[2023-03-17 22:53:09,078] [INFO] DFAST_QC pipeline started.
[2023-03-17 22:53:09,078] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 22:53:09,078] [INFO] DQC Reference Directory: /var/lib/cwl/stg63290033-adea-43a9-a419-d377befb28f2/dqc_reference
[2023-03-17 22:53:12,179] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 22:53:12,179] [INFO] Task started: Prodigal
[2023-03-17 22:53:12,179] [INFO] Running command: cat /var/lib/cwl/stg243a77c4-93db-44bd-a4f1-088c4679c08d/OceanDNA-b24620.fa | prodigal -d OceanDNA-b24620/cds.fna -a OceanDNA-b24620/protein.faa -g 11 -q > /dev/null
[2023-03-17 22:53:18,645] [INFO] Task succeeded: Prodigal
[2023-03-17 22:53:18,646] [INFO] Task started: HMMsearch
[2023-03-17 22:53:18,646] [INFO] Running command: hmmsearch --tblout OceanDNA-b24620/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg63290033-adea-43a9-a419-d377befb28f2/dqc_reference/reference_markers.hmm OceanDNA-b24620/protein.faa > /dev/null
[2023-03-17 22:53:18,871] [INFO] Task succeeded: HMMsearch
[2023-03-17 22:53:18,872] [INFO] Found 6/6 markers.
[2023-03-17 22:53:18,886] [INFO] Query marker FASTA was written to OceanDNA-b24620/markers.fasta
[2023-03-17 22:53:18,888] [INFO] Task started: Blastn
[2023-03-17 22:53:18,888] [INFO] Running command: blastn -query OceanDNA-b24620/markers.fasta -db /var/lib/cwl/stg63290033-adea-43a9-a419-d377befb28f2/dqc_reference/reference_markers.fasta -out OceanDNA-b24620/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 22:53:22,664] [INFO] Task succeeded: Blastn
[2023-03-17 22:53:22,665] [INFO] Selected 34 target genomes.
[2023-03-17 22:53:22,665] [INFO] Target genome list was writen to OceanDNA-b24620/target_genomes.txt
[2023-03-17 22:53:22,688] [INFO] Task started: fastANI
[2023-03-17 22:53:22,688] [INFO] Running command: fastANI --query /var/lib/cwl/stg243a77c4-93db-44bd-a4f1-088c4679c08d/OceanDNA-b24620.fa --refList OceanDNA-b24620/target_genomes.txt --output OceanDNA-b24620/fastani_result.tsv --threads 1
[2023-03-17 22:53:39,423] [INFO] Task succeeded: fastANI
[2023-03-17 22:53:39,423] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg63290033-adea-43a9-a419-d377befb28f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 22:53:39,423] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg63290033-adea-43a9-a419-d377befb28f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 22:53:39,423] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 22:53:39,423] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 22:53:39,424] [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
--------------------------------------------------------------------------------
[2023-03-17 22:53:39,424] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24620/tc_result.tsv
[2023-03-17 22:53:39,424] [INFO] ===== Taxonomy check completed =====
[2023-03-17 22:53:39,424] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 22:53:39,424] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg63290033-adea-43a9-a419-d377befb28f2/dqc_reference/checkm_data
[2023-03-17 22:53:39,434] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 22:53:39,437] [INFO] Task started: CheckM
[2023-03-17 22:53:39,437] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24620/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24620/checkm_input OceanDNA-b24620/checkm_result
[2023-03-17 22:54:04,638] [INFO] Task succeeded: CheckM
[2023-03-17 22:54:04,638] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.62%
Contamintation: 16.50%
Strain heterogeneity: 60.00%
--------------------------------------------------------------------------------
[2023-03-17 22:54:04,641] [INFO] ===== Completeness check finished =====
[2023-03-17 22:54:04,641] [INFO] ===== Start GTDB Search =====
[2023-03-17 22:54:04,641] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24620/markers.fasta)
[2023-03-17 22:54:04,642] [INFO] Task started: Blastn
[2023-03-17 22:54:04,642] [INFO] Running command: blastn -query OceanDNA-b24620/markers.fasta -db /var/lib/cwl/stg63290033-adea-43a9-a419-d377befb28f2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24620/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 22:54:05,652] [INFO] Task succeeded: Blastn
[2023-03-17 22:54:05,653] [INFO] Selected 29 target genomes.
[2023-03-17 22:54:05,653] [INFO] Target genome list was writen to OceanDNA-b24620/target_genomes_gtdb.txt
[2023-03-17 22:54:05,674] [INFO] Task started: fastANI
[2023-03-17 22:54:05,674] [INFO] Running command: fastANI --query /var/lib/cwl/stg243a77c4-93db-44bd-a4f1-088c4679c08d/OceanDNA-b24620.fa --refList OceanDNA-b24620/target_genomes_gtdb.txt --output OceanDNA-b24620/fastani_result_gtdb.tsv --threads 1
[2023-03-17 22:54:18,608] [INFO] Task succeeded: fastANI
[2023-03-17 22:54:18,610] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 22:54:18,610] [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_009995045.1	s__TMED27 sp009995045	77.5768	86	307	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Micavibrionales;f__Micavibrionaceae;g__TMED27	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 22:54:18,610] [INFO] GTDB search result was written to OceanDNA-b24620/result_gtdb.tsv
[2023-03-17 22:54:18,610] [INFO] ===== GTDB Search completed =====
[2023-03-17 22:54:18,611] [INFO] DFAST_QC result json was written to OceanDNA-b24620/dqc_result.json
[2023-03-17 22:54:18,611] [INFO] DFAST_QC completed!
[2023-03-17 22:54:18,611] [INFO] Total running time: 0h1m10s