[2023-03-18 00:35:04,592] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:35:04,592] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:35:04,592] [INFO] DQC Reference Directory: /var/lib/cwl/stg16996457-2ef9-4406-a768-95b201c6bd46/dqc_reference
[2023-03-18 00:35:05,671] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:35:05,672] [INFO] Task started: Prodigal
[2023-03-18 00:35:05,672] [INFO] Running command: cat /var/lib/cwl/stg1717d887-e77d-4c4d-9fc4-3b2f2d31c903/OceanDNA-b26605.fa | prodigal -d OceanDNA-b26605/cds.fna -a OceanDNA-b26605/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:35:14,903] [INFO] Task succeeded: Prodigal
[2023-03-18 00:35:14,903] [INFO] Task started: HMMsearch
[2023-03-18 00:35:14,903] [INFO] Running command: hmmsearch --tblout OceanDNA-b26605/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg16996457-2ef9-4406-a768-95b201c6bd46/dqc_reference/reference_markers.hmm OceanDNA-b26605/protein.faa > /dev/null
[2023-03-18 00:35:15,154] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:35:15,155] [INFO] Found 6/6 markers.
[2023-03-18 00:35:15,168] [INFO] Query marker FASTA was written to OceanDNA-b26605/markers.fasta
[2023-03-18 00:35:15,168] [INFO] Task started: Blastn
[2023-03-18 00:35:15,168] [INFO] Running command: blastn -query OceanDNA-b26605/markers.fasta -db /var/lib/cwl/stg16996457-2ef9-4406-a768-95b201c6bd46/dqc_reference/reference_markers.fasta -out OceanDNA-b26605/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:35:15,759] [INFO] Task succeeded: Blastn
[2023-03-18 00:35:15,760] [INFO] Selected 30 target genomes.
[2023-03-18 00:35:15,760] [INFO] Target genome list was writen to OceanDNA-b26605/target_genomes.txt
[2023-03-18 00:35:15,775] [INFO] Task started: fastANI
[2023-03-18 00:35:15,775] [INFO] Running command: fastANI --query /var/lib/cwl/stg1717d887-e77d-4c4d-9fc4-3b2f2d31c903/OceanDNA-b26605.fa --refList OceanDNA-b26605/target_genomes.txt --output OceanDNA-b26605/fastani_result.tsv --threads 1
[2023-03-18 00:35:33,704] [INFO] Task succeeded: fastANI
[2023-03-18 00:35:33,704] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg16996457-2ef9-4406-a768-95b201c6bd46/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:35:33,705] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg16996457-2ef9-4406-a768-95b201c6bd46/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:35:33,705] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 00:35:33,705] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 00:35:33,705] [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
--------------------------------------------------------------------------------
[2023-03-18 00:35:33,705] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26605/tc_result.tsv
[2023-03-18 00:35:33,705] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:35:33,705] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:35:33,705] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg16996457-2ef9-4406-a768-95b201c6bd46/dqc_reference/checkm_data
[2023-03-18 00:35:33,708] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:35:33,712] [INFO] Task started: CheckM
[2023-03-18 00:35:33,712] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26605/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26605/checkm_input OceanDNA-b26605/checkm_result
[2023-03-18 00:36:02,007] [INFO] Task succeeded: CheckM
[2023-03-18 00:36:02,008] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 00:36:02,009] [INFO] ===== Completeness check finished =====
[2023-03-18 00:36:02,010] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:36:02,010] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26605/markers.fasta)
[2023-03-18 00:36:02,010] [INFO] Task started: Blastn
[2023-03-18 00:36:02,010] [INFO] Running command: blastn -query OceanDNA-b26605/markers.fasta -db /var/lib/cwl/stg16996457-2ef9-4406-a768-95b201c6bd46/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26605/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:36:03,027] [INFO] Task succeeded: Blastn
[2023-03-18 00:36:03,028] [INFO] Selected 14 target genomes.
[2023-03-18 00:36:03,028] [INFO] Target genome list was writen to OceanDNA-b26605/target_genomes_gtdb.txt
[2023-03-18 00:36:03,038] [INFO] Task started: fastANI
[2023-03-18 00:36:03,038] [INFO] Running command: fastANI --query /var/lib/cwl/stg1717d887-e77d-4c4d-9fc4-3b2f2d31c903/OceanDNA-b26605.fa --refList OceanDNA-b26605/target_genomes_gtdb.txt --output OceanDNA-b26605/fastani_result_gtdb.tsv --threads 1
[2023-03-18 00:36:07,068] [INFO] Task succeeded: fastANI
[2023-03-18 00:36:07,071] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 00:36:07,071] [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_018701255.1	s__UBA12202 sp018701255	99.3341	442	518	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__UBA1172;g__UBA12202	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002691725.1	s__UBA12202 sp002691725	78.7859	282	518	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__UBA1172;g__UBA12202	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016778985.1	s__UBA12202 sp016778985	78.7697	318	518	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__UBA1172;g__UBA12202	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011522975.1	s__UBA1172 sp011522975	75.9909	58	518	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__UBA1172;g__UBA1172	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 00:36:07,071] [INFO] GTDB search result was written to OceanDNA-b26605/result_gtdb.tsv
[2023-03-18 00:36:07,071] [INFO] ===== GTDB Search completed =====
[2023-03-18 00:36:07,072] [INFO] DFAST_QC result json was written to OceanDNA-b26605/dqc_result.json
[2023-03-18 00:36:07,072] [INFO] DFAST_QC completed!
[2023-03-18 00:36:07,072] [INFO] Total running time: 0h1m2s