[2023-03-16 20:47:10,546] [INFO] DFAST_QC pipeline started.
[2023-03-16 20:47:10,547] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 20:47:10,547] [INFO] DQC Reference Directory: /var/lib/cwl/stgd783cc83-db2f-4f2b-b449-354a18c5e805/dqc_reference
[2023-03-16 20:47:11,680] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 20:47:11,680] [INFO] Task started: Prodigal
[2023-03-16 20:47:11,680] [INFO] Running command: cat /var/lib/cwl/stg485b44a3-026c-4d8a-bf81-bae7c9474fa4/OceanDNA-b43072.fa | prodigal -d OceanDNA-b43072/cds.fna -a OceanDNA-b43072/protein.faa -g 11 -q > /dev/null
[2023-03-16 20:47:13,692] [INFO] Task succeeded: Prodigal
[2023-03-16 20:47:13,692] [INFO] Task started: HMMsearch
[2023-03-16 20:47:13,692] [INFO] Running command: hmmsearch --tblout OceanDNA-b43072/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd783cc83-db2f-4f2b-b449-354a18c5e805/dqc_reference/reference_markers.hmm OceanDNA-b43072/protein.faa > /dev/null
[2023-03-16 20:47:13,825] [INFO] Task succeeded: HMMsearch
[2023-03-16 20:47:13,826] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg485b44a3-026c-4d8a-bf81-bae7c9474fa4/OceanDNA-b43072.fa]
[2023-03-16 20:47:13,832] [INFO] Query marker FASTA was written to OceanDNA-b43072/markers.fasta
[2023-03-16 20:47:13,857] [INFO] Task started: Blastn
[2023-03-16 20:47:13,857] [INFO] Running command: blastn -query OceanDNA-b43072/markers.fasta -db /var/lib/cwl/stgd783cc83-db2f-4f2b-b449-354a18c5e805/dqc_reference/reference_markers.fasta -out OceanDNA-b43072/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 20:47:14,295] [INFO] Task succeeded: Blastn
[2023-03-16 20:47:14,296] [INFO] Selected 10 target genomes.
[2023-03-16 20:47:14,296] [INFO] Target genome list was writen to OceanDNA-b43072/target_genomes.txt
[2023-03-16 20:47:14,302] [INFO] Task started: fastANI
[2023-03-16 20:47:14,302] [INFO] Running command: fastANI --query /var/lib/cwl/stg485b44a3-026c-4d8a-bf81-bae7c9474fa4/OceanDNA-b43072.fa --refList OceanDNA-b43072/target_genomes.txt --output OceanDNA-b43072/fastani_result.tsv --threads 1
[2023-03-16 20:47:18,285] [INFO] Task succeeded: fastANI
[2023-03-16 20:47:18,285] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd783cc83-db2f-4f2b-b449-354a18c5e805/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 20:47:18,286] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd783cc83-db2f-4f2b-b449-354a18c5e805/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 20:47:18,286] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 20:47:18,286] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 20:47:18,286] [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 20:47:18,286] [INFO] DFAST Taxonomy check result was written to OceanDNA-b43072/tc_result.tsv
[2023-03-16 20:47:18,286] [INFO] ===== Taxonomy check completed =====
[2023-03-16 20:47:18,286] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 20:47:18,286] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd783cc83-db2f-4f2b-b449-354a18c5e805/dqc_reference/checkm_data
[2023-03-16 20:47:18,289] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 20:47:18,292] [INFO] Task started: CheckM
[2023-03-16 20:47:18,292] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b43072/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b43072/checkm_input OceanDNA-b43072/checkm_result
[2023-03-16 20:47:30,505] [INFO] Task succeeded: CheckM
[2023-03-16 20:47:30,505] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 65.88%
Contamintation: 10.80%
Strain heterogeneity: 75.00%
--------------------------------------------------------------------------------
[2023-03-16 20:47:30,507] [INFO] ===== Completeness check finished =====
[2023-03-16 20:47:30,507] [INFO] ===== Start GTDB Search =====
[2023-03-16 20:47:30,507] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b43072/markers.fasta)
[2023-03-16 20:47:30,507] [INFO] Task started: Blastn
[2023-03-16 20:47:30,507] [INFO] Running command: blastn -query OceanDNA-b43072/markers.fasta -db /var/lib/cwl/stgd783cc83-db2f-4f2b-b449-354a18c5e805/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b43072/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 20:47:30,928] [INFO] Task succeeded: Blastn
[2023-03-16 20:47:30,929] [INFO] Selected 12 target genomes.
[2023-03-16 20:47:30,929] [INFO] Target genome list was writen to OceanDNA-b43072/target_genomes_gtdb.txt
[2023-03-16 20:47:30,957] [INFO] Task started: fastANI
[2023-03-16 20:47:30,957] [INFO] Running command: fastANI --query /var/lib/cwl/stg485b44a3-026c-4d8a-bf81-bae7c9474fa4/OceanDNA-b43072.fa --refList OceanDNA-b43072/target_genomes_gtdb.txt --output OceanDNA-b43072/fastani_result_gtdb.tsv --threads 1
[2023-03-16 20:47:33,826] [INFO] Task succeeded: fastANI
[2023-03-16 20:47:33,828] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 20:47:33,828] [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_902606745.1	s__Pseudothioglobus sp902606745	90.6423	55	75	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 20:47:33,828] [INFO] GTDB search result was written to OceanDNA-b43072/result_gtdb.tsv
[2023-03-16 20:47:33,828] [INFO] ===== GTDB Search completed =====
[2023-03-16 20:47:33,829] [INFO] DFAST_QC result json was written to OceanDNA-b43072/dqc_result.json
[2023-03-16 20:47:33,829] [INFO] DFAST_QC completed!
[2023-03-16 20:47:33,829] [INFO] Total running time: 0h0m23s