] [INFO] Found 6/6 markers.
[2023-03-17 23:54:27,480] [INFO] Query marker FASTA was written to OceanDNA-b13496/markers.fasta
[2023-03-17 23:54:27,480] [INFO] Task started: Blastn
[2023-03-17 23:54:27,480] [INFO] Running command: blastn -query OceanDNA-b13496/markers.fasta -db /var/lib/cwl/stga2020ff5-6b07-4685-ac5e-ac8d26a583c6/dqc_reference/reference_markers.fasta -out OceanDNA-b13496/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:54:27,988] [INFO] Task succeeded: Blastn
[2023-03-17 23:54:27,991] [INFO] Selected 21 target genomes.
[2023-03-17 23:54:27,991] [INFO] Target genome list was writen to OceanDNA-b13496/target_genomes.txt
[2023-03-17 23:54:28,012] [INFO] Task started: fastANI
[2023-03-17 23:54:28,012] [INFO] Running command: fastANI --query /var/lib/cwl/stgb561fab0-c6e8-40f0-b391-f69865eb088f/OceanDNA-b13496.fa --refList OceanDNA-b13496/target_genomes.txt --output OceanDNA-b13496/fastani_result.tsv --threads 1
[2023-03-17 23:54:39,364] [INFO] Task succeeded: fastANI
[2023-03-17 23:54:39,365] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga2020ff5-6b07-4685-ac5e-ac8d26a583c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 23:54:39,365] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga2020ff5-6b07-4685-ac5e-ac8d26a583c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 23:54:39,365] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 23:54:39,365] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 23:54:39,365] [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 23:54:39,368] [INFO] DFAST Taxonomy check result was written to OceanDNA-b13496/tc_result.tsv
[2023-03-17 23:54:39,371] [INFO] ===== Taxonomy check completed =====
[2023-03-17 23:54:39,371] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 23:54:39,371] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga2020ff5-6b07-4685-ac5e-ac8d26a583c6/dqc_reference/checkm_data
[2023-03-17 23:54:39,374] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 23:54:39,378] [INFO] Task started: CheckM
[2023-03-17 23:54:39,378] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b13496/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b13496/checkm_input OceanDNA-b13496/checkm_result
[2023-03-17 23:55:20,016] [INFO] Task succeeded: CheckM
[2023-03-17 23:55:20,016] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 23:55:20,046] [INFO] ===== Completeness check finished =====
[2023-03-17 23:55:20,046] [INFO] ===== Start GTDB Search =====
[2023-03-17 23:55:20,047] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b13496/markers.fasta)
[2023-03-17 23:55:20,048] [INFO] Task started: Blastn
[2023-03-17 23:55:20,048] [INFO] Running command: blastn -query OceanDNA-b13496/markers.fasta -db /var/lib/cwl/stga2020ff5-6b07-4685-ac5e-ac8d26a583c6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b13496/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:55:20,739] [INFO] Task succeeded: Blastn
[2023-03-17 23:55:20,745] [INFO] Selected 26 target genomes.
[2023-03-17 23:55:20,745] [INFO] Target genome list was writen to OceanDNA-b13496/target_genomes_gtdb.txt
[2023-03-17 23:55:20,772] [INFO] Task started: fastANI
[2023-03-17 23:55:20,772] [INFO] Running command: fastANI --query /var/lib/cwl/stgb561fab0-c6e8-40f0-b391-f69865eb088f/OceanDNA-b13496.fa --refList OceanDNA-b13496/target_genomes_gtdb.txt --output OceanDNA-b13496/fastani_result_gtdb.tsv --threads 1
[2023-03-17 23:55:33,293] [INFO] Task succeeded: fastANI
[2023-03-17 23:55:33,295] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 23:55:33,295] [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_018662365.1	s__JABJGH01 sp018662365	99.8971	831	896	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__UBA11579;g__JABJGH01	95.0	99.95	99.92	0.97	0.94	12	conclusive
--------------------------------------------------------------------------------
[2023-03-17 23:55:33,297] [INFO] GTDB search result was written to OceanDNA-b13496/result_gtdb.tsv
[2023-03-17 23:55:33,300] [INFO] ===== GTDB Search completed =====
[2023-03-17 23:55:33,304] [INFO] DFAST_QC result json was written to OceanDNA-b13496/dqc_result.json
[2023-03-17 23:55:33,304] [INFO] DFAST_QC completed!
[2023-03-17 23:55:33,304] [INFO] Total running time: 0h1m23s