[2023-03-16 17:31:39,690] [INFO] DFAST_QC pipeline started.
[2023-03-16 17:31:39,690] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 17:31:39,690] [INFO] DQC Reference Directory: /var/lib/cwl/stg387aabcd-b0f6-4226-aaaa-2d3c335a68d8/dqc_reference
[2023-03-16 17:31:42,514] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 17:31:42,515] [INFO] Task started: Prodigal
[2023-03-16 17:31:42,515] [INFO] Running command: cat /var/lib/cwl/stga3bf12af-255d-4b14-91ca-b3da7c8f1a96/OceanDNA-b45275.fa | prodigal -d OceanDNA-b45275/cds.fna -a OceanDNA-b45275/protein.faa -g 11 -q > /dev/null
[2023-03-16 17:31:48,587] [INFO] Task succeeded: Prodigal
[2023-03-16 17:31:48,587] [INFO] Task started: HMMsearch
[2023-03-16 17:31:48,587] [INFO] Running command: hmmsearch --tblout OceanDNA-b45275/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg387aabcd-b0f6-4226-aaaa-2d3c335a68d8/dqc_reference/reference_markers.hmm OceanDNA-b45275/protein.faa > /dev/null
[2023-03-16 17:31:48,746] [INFO] Task succeeded: HMMsearch
[2023-03-16 17:31:48,746] [WARNING] Found 5/6 markers. [/var/lib/cwl/stga3bf12af-255d-4b14-91ca-b3da7c8f1a96/OceanDNA-b45275.fa]
[2023-03-16 17:31:48,758] [INFO] Query marker FASTA was written to OceanDNA-b45275/markers.fasta
[2023-03-16 17:31:48,759] [INFO] Task started: Blastn
[2023-03-16 17:31:48,760] [INFO] Running command: blastn -query OceanDNA-b45275/markers.fasta -db /var/lib/cwl/stg387aabcd-b0f6-4226-aaaa-2d3c335a68d8/dqc_reference/reference_markers.fasta -out OceanDNA-b45275/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:31:49,248] [INFO] Task succeeded: Blastn
[2023-03-16 17:31:49,251] [INFO] Selected 11 target genomes.
[2023-03-16 17:31:49,251] [INFO] Target genome list was writen to OceanDNA-b45275/target_genomes.txt
[2023-03-16 17:31:49,258] [INFO] Task started: fastANI
[2023-03-16 17:31:49,258] [INFO] Running command: fastANI --query /var/lib/cwl/stga3bf12af-255d-4b14-91ca-b3da7c8f1a96/OceanDNA-b45275.fa --refList OceanDNA-b45275/target_genomes.txt --output OceanDNA-b45275/fastani_result.tsv --threads 1
[2023-03-16 17:31:56,376] [INFO] Task succeeded: fastANI
[2023-03-16 17:31:56,376] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg387aabcd-b0f6-4226-aaaa-2d3c335a68d8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 17:31:56,376] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg387aabcd-b0f6-4226-aaaa-2d3c335a68d8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 17:31:56,377] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 17:31:56,377] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 17:31:56,377] [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 17:31:56,378] [INFO] DFAST Taxonomy check result was written to OceanDNA-b45275/tc_result.tsv
[2023-03-16 17:31:56,378] [INFO] ===== Taxonomy check completed =====
[2023-03-16 17:31:56,378] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 17:31:56,378] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg387aabcd-b0f6-4226-aaaa-2d3c335a68d8/dqc_reference/checkm_data
[2023-03-16 17:31:56,431] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 17:31:56,434] [INFO] Task started: CheckM
[2023-03-16 17:31:56,434] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b45275/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b45275/checkm_input OceanDNA-b45275/checkm_result
[2023-03-16 17:32:20,011] [INFO] Task succeeded: CheckM
[2023-03-16 17:32:20,011] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.88%
Contamintation: 1.04%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 17:32:20,017] [INFO] ===== Completeness check finished =====
[2023-03-16 17:32:20,017] [INFO] ===== Start GTDB Search =====
[2023-03-16 17:32:20,017] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b45275/markers.fasta)
[2023-03-16 17:32:20,018] [INFO] Task started: Blastn
[2023-03-16 17:32:20,019] [INFO] Running command: blastn -query OceanDNA-b45275/markers.fasta -db /var/lib/cwl/stg387aabcd-b0f6-4226-aaaa-2d3c335a68d8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b45275/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:32:21,651] [INFO] Task succeeded: Blastn
[2023-03-16 17:32:21,653] [INFO] Selected 16 target genomes.
[2023-03-16 17:32:21,653] [INFO] Target genome list was writen to OceanDNA-b45275/target_genomes_gtdb.txt
[2023-03-16 17:32:21,673] [INFO] Task started: fastANI
[2023-03-16 17:32:21,673] [INFO] Running command: fastANI --query /var/lib/cwl/stga3bf12af-255d-4b14-91ca-b3da7c8f1a96/OceanDNA-b45275.fa --refList OceanDNA-b45275/target_genomes_gtdb.txt --output OceanDNA-b45275/fastani_result_gtdb.tsv --threads 1
[2023-03-16 17:32:34,443] [INFO] Task succeeded: fastANI
[2023-03-16 17:32:34,445] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 17:32:34,445] [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_002377645.1	s__UBA3496 sp002377645	80.8201	225	272	d__Bacteria;p__UBA8248;c__UBA8248;o__UBA8248;f__UBA3496;g__UBA3496	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 17:32:34,447] [INFO] GTDB search result was written to OceanDNA-b45275/result_gtdb.tsv
[2023-03-16 17:32:34,447] [INFO] ===== GTDB Search completed =====
[2023-03-16 17:32:34,449] [INFO] DFAST_QC result json was written to OceanDNA-b45275/dqc_result.json
[2023-03-16 17:32:34,449] [INFO] DFAST_QC completed!
[2023-03-16 17:32:34,449] [INFO] Total running time: 0h0m55s