[2023-03-15 21:24:36,533] [INFO] DFAST_QC pipeline started.
[2023-03-15 21:24:36,533] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 21:24:36,533] [INFO] DQC Reference Directory: /var/lib/cwl/stg619ca3a0-7a11-404f-9925-1e8b6bedad1e/dqc_reference
[2023-03-15 21:24:37,638] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 21:24:37,638] [INFO] Task started: Prodigal
[2023-03-15 21:24:37,638] [INFO] Running command: cat /var/lib/cwl/stg93052573-7c19-48a7-b811-3957daf00210/OceanDNA-b43636.fa | prodigal -d OceanDNA-b43636/cds.fna -a OceanDNA-b43636/protein.faa -g 11 -q > /dev/null
[2023-03-15 21:24:49,444] [INFO] Task succeeded: Prodigal
[2023-03-15 21:24:49,444] [INFO] Task started: HMMsearch
[2023-03-15 21:24:49,444] [INFO] Running command: hmmsearch --tblout OceanDNA-b43636/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg619ca3a0-7a11-404f-9925-1e8b6bedad1e/dqc_reference/reference_markers.hmm OceanDNA-b43636/protein.faa > /dev/null
[2023-03-15 21:24:49,642] [INFO] Task succeeded: HMMsearch
[2023-03-15 21:24:49,643] [INFO] Found 6/6 markers.
[2023-03-15 21:24:49,660] [INFO] Query marker FASTA was written to OceanDNA-b43636/markers.fasta
[2023-03-15 21:24:49,660] [INFO] Task started: Blastn
[2023-03-15 21:24:49,660] [INFO] Running command: blastn -query OceanDNA-b43636/markers.fasta -db /var/lib/cwl/stg619ca3a0-7a11-404f-9925-1e8b6bedad1e/dqc_reference/reference_markers.fasta -out OceanDNA-b43636/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:24:50,177] [INFO] Task succeeded: Blastn
[2023-03-15 21:24:50,177] [INFO] Selected 25 target genomes.
[2023-03-15 21:24:50,178] [INFO] Target genome list was writen to OceanDNA-b43636/target_genomes.txt
[2023-03-15 21:24:50,192] [INFO] Task started: fastANI
[2023-03-15 21:24:50,192] [INFO] Running command: fastANI --query /var/lib/cwl/stg93052573-7c19-48a7-b811-3957daf00210/OceanDNA-b43636.fa --refList OceanDNA-b43636/target_genomes.txt --output OceanDNA-b43636/fastani_result.tsv --threads 1
[2023-03-15 21:25:04,721] [INFO] Task succeeded: fastANI
[2023-03-15 21:25:04,721] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg619ca3a0-7a11-404f-9925-1e8b6bedad1e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 21:25:04,721] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg619ca3a0-7a11-404f-9925-1e8b6bedad1e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 21:25:04,721] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 21:25:04,721] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 21:25:04,721] [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
--------------------------------------------------------------------------------
[2023-03-15 21:25:04,722] [INFO] DFAST Taxonomy check result was written to OceanDNA-b43636/tc_result.tsv
[2023-03-15 21:25:04,722] [INFO] ===== Taxonomy check completed =====
[2023-03-15 21:25:04,722] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 21:25:04,722] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg619ca3a0-7a11-404f-9925-1e8b6bedad1e/dqc_reference/checkm_data
[2023-03-15 21:25:04,725] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 21:25:04,728] [INFO] Task started: CheckM
[2023-03-15 21:25:04,728] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b43636/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b43636/checkm_input OceanDNA-b43636/checkm_result
[2023-03-15 21:25:38,418] [INFO] Task succeeded: CheckM
[2023-03-15 21:25:38,418] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.74%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 21:25:38,516] [INFO] ===== Completeness check finished =====
[2023-03-15 21:25:38,516] [INFO] ===== Start GTDB Search =====
[2023-03-15 21:25:38,517] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b43636/markers.fasta)
[2023-03-15 21:25:38,518] [INFO] Task started: Blastn
[2023-03-15 21:25:38,518] [INFO] Running command: blastn -query OceanDNA-b43636/markers.fasta -db /var/lib/cwl/stg619ca3a0-7a11-404f-9925-1e8b6bedad1e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b43636/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:25:39,221] [INFO] Task succeeded: Blastn
[2023-03-15 21:25:39,222] [INFO] Selected 23 target genomes.
[2023-03-15 21:25:39,222] [INFO] Target genome list was writen to OceanDNA-b43636/target_genomes_gtdb.txt
[2023-03-15 21:25:39,451] [INFO] Task started: fastANI
[2023-03-15 21:25:39,451] [INFO] Running command: fastANI --query /var/lib/cwl/stg93052573-7c19-48a7-b811-3957daf00210/OceanDNA-b43636.fa --refList OceanDNA-b43636/target_genomes_gtdb.txt --output OceanDNA-b43636/fastani_result_gtdb.tsv --threads 1
[2023-03-15 21:25:51,867] [INFO] Task succeeded: fastANI
[2023-03-15 21:25:51,870] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 21:25:51,870] [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_002714255.1	s__UBA11791 sp002714255	89.7144	361	613	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Arenicellales;f__UBA868;g__UBA11791	95.0	98.20	98.17	0.64	0.59	4	-
GCA_012960345.1	s__UBA11791 sp012960345	88.6849	504	613	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Arenicellales;f__UBA868;g__UBA11791	95.0	99.31	99.31	0.83	0.83	2	-
GCA_905612355.1	s__UBA11791 sp905612355	87.7642	301	613	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Arenicellales;f__UBA868;g__UBA11791	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 21:25:51,870] [INFO] GTDB search result was written to OceanDNA-b43636/result_gtdb.tsv
[2023-03-15 21:25:51,870] [INFO] ===== GTDB Search completed =====
[2023-03-15 21:25:51,871] [INFO] DFAST_QC result json was written to OceanDNA-b43636/dqc_result.json
[2023-03-15 21:25:51,871] [INFO] DFAST_QC completed!
[2023-03-15 21:25:51,871] [INFO] Total running time: 0h1m15s