[2023-03-15 16:14:47,334] [INFO] DFAST_QC pipeline started.
[2023-03-15 16:14:47,336] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 16:14:47,336] [INFO] DQC Reference Directory: /var/lib/cwl/stg8ab42df0-04d2-489c-8353-db3d62080d09/dqc_reference
[2023-03-15 16:14:49,238] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 16:14:49,239] [INFO] Task started: Prodigal
[2023-03-15 16:14:49,239] [INFO] Running command: cat /var/lib/cwl/stg88b5c5a6-f7ab-40f6-bd13-ccafa809e968/OceanDNA-b20953.fa | prodigal -d OceanDNA-b20953/cds.fna -a OceanDNA-b20953/protein.faa -g 11 -q > /dev/null
[2023-03-15 16:15:05,275] [INFO] Task succeeded: Prodigal
[2023-03-15 16:15:05,275] [INFO] Task started: HMMsearch
[2023-03-15 16:15:05,275] [INFO] Running command: hmmsearch --tblout OceanDNA-b20953/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8ab42df0-04d2-489c-8353-db3d62080d09/dqc_reference/reference_markers.hmm OceanDNA-b20953/protein.faa > /dev/null
[2023-03-15 16:15:05,478] [INFO] Task succeeded: HMMsearch
[2023-03-15 16:15:05,479] [INFO] Found 6/6 markers.
[2023-03-15 16:15:05,512] [INFO] Query marker FASTA was written to OceanDNA-b20953/markers.fasta
[2023-03-15 16:15:05,512] [INFO] Task started: Blastn
[2023-03-15 16:15:05,512] [INFO] Running command: blastn -query OceanDNA-b20953/markers.fasta -db /var/lib/cwl/stg8ab42df0-04d2-489c-8353-db3d62080d09/dqc_reference/reference_markers.fasta -out OceanDNA-b20953/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 16:15:06,078] [INFO] Task succeeded: Blastn
[2023-03-15 16:15:06,084] [INFO] Selected 17 target genomes.
[2023-03-15 16:15:06,084] [INFO] Target genome list was writen to OceanDNA-b20953/target_genomes.txt
[2023-03-15 16:15:06,095] [INFO] Task started: fastANI
[2023-03-15 16:15:06,095] [INFO] Running command: fastANI --query /var/lib/cwl/stg88b5c5a6-f7ab-40f6-bd13-ccafa809e968/OceanDNA-b20953.fa --refList OceanDNA-b20953/target_genomes.txt --output OceanDNA-b20953/fastani_result.tsv --threads 1
[2023-03-15 16:15:14,237] [INFO] Task succeeded: fastANI
[2023-03-15 16:15:14,238] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8ab42df0-04d2-489c-8353-db3d62080d09/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 16:15:14,238] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8ab42df0-04d2-489c-8353-db3d62080d09/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 16:15:14,238] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 16:15:14,238] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 16:15:14,238] [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 16:15:14,242] [INFO] DFAST Taxonomy check result was written to OceanDNA-b20953/tc_result.tsv
[2023-03-15 16:15:14,245] [INFO] ===== Taxonomy check completed =====
[2023-03-15 16:15:14,245] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 16:15:14,246] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8ab42df0-04d2-489c-8353-db3d62080d09/dqc_reference/checkm_data
[2023-03-15 16:15:14,248] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 16:15:14,262] [INFO] Task started: CheckM
[2023-03-15 16:15:14,262] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b20953/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b20953/checkm_input OceanDNA-b20953/checkm_result
[2023-03-15 16:15:56,980] [INFO] Task succeeded: CheckM
[2023-03-15 16:15:56,981] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 16:15:56,983] [INFO] ===== Completeness check finished =====
[2023-03-15 16:15:56,984] [INFO] ===== Start GTDB Search =====
[2023-03-15 16:15:56,984] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b20953/markers.fasta)
[2023-03-15 16:15:56,985] [INFO] Task started: Blastn
[2023-03-15 16:15:56,985] [INFO] Running command: blastn -query OceanDNA-b20953/markers.fasta -db /var/lib/cwl/stg8ab42df0-04d2-489c-8353-db3d62080d09/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b20953/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 16:15:57,874] [INFO] Task succeeded: Blastn
[2023-03-15 16:15:57,875] [INFO] Selected 30 target genomes.
[2023-03-15 16:15:57,875] [INFO] Target genome list was writen to OceanDNA-b20953/target_genomes_gtdb.txt
[2023-03-15 16:15:57,899] [INFO] Task started: fastANI
[2023-03-15 16:15:57,899] [INFO] Running command: fastANI --query /var/lib/cwl/stg88b5c5a6-f7ab-40f6-bd13-ccafa809e968/OceanDNA-b20953.fa --refList OceanDNA-b20953/target_genomes_gtdb.txt --output OceanDNA-b20953/fastani_result_gtdb.tsv --threads 1
[2023-03-15 16:16:11,465] [INFO] Task succeeded: fastANI
[2023-03-15 16:16:11,465] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 16:16:11,465] [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
--------------------------------------------------------------------------------
[2023-03-15 16:16:11,466] [INFO] GTDB search result was written to OceanDNA-b20953/result_gtdb.tsv
[2023-03-15 16:16:11,466] [INFO] ===== GTDB Search completed =====
[2023-03-15 16:16:11,467] [INFO] DFAST_QC result json was written to OceanDNA-b20953/dqc_result.json
[2023-03-15 16:16:11,467] [INFO] DFAST_QC completed!
[2023-03-15 16:16:11,467] [INFO] Total running time: 0h1m24s