[2023-03-14 11:14:12,735] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:14:12,735] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:14:12,736] [INFO] DQC Reference Directory: /var/lib/cwl/stg1d21d6b4-c56d-4fc6-a9c7-4a96d9717ce6/dqc_reference
[2023-03-14 11:14:14,204] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:14:14,204] [INFO] Task started: Prodigal
[2023-03-14 11:14:14,205] [INFO] Running command: cat /var/lib/cwl/stgbbba0eec-a753-44b4-b07f-c846f9d296db/OceanDNA-b33590.fa | prodigal -d OceanDNA-b33590/cds.fna -a OceanDNA-b33590/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:14:18,067] [INFO] Task succeeded: Prodigal
[2023-03-14 11:14:18,067] [INFO] Task started: HMMsearch
[2023-03-14 11:14:18,067] [INFO] Running command: hmmsearch --tblout OceanDNA-b33590/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1d21d6b4-c56d-4fc6-a9c7-4a96d9717ce6/dqc_reference/reference_markers.hmm OceanDNA-b33590/protein.faa > /dev/null
[2023-03-14 11:14:18,225] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:14:18,225] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgbbba0eec-a753-44b4-b07f-c846f9d296db/OceanDNA-b33590.fa]
[2023-03-14 11:14:18,235] [INFO] Query marker FASTA was written to OceanDNA-b33590/markers.fasta
[2023-03-14 11:14:18,235] [INFO] Task started: Blastn
[2023-03-14 11:14:18,235] [INFO] Running command: blastn -query OceanDNA-b33590/markers.fasta -db /var/lib/cwl/stg1d21d6b4-c56d-4fc6-a9c7-4a96d9717ce6/dqc_reference/reference_markers.fasta -out OceanDNA-b33590/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:14:18,687] [INFO] Task succeeded: Blastn
[2023-03-14 11:14:18,688] [INFO] Selected 4 target genomes.
[2023-03-14 11:14:18,688] [INFO] Target genome list was writen to OceanDNA-b33590/target_genomes.txt
[2023-03-14 11:14:18,692] [INFO] Task started: fastANI
[2023-03-14 11:14:18,692] [INFO] Running command: fastANI --query /var/lib/cwl/stgbbba0eec-a753-44b4-b07f-c846f9d296db/OceanDNA-b33590.fa --refList OceanDNA-b33590/target_genomes.txt --output OceanDNA-b33590/fastani_result.tsv --threads 1
[2023-03-14 11:14:19,809] [INFO] Task succeeded: fastANI
[2023-03-14 11:14:19,809] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1d21d6b4-c56d-4fc6-a9c7-4a96d9717ce6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 11:14:19,809] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1d21d6b4-c56d-4fc6-a9c7-4a96d9717ce6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 11:14:19,809] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 11:14:19,809] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 11:14:19,809] [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 11:14:19,810] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33590/tc_result.tsv
[2023-03-14 11:14:19,810] [INFO] ===== Taxonomy check completed =====
[2023-03-14 11:14:19,810] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:14:19,810] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1d21d6b4-c56d-4fc6-a9c7-4a96d9717ce6/dqc_reference/checkm_data
[2023-03-14 11:14:19,812] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:14:20,352] [INFO] Task started: CheckM
[2023-03-14 11:14:20,352] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33590/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33590/checkm_input OceanDNA-b33590/checkm_result
[2023-03-14 11:14:37,209] [INFO] Task succeeded: CheckM
[2023-03-14 11:14:37,209] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 61.08%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-14 11:14:37,211] [INFO] ===== Completeness check finished =====
[2023-03-14 11:14:37,211] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:14:37,211] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33590/markers.fasta)
[2023-03-14 11:14:37,212] [INFO] Task started: Blastn
[2023-03-14 11:14:37,212] [INFO] Running command: blastn -query OceanDNA-b33590/markers.fasta -db /var/lib/cwl/stg1d21d6b4-c56d-4fc6-a9c7-4a96d9717ce6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33590/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:14:37,670] [INFO] Task succeeded: Blastn
[2023-03-14 11:14:37,671] [INFO] Selected 14 target genomes.
[2023-03-14 11:14:37,671] [INFO] Target genome list was writen to OceanDNA-b33590/target_genomes_gtdb.txt
[2023-03-14 11:14:37,697] [INFO] Task started: fastANI
[2023-03-14 11:14:37,697] [INFO] Running command: fastANI --query /var/lib/cwl/stgbbba0eec-a753-44b4-b07f-c846f9d296db/OceanDNA-b33590.fa --refList OceanDNA-b33590/target_genomes_gtdb.txt --output OceanDNA-b33590/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:14:41,741] [INFO] Task succeeded: fastANI
[2023-03-14 11:14:41,743] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 11:14:41,744] [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_002170285.1	s__UBA7377 sp002170285	81.1056	144	196	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae_A;g__UBA7377	95.0	98.55	98.55	0.77	0.77	2	-
--------------------------------------------------------------------------------
[2023-03-14 11:14:41,744] [INFO] GTDB search result was written to OceanDNA-b33590/result_gtdb.tsv
[2023-03-14 11:14:41,744] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:14:41,744] [INFO] DFAST_QC result json was written to OceanDNA-b33590/dqc_result.json
[2023-03-14 11:14:41,744] [INFO] DFAST_QC completed!
[2023-03-14 11:14:41,745] [INFO] Total running time: 0h0m29s