[2023-03-19 04:29:37,740] [INFO] DFAST_QC pipeline started.
[2023-03-19 04:29:37,740] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 04:29:37,741] [INFO] DQC Reference Directory: /var/lib/cwl/stg8ac7a6dc-663e-4568-a6f2-20a673cc03cb/dqc_reference
[2023-03-19 04:29:38,863] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 04:29:38,863] [INFO] Task started: Prodigal
[2023-03-19 04:29:38,864] [INFO] Running command: cat /var/lib/cwl/stg1b4d0393-1160-4aaa-a16c-353b98a977ee/OceanDNA-b19813.fa | prodigal -d OceanDNA-b19813/cds.fna -a OceanDNA-b19813/protein.faa -g 11 -q > /dev/null
[2023-03-19 04:29:47,100] [INFO] Task succeeded: Prodigal
[2023-03-19 04:29:47,100] [INFO] Task started: HMMsearch
[2023-03-19 04:29:47,100] [INFO] Running command: hmmsearch --tblout OceanDNA-b19813/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8ac7a6dc-663e-4568-a6f2-20a673cc03cb/dqc_reference/reference_markers.hmm OceanDNA-b19813/protein.faa > /dev/null
[2023-03-19 04:29:47,267] [INFO] Task succeeded: HMMsearch
[2023-03-19 04:29:47,268] [INFO] Found 6/6 markers.
[2023-03-19 04:29:47,283] [INFO] Query marker FASTA was written to OceanDNA-b19813/markers.fasta
[2023-03-19 04:29:47,283] [INFO] Task started: Blastn
[2023-03-19 04:29:47,283] [INFO] Running command: blastn -query OceanDNA-b19813/markers.fasta -db /var/lib/cwl/stg8ac7a6dc-663e-4568-a6f2-20a673cc03cb/dqc_reference/reference_markers.fasta -out OceanDNA-b19813/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:29:47,783] [INFO] Task succeeded: Blastn
[2023-03-19 04:29:47,783] [INFO] Selected 16 target genomes.
[2023-03-19 04:29:47,784] [INFO] Target genome list was writen to OceanDNA-b19813/target_genomes.txt
[2023-03-19 04:29:47,792] [INFO] Task started: fastANI
[2023-03-19 04:29:47,793] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b4d0393-1160-4aaa-a16c-353b98a977ee/OceanDNA-b19813.fa --refList OceanDNA-b19813/target_genomes.txt --output OceanDNA-b19813/fastani_result.tsv --threads 1
[2023-03-19 04:29:54,200] [INFO] Task succeeded: fastANI
[2023-03-19 04:29:54,200] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8ac7a6dc-663e-4568-a6f2-20a673cc03cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 04:29:54,200] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8ac7a6dc-663e-4568-a6f2-20a673cc03cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 04:29:54,201] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 04:29:54,201] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 04:29:54,201] [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
--------------------------------------------------------------------------------
[2023-03-19 04:29:54,201] [INFO] DFAST Taxonomy check result was written to OceanDNA-b19813/tc_result.tsv
[2023-03-19 04:29:54,201] [INFO] ===== Taxonomy check completed =====
[2023-03-19 04:29:54,201] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 04:29:54,201] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8ac7a6dc-663e-4568-a6f2-20a673cc03cb/dqc_reference/checkm_data
[2023-03-19 04:29:54,204] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 04:29:54,207] [INFO] Task started: CheckM
[2023-03-19 04:29:54,207] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b19813/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b19813/checkm_input OceanDNA-b19813/checkm_result
[2023-03-19 04:30:19,560] [INFO] Task succeeded: CheckM
[2023-03-19 04:30:19,560] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.44%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-19 04:30:19,562] [INFO] ===== Completeness check finished =====
[2023-03-19 04:30:19,562] [INFO] ===== Start GTDB Search =====
[2023-03-19 04:30:19,562] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b19813/markers.fasta)
[2023-03-19 04:30:19,562] [INFO] Task started: Blastn
[2023-03-19 04:30:19,562] [INFO] Running command: blastn -query OceanDNA-b19813/markers.fasta -db /var/lib/cwl/stg8ac7a6dc-663e-4568-a6f2-20a673cc03cb/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b19813/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:30:20,289] [INFO] Task succeeded: Blastn
[2023-03-19 04:30:20,290] [INFO] Selected 25 target genomes.
[2023-03-19 04:30:20,290] [INFO] Target genome list was writen to OceanDNA-b19813/target_genomes_gtdb.txt
[2023-03-19 04:30:20,380] [INFO] Task started: fastANI
[2023-03-19 04:30:20,381] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b4d0393-1160-4aaa-a16c-353b98a977ee/OceanDNA-b19813.fa --refList OceanDNA-b19813/target_genomes_gtdb.txt --output OceanDNA-b19813/fastani_result_gtdb.tsv --threads 1
[2023-03-19 04:30:27,927] [INFO] Task succeeded: fastANI
[2023-03-19 04:30:27,929] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 04:30:27,929] [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_002167345.2	s__CACEUX01 sp002167345	76.0908	57	536	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA1611;g__CACEUX01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 04:30:27,929] [INFO] GTDB search result was written to OceanDNA-b19813/result_gtdb.tsv
[2023-03-19 04:30:27,930] [INFO] ===== GTDB Search completed =====
[2023-03-19 04:30:27,930] [INFO] DFAST_QC result json was written to OceanDNA-b19813/dqc_result.json
[2023-03-19 04:30:27,930] [INFO] DFAST_QC completed!
[2023-03-19 04:30:27,930] [INFO] Total running time: 0h0m50s