[2023-03-16 07:15:38,893] [INFO] DFAST_QC pipeline started.
[2023-03-16 07:15:38,893] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 07:15:38,893] [INFO] DQC Reference Directory: /var/lib/cwl/stg2e8f3348-90e7-40b5-9d30-8db8f2b0b875/dqc_reference
[2023-03-16 07:15:39,968] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 07:15:39,969] [INFO] Task started: Prodigal
[2023-03-16 07:15:39,969] [INFO] Running command: cat /var/lib/cwl/stgda57eb8b-236d-4237-a726-c101bd359555/OceanDNA-b35873.fa | prodigal -d OceanDNA-b35873/cds.fna -a OceanDNA-b35873/protein.faa -g 11 -q > /dev/null
[2023-03-16 07:15:45,903] [INFO] Task succeeded: Prodigal
[2023-03-16 07:15:45,903] [INFO] Task started: HMMsearch
[2023-03-16 07:15:45,903] [INFO] Running command: hmmsearch --tblout OceanDNA-b35873/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2e8f3348-90e7-40b5-9d30-8db8f2b0b875/dqc_reference/reference_markers.hmm OceanDNA-b35873/protein.faa > /dev/null
[2023-03-16 07:15:46,075] [INFO] Task succeeded: HMMsearch
[2023-03-16 07:15:46,076] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgda57eb8b-236d-4237-a726-c101bd359555/OceanDNA-b35873.fa]
[2023-03-16 07:15:46,088] [INFO] Query marker FASTA was written to OceanDNA-b35873/markers.fasta
[2023-03-16 07:15:46,089] [INFO] Task started: Blastn
[2023-03-16 07:15:46,089] [INFO] Running command: blastn -query OceanDNA-b35873/markers.fasta -db /var/lib/cwl/stg2e8f3348-90e7-40b5-9d30-8db8f2b0b875/dqc_reference/reference_markers.fasta -out OceanDNA-b35873/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:15:46,640] [INFO] Task succeeded: Blastn
[2023-03-16 07:15:46,641] [INFO] Selected 21 target genomes.
[2023-03-16 07:15:46,642] [INFO] Target genome list was writen to OceanDNA-b35873/target_genomes.txt
[2023-03-16 07:15:46,655] [INFO] Task started: fastANI
[2023-03-16 07:15:46,655] [INFO] Running command: fastANI --query /var/lib/cwl/stgda57eb8b-236d-4237-a726-c101bd359555/OceanDNA-b35873.fa --refList OceanDNA-b35873/target_genomes.txt --output OceanDNA-b35873/fastani_result.tsv --threads 1
[2023-03-16 07:15:55,263] [INFO] Task succeeded: fastANI
[2023-03-16 07:15:55,264] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2e8f3348-90e7-40b5-9d30-8db8f2b0b875/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 07:15:55,264] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2e8f3348-90e7-40b5-9d30-8db8f2b0b875/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 07:15:55,264] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 07:15:55,264] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 07:15:55,264] [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 07:15:55,265] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35873/tc_result.tsv
[2023-03-16 07:15:55,265] [INFO] ===== Taxonomy check completed =====
[2023-03-16 07:15:55,265] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 07:15:55,265] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2e8f3348-90e7-40b5-9d30-8db8f2b0b875/dqc_reference/checkm_data
[2023-03-16 07:15:55,267] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 07:15:55,271] [INFO] Task started: CheckM
[2023-03-16 07:15:55,271] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35873/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35873/checkm_input OceanDNA-b35873/checkm_result
[2023-03-16 07:16:15,750] [INFO] Task succeeded: CheckM
[2023-03-16 07:16:15,751] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 67.13%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 07:16:15,753] [INFO] ===== Completeness check finished =====
[2023-03-16 07:16:15,753] [INFO] ===== Start GTDB Search =====
[2023-03-16 07:16:15,753] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35873/markers.fasta)
[2023-03-16 07:16:15,754] [INFO] Task started: Blastn
[2023-03-16 07:16:15,754] [INFO] Running command: blastn -query OceanDNA-b35873/markers.fasta -db /var/lib/cwl/stg2e8f3348-90e7-40b5-9d30-8db8f2b0b875/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35873/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:16:16,624] [INFO] Task succeeded: Blastn
[2023-03-16 07:16:16,626] [INFO] Selected 24 target genomes.
[2023-03-16 07:16:16,626] [INFO] Target genome list was writen to OceanDNA-b35873/target_genomes_gtdb.txt
[2023-03-16 07:16:16,669] [INFO] Task started: fastANI
[2023-03-16 07:16:16,669] [INFO] Running command: fastANI --query /var/lib/cwl/stgda57eb8b-236d-4237-a726-c101bd359555/OceanDNA-b35873.fa --refList OceanDNA-b35873/target_genomes_gtdb.txt --output OceanDNA-b35873/fastani_result_gtdb.tsv --threads 1
[2023-03-16 07:16:26,089] [INFO] Task succeeded: fastANI
[2023-03-16 07:16:26,092] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 07:16:26,092] [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_902597385.1	s__CACJXQ01 sp902597385	92.8935	262	355	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__CACJXQ01;f__CACJXQ01;g__CACJXQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902551695.1	s__CACJXQ01 sp902551695	91.5744	210	355	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__CACJXQ01;f__CACJXQ01;g__CACJXQ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 07:16:26,092] [INFO] GTDB search result was written to OceanDNA-b35873/result_gtdb.tsv
[2023-03-16 07:16:26,093] [INFO] ===== GTDB Search completed =====
[2023-03-16 07:16:26,093] [INFO] DFAST_QC result json was written to OceanDNA-b35873/dqc_result.json
[2023-03-16 07:16:26,093] [INFO] DFAST_QC completed!
[2023-03-16 07:16:26,093] [INFO] Total running time: 0h0m47s