[2023-03-16 03:47:32,867] [INFO] DFAST_QC pipeline started.
[2023-03-16 03:47:32,867] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 03:47:32,867] [INFO] DQC Reference Directory: /var/lib/cwl/stg56b55597-e8d4-4816-bc76-029c3a0bbe63/dqc_reference
[2023-03-16 03:47:34,530] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 03:47:34,531] [INFO] Task started: Prodigal
[2023-03-16 03:47:34,531] [INFO] Running command: cat /var/lib/cwl/stgec7173ea-38d8-4b86-884d-2271c96d3229/OceanDNA-a1794.fa | prodigal -d OceanDNA-a1794/cds.fna -a OceanDNA-a1794/protein.faa -g 11 -q > /dev/null
[2023-03-16 03:47:38,844] [INFO] Task succeeded: Prodigal
[2023-03-16 03:47:38,844] [INFO] Task started: HMMsearch
[2023-03-16 03:47:38,844] [INFO] Running command: hmmsearch --tblout OceanDNA-a1794/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg56b55597-e8d4-4816-bc76-029c3a0bbe63/dqc_reference/reference_markers.hmm OceanDNA-a1794/protein.faa > /dev/null
[2023-03-16 03:47:39,013] [INFO] Task succeeded: HMMsearch
[2023-03-16 03:47:39,014] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgec7173ea-38d8-4b86-884d-2271c96d3229/OceanDNA-a1794.fa]
[2023-03-16 03:47:39,021] [INFO] Query marker FASTA was written to OceanDNA-a1794/markers.fasta
[2023-03-16 03:47:39,021] [INFO] Task started: Blastn
[2023-03-16 03:47:39,021] [INFO] Running command: blastn -query OceanDNA-a1794/markers.fasta -db /var/lib/cwl/stg56b55597-e8d4-4816-bc76-029c3a0bbe63/dqc_reference/reference_markers.fasta -out OceanDNA-a1794/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 03:47:39,832] [INFO] Task succeeded: Blastn
[2023-03-16 03:47:39,833] [INFO] Selected 5 target genomes.
[2023-03-16 03:47:39,833] [INFO] Target genome list was writen to OceanDNA-a1794/target_genomes.txt
[2023-03-16 03:47:39,837] [INFO] Task started: fastANI
[2023-03-16 03:47:39,837] [INFO] Running command: fastANI --query /var/lib/cwl/stgec7173ea-38d8-4b86-884d-2271c96d3229/OceanDNA-a1794.fa --refList OceanDNA-a1794/target_genomes.txt --output OceanDNA-a1794/fastani_result.tsv --threads 1
[2023-03-16 03:47:41,419] [INFO] Task succeeded: fastANI
[2023-03-16 03:47:41,419] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg56b55597-e8d4-4816-bc76-029c3a0bbe63/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 03:47:41,419] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg56b55597-e8d4-4816-bc76-029c3a0bbe63/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 03:47:41,420] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 03:47:41,420] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 03:47:41,420] [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 03:47:41,420] [INFO] DFAST Taxonomy check result was written to OceanDNA-a1794/tc_result.tsv
[2023-03-16 03:47:41,420] [INFO] ===== Taxonomy check completed =====
[2023-03-16 03:47:41,420] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 03:47:41,420] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg56b55597-e8d4-4816-bc76-029c3a0bbe63/dqc_reference/checkm_data
[2023-03-16 03:47:41,431] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 03:47:41,606] [INFO] Task started: CheckM
[2023-03-16 03:47:41,606] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a1794/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a1794/checkm_input OceanDNA-a1794/checkm_result
[2023-03-16 03:48:00,378] [INFO] Task succeeded: CheckM
[2023-03-16 03:48:00,378] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 84.72%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 03:48:00,379] [INFO] ===== Completeness check finished =====
[2023-03-16 03:48:00,380] [INFO] ===== Start GTDB Search =====
[2023-03-16 03:48:00,380] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a1794/markers.fasta)
[2023-03-16 03:48:00,380] [INFO] Task started: Blastn
[2023-03-16 03:48:00,380] [INFO] Running command: blastn -query OceanDNA-a1794/markers.fasta -db /var/lib/cwl/stg56b55597-e8d4-4816-bc76-029c3a0bbe63/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a1794/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 03:48:00,852] [INFO] Task succeeded: Blastn
[2023-03-16 03:48:00,853] [INFO] Selected 11 target genomes.
[2023-03-16 03:48:00,853] [INFO] Target genome list was writen to OceanDNA-a1794/target_genomes_gtdb.txt
[2023-03-16 03:48:00,891] [INFO] Task started: fastANI
[2023-03-16 03:48:00,892] [INFO] Running command: fastANI --query /var/lib/cwl/stgec7173ea-38d8-4b86-884d-2271c96d3229/OceanDNA-a1794.fa --refList OceanDNA-a1794/target_genomes_gtdb.txt --output OceanDNA-a1794/fastani_result_gtdb.tsv --threads 1
[2023-03-16 03:48:03,723] [INFO] Task succeeded: fastANI
[2023-03-16 03:48:03,726] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 03:48:03,726] [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_002509225.1	s__UBA102 sp002509225	94.206	231	266	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__MGIII;f__CG-Epi1;g__UBA102	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001875425.1	s__UBA102 sp001875425	88.0769	213	266	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__MGIII;f__CG-Epi1;g__UBA102	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 03:48:03,726] [INFO] GTDB search result was written to OceanDNA-a1794/result_gtdb.tsv
[2023-03-16 03:48:03,727] [INFO] ===== GTDB Search completed =====
[2023-03-16 03:48:03,727] [INFO] DFAST_QC result json was written to OceanDNA-a1794/dqc_result.json
[2023-03-16 03:48:03,727] [INFO] DFAST_QC completed!
[2023-03-16 03:48:03,727] [INFO] Total running time: 0h0m31s