[2023-03-18 09:41:09,185] [INFO] DFAST_QC pipeline started.
[2023-03-18 09:41:09,185] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 09:41:09,185] [INFO] DQC Reference Directory: /var/lib/cwl/stgbd2755cc-b860-4dea-9bbb-ea0ceaefe4c9/dqc_reference
[2023-03-18 09:41:10,436] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 09:41:10,436] [INFO] Task started: Prodigal
[2023-03-18 09:41:10,436] [INFO] Running command: cat /var/lib/cwl/stg9ae9f3d0-3b1b-44c3-82cc-b6fce2c6abb6/OceanDNA-b40202.fa | prodigal -d OceanDNA-b40202/cds.fna -a OceanDNA-b40202/protein.faa -g 11 -q > /dev/null
[2023-03-18 09:41:15,949] [INFO] Task succeeded: Prodigal
[2023-03-18 09:41:15,949] [INFO] Task started: HMMsearch
[2023-03-18 09:41:15,949] [INFO] Running command: hmmsearch --tblout OceanDNA-b40202/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbd2755cc-b860-4dea-9bbb-ea0ceaefe4c9/dqc_reference/reference_markers.hmm OceanDNA-b40202/protein.faa > /dev/null
[2023-03-18 09:41:16,122] [INFO] Task succeeded: HMMsearch
[2023-03-18 09:41:16,122] [INFO] Found 6/6 markers.
[2023-03-18 09:41:16,132] [INFO] Query marker FASTA was written to OceanDNA-b40202/markers.fasta
[2023-03-18 09:41:16,132] [INFO] Task started: Blastn
[2023-03-18 09:41:16,132] [INFO] Running command: blastn -query OceanDNA-b40202/markers.fasta -db /var/lib/cwl/stgbd2755cc-b860-4dea-9bbb-ea0ceaefe4c9/dqc_reference/reference_markers.fasta -out OceanDNA-b40202/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:41:16,651] [INFO] Task succeeded: Blastn
[2023-03-18 09:41:16,651] [INFO] Selected 24 target genomes.
[2023-03-18 09:41:16,652] [INFO] Target genome list was writen to OceanDNA-b40202/target_genomes.txt
[2023-03-18 09:41:16,665] [INFO] Task started: fastANI
[2023-03-18 09:41:16,665] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ae9f3d0-3b1b-44c3-82cc-b6fce2c6abb6/OceanDNA-b40202.fa --refList OceanDNA-b40202/target_genomes.txt --output OceanDNA-b40202/fastani_result.tsv --threads 1
[2023-03-18 09:41:29,795] [INFO] Task succeeded: fastANI
[2023-03-18 09:41:29,796] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbd2755cc-b860-4dea-9bbb-ea0ceaefe4c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 09:41:29,796] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbd2755cc-b860-4dea-9bbb-ea0ceaefe4c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 09:41:29,796] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 09:41:29,796] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 09:41:29,796] [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 09:41:29,796] [INFO] DFAST Taxonomy check result was written to OceanDNA-b40202/tc_result.tsv
[2023-03-18 09:41:29,796] [INFO] ===== Taxonomy check completed =====
[2023-03-18 09:41:29,796] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 09:41:29,797] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbd2755cc-b860-4dea-9bbb-ea0ceaefe4c9/dqc_reference/checkm_data
[2023-03-18 09:41:29,799] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 09:41:29,802] [INFO] Task started: CheckM
[2023-03-18 09:41:29,802] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b40202/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b40202/checkm_input OceanDNA-b40202/checkm_result
[2023-03-18 09:41:49,385] [INFO] Task succeeded: CheckM
[2023-03-18 09:41:49,385] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.19%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 09:41:49,387] [INFO] ===== Completeness check finished =====
[2023-03-18 09:41:49,387] [INFO] ===== Start GTDB Search =====
[2023-03-18 09:41:49,387] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b40202/markers.fasta)
[2023-03-18 09:41:49,387] [INFO] Task started: Blastn
[2023-03-18 09:41:49,387] [INFO] Running command: blastn -query OceanDNA-b40202/markers.fasta -db /var/lib/cwl/stgbd2755cc-b860-4dea-9bbb-ea0ceaefe4c9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b40202/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:41:50,115] [INFO] Task succeeded: Blastn
[2023-03-18 09:41:50,116] [INFO] Selected 8 target genomes.
[2023-03-18 09:41:50,116] [INFO] Target genome list was writen to OceanDNA-b40202/target_genomes_gtdb.txt
[2023-03-18 09:41:50,144] [INFO] Task started: fastANI
[2023-03-18 09:41:50,144] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ae9f3d0-3b1b-44c3-82cc-b6fce2c6abb6/OceanDNA-b40202.fa --refList OceanDNA-b40202/target_genomes_gtdb.txt --output OceanDNA-b40202/fastani_result_gtdb.tsv --threads 1
[2023-03-18 09:41:53,248] [INFO] Task succeeded: fastANI
[2023-03-18 09:41:53,253] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 09:41:53,253] [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_002689135.1	s__TMED48 sp002689135	99.6467	267	337	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__TMED48	95.0	99.93	99.93	0.80	0.80	2	conclusive
GCA_002731695.1	s__TMED48 sp002731695	83.4668	266	337	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__TMED48	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002691825.1	s__TMED48 sp002691825	83.2322	239	337	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__TMED48	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002338445.1	s__TMED48 sp002338445	81.7307	283	337	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__TMED48	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002720735.1	s__TMED48 sp002720735	81.2262	259	337	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__TMED48	95.0	97.48	96.80	0.75	0.75	3	-
GCA_902562425.1	s__TMED48 sp902562425	81.0957	259	337	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__TMED48	95.0	99.92	99.92	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2023-03-18 09:41:53,253] [INFO] GTDB search result was written to OceanDNA-b40202/result_gtdb.tsv
[2023-03-18 09:41:53,253] [INFO] ===== GTDB Search completed =====
[2023-03-18 09:41:53,254] [INFO] DFAST_QC result json was written to OceanDNA-b40202/dqc_result.json
[2023-03-18 09:41:53,254] [INFO] DFAST_QC completed!
[2023-03-18 09:41:53,254] [INFO] Total running time: 0h0m44s