[2023-03-16 11:37:45,081] [INFO] DFAST_QC pipeline started.
[2023-03-16 11:37:45,081] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 11:37:45,081] [INFO] DQC Reference Directory: /var/lib/cwl/stg3235ff67-8444-492c-babd-3a955df4090e/dqc_reference
[2023-03-16 11:37:47,982] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 11:37:47,983] [INFO] Task started: Prodigal
[2023-03-16 11:37:47,983] [INFO] Running command: cat /var/lib/cwl/stg36cb2da7-79ff-4931-b00d-59696888891a/OceanDNA-b33096.fa | prodigal -d OceanDNA-b33096/cds.fna -a OceanDNA-b33096/protein.faa -g 11 -q > /dev/null
[2023-03-16 11:38:07,075] [INFO] Task succeeded: Prodigal
[2023-03-16 11:38:07,075] [INFO] Task started: HMMsearch
[2023-03-16 11:38:07,075] [INFO] Running command: hmmsearch --tblout OceanDNA-b33096/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3235ff67-8444-492c-babd-3a955df4090e/dqc_reference/reference_markers.hmm OceanDNA-b33096/protein.faa > /dev/null
[2023-03-16 11:38:07,233] [INFO] Task succeeded: HMMsearch
[2023-03-16 11:38:07,233] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg36cb2da7-79ff-4931-b00d-59696888891a/OceanDNA-b33096.fa]
[2023-03-16 11:38:07,252] [INFO] Query marker FASTA was written to OceanDNA-b33096/markers.fasta
[2023-03-16 11:38:07,252] [INFO] Task started: Blastn
[2023-03-16 11:38:07,252] [INFO] Running command: blastn -query OceanDNA-b33096/markers.fasta -db /var/lib/cwl/stg3235ff67-8444-492c-babd-3a955df4090e/dqc_reference/reference_markers.fasta -out OceanDNA-b33096/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 11:38:07,755] [INFO] Task succeeded: Blastn
[2023-03-16 11:38:07,756] [INFO] Selected 20 target genomes.
[2023-03-16 11:38:07,756] [INFO] Target genome list was writen to OceanDNA-b33096/target_genomes.txt
[2023-03-16 11:38:07,767] [INFO] Task started: fastANI
[2023-03-16 11:38:07,767] [INFO] Running command: fastANI --query /var/lib/cwl/stg36cb2da7-79ff-4931-b00d-59696888891a/OceanDNA-b33096.fa --refList OceanDNA-b33096/target_genomes.txt --output OceanDNA-b33096/fastani_result.tsv --threads 1
[2023-03-16 11:38:19,380] [INFO] Task succeeded: fastANI
[2023-03-16 11:38:19,380] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3235ff67-8444-492c-babd-3a955df4090e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 11:38:19,380] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3235ff67-8444-492c-babd-3a955df4090e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 11:38:19,381] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 11:38:19,381] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 11:38:19,381] [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 11:38:19,381] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33096/tc_result.tsv
[2023-03-16 11:38:19,381] [INFO] ===== Taxonomy check completed =====
[2023-03-16 11:38:19,381] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 11:38:19,381] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3235ff67-8444-492c-babd-3a955df4090e/dqc_reference/checkm_data
[2023-03-16 11:38:19,384] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 11:38:19,389] [INFO] Task started: CheckM
[2023-03-16 11:38:19,389] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33096/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33096/checkm_input OceanDNA-b33096/checkm_result
[2023-03-16 11:38:57,424] [INFO] Task succeeded: CheckM
[2023-03-16 11:38:57,424] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.93%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 11:38:57,427] [INFO] ===== Completeness check finished =====
[2023-03-16 11:38:57,427] [INFO] ===== Start GTDB Search =====
[2023-03-16 11:38:57,427] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33096/markers.fasta)
[2023-03-16 11:38:57,427] [INFO] Task started: Blastn
[2023-03-16 11:38:57,427] [INFO] Running command: blastn -query OceanDNA-b33096/markers.fasta -db /var/lib/cwl/stg3235ff67-8444-492c-babd-3a955df4090e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33096/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 11:38:58,102] [INFO] Task succeeded: Blastn
[2023-03-16 11:38:58,103] [INFO] Selected 20 target genomes.
[2023-03-16 11:38:58,103] [INFO] Target genome list was writen to OceanDNA-b33096/target_genomes_gtdb.txt
[2023-03-16 11:38:58,791] [INFO] Task started: fastANI
[2023-03-16 11:38:58,791] [INFO] Running command: fastANI --query /var/lib/cwl/stg36cb2da7-79ff-4931-b00d-59696888891a/OceanDNA-b33096.fa --refList OceanDNA-b33096/target_genomes_gtdb.txt --output OceanDNA-b33096/fastani_result_gtdb.tsv --threads 1
[2023-03-16 11:39:11,397] [INFO] Task succeeded: fastANI
[2023-03-16 11:39:11,399] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 11:39:11,399] [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_002434595.1	s__UBA6544 sp002434595	76.5661	79	779	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__UBA8366;g__UBA6544	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 11:39:11,399] [INFO] GTDB search result was written to OceanDNA-b33096/result_gtdb.tsv
[2023-03-16 11:39:11,399] [INFO] ===== GTDB Search completed =====
[2023-03-16 11:39:11,400] [INFO] DFAST_QC result json was written to OceanDNA-b33096/dqc_result.json
[2023-03-16 11:39:11,400] [INFO] DFAST_QC completed!
[2023-03-16 11:39:11,400] [INFO] Total running time: 0h1m26s