[2023-03-16 08:30:41,521] [INFO] DFAST_QC pipeline started.
[2023-03-16 08:30:41,522] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 08:30:41,522] [INFO] DQC Reference Directory: /var/lib/cwl/stgaaac87a4-6d0e-4068-9718-0e6f1ccb6085/dqc_reference
[2023-03-16 08:30:42,646] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 08:30:42,647] [INFO] Task started: Prodigal
[2023-03-16 08:30:42,647] [INFO] Running command: cat /var/lib/cwl/stg6a9965ff-67af-45a6-8775-3a0ee90e2953/OceanDNA-b45369.fa | prodigal -d OceanDNA-b45369/cds.fna -a OceanDNA-b45369/protein.faa -g 11 -q > /dev/null
[2023-03-16 08:30:59,050] [INFO] Task succeeded: Prodigal
[2023-03-16 08:30:59,050] [INFO] Task started: HMMsearch
[2023-03-16 08:30:59,050] [INFO] Running command: hmmsearch --tblout OceanDNA-b45369/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaaac87a4-6d0e-4068-9718-0e6f1ccb6085/dqc_reference/reference_markers.hmm OceanDNA-b45369/protein.faa > /dev/null
[2023-03-16 08:30:59,281] [INFO] Task succeeded: HMMsearch
[2023-03-16 08:30:59,282] [INFO] Found 6/6 markers.
[2023-03-16 08:30:59,325] [INFO] Query marker FASTA was written to OceanDNA-b45369/markers.fasta
[2023-03-16 08:30:59,326] [INFO] Task started: Blastn
[2023-03-16 08:30:59,326] [INFO] Running command: blastn -query OceanDNA-b45369/markers.fasta -db /var/lib/cwl/stgaaac87a4-6d0e-4068-9718-0e6f1ccb6085/dqc_reference/reference_markers.fasta -out OceanDNA-b45369/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:30:59,830] [INFO] Task succeeded: Blastn
[2023-03-16 08:30:59,833] [INFO] Selected 21 target genomes.
[2023-03-16 08:30:59,834] [INFO] Target genome list was writen to OceanDNA-b45369/target_genomes.txt
[2023-03-16 08:30:59,873] [INFO] Task started: fastANI
[2023-03-16 08:30:59,873] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a9965ff-67af-45a6-8775-3a0ee90e2953/OceanDNA-b45369.fa --refList OceanDNA-b45369/target_genomes.txt --output OceanDNA-b45369/fastani_result.tsv --threads 1
[2023-03-16 08:31:12,904] [INFO] Task succeeded: fastANI
[2023-03-16 08:31:12,904] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaaac87a4-6d0e-4068-9718-0e6f1ccb6085/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 08:31:12,904] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaaac87a4-6d0e-4068-9718-0e6f1ccb6085/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 08:31:12,904] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 08:31:12,905] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 08:31:12,905] [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
--------------------------------------------------------------------------------
[2023-03-16 08:31:12,906] [INFO] DFAST Taxonomy check result was written to OceanDNA-b45369/tc_result.tsv
[2023-03-16 08:31:12,909] [INFO] ===== Taxonomy check completed =====
[2023-03-16 08:31:12,909] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 08:31:12,909] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaaac87a4-6d0e-4068-9718-0e6f1ccb6085/dqc_reference/checkm_data
[2023-03-16 08:31:12,912] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 08:31:12,984] [INFO] Task started: CheckM
[2023-03-16 08:31:12,984] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b45369/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b45369/checkm_input OceanDNA-b45369/checkm_result
[2023-03-16 08:31:57,815] [INFO] Task succeeded: CheckM
[2023-03-16 08:31:57,816] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 08:31:57,976] [INFO] ===== Completeness check finished =====
[2023-03-16 08:31:57,976] [INFO] ===== Start GTDB Search =====
[2023-03-16 08:31:57,976] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b45369/markers.fasta)
[2023-03-16 08:31:57,977] [INFO] Task started: Blastn
[2023-03-16 08:31:57,977] [INFO] Running command: blastn -query OceanDNA-b45369/markers.fasta -db /var/lib/cwl/stgaaac87a4-6d0e-4068-9718-0e6f1ccb6085/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b45369/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:31:58,683] [INFO] Task succeeded: Blastn
[2023-03-16 08:31:58,686] [INFO] Selected 29 target genomes.
[2023-03-16 08:31:58,686] [INFO] Target genome list was writen to OceanDNA-b45369/target_genomes_gtdb.txt
[2023-03-16 08:31:58,858] [INFO] Task started: fastANI
[2023-03-16 08:31:58,858] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a9965ff-67af-45a6-8775-3a0ee90e2953/OceanDNA-b45369.fa --refList OceanDNA-b45369/target_genomes_gtdb.txt --output OceanDNA-b45369/fastani_result_gtdb.tsv --threads 1
[2023-03-16 08:32:13,440] [INFO] Task succeeded: fastANI
[2023-03-16 08:32:13,441] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 08:32:13,441] [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
--------------------------------------------------------------------------------
[2023-03-16 08:32:13,443] [INFO] GTDB search result was written to OceanDNA-b45369/result_gtdb.tsv
[2023-03-16 08:32:13,444] [INFO] ===== GTDB Search completed =====
[2023-03-16 08:32:13,446] [INFO] DFAST_QC result json was written to OceanDNA-b45369/dqc_result.json
[2023-03-16 08:32:13,446] [INFO] DFAST_QC completed!
[2023-03-16 08:32:13,446] [INFO] Total running time: 0h1m32s