[2023-06-04 17:43:46,353] [INFO] DFAST_QC pipeline started.
[2023-06-04 17:43:46,359] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 17:43:46,359] [INFO] DQC Reference Directory: /var/lib/cwl/stgeb97146d-e6d4-4ba3-ab13-cdf2754b9ca8/dqc_reference
[2023-06-04 17:43:48,149] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 17:43:48,149] [INFO] Task started: Prodigal
[2023-06-04 17:43:48,150] [INFO] Running command: gunzip -c /var/lib/cwl/stg3410b803-ce30-49da-b7fa-731319ac02fa/GCA_902617595.1_AG-919-N16_genomic.fna.gz | prodigal -d GCA_902617595.1_AG-919-N16_genomic.fna/cds.fna -a GCA_902617595.1_AG-919-N16_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 17:43:50,760] [INFO] Task succeeded: Prodigal
[2023-06-04 17:43:50,760] [INFO] Task started: HMMsearch
[2023-06-04 17:43:50,760] [INFO] Running command: hmmsearch --tblout GCA_902617595.1_AG-919-N16_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeb97146d-e6d4-4ba3-ab13-cdf2754b9ca8/dqc_reference/reference_markers.hmm GCA_902617595.1_AG-919-N16_genomic.fna/protein.faa > /dev/null
[2023-06-04 17:43:50,986] [INFO] Task succeeded: HMMsearch
[2023-06-04 17:43:50,988] [INFO] Found 6/6 markers.
[2023-06-04 17:43:51,011] [INFO] Query marker FASTA was written to GCA_902617595.1_AG-919-N16_genomic.fna/markers.fasta
[2023-06-04 17:43:51,011] [INFO] Task started: Blastn
[2023-06-04 17:43:51,011] [INFO] Running command: blastn -query GCA_902617595.1_AG-919-N16_genomic.fna/markers.fasta -db /var/lib/cwl/stgeb97146d-e6d4-4ba3-ab13-cdf2754b9ca8/dqc_reference/reference_markers.fasta -out GCA_902617595.1_AG-919-N16_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 17:43:51,665] [INFO] Task succeeded: Blastn
[2023-06-04 17:43:51,669] [INFO] Selected 15 target genomes.
[2023-06-04 17:43:51,670] [INFO] Target genome list was writen to GCA_902617595.1_AG-919-N16_genomic.fna/target_genomes.txt
[2023-06-04 17:43:52,056] [INFO] Task started: fastANI
[2023-06-04 17:43:52,056] [INFO] Running command: fastANI --query /var/lib/cwl/stg3410b803-ce30-49da-b7fa-731319ac02fa/GCA_902617595.1_AG-919-N16_genomic.fna.gz --refList GCA_902617595.1_AG-919-N16_genomic.fna/target_genomes.txt --output GCA_902617595.1_AG-919-N16_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 17:43:59,361] [INFO] Task succeeded: fastANI
[2023-06-04 17:43:59,362] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeb97146d-e6d4-4ba3-ab13-cdf2754b9ca8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 17:43:59,362] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeb97146d-e6d4-4ba3-ab13-cdf2754b9ca8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 17:43:59,364] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 17:43:59,364] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-04 17:43:59,364] [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
--------------------------------------------------------------------------------
[2023-06-04 17:43:59,367] [INFO] DFAST Taxonomy check result was written to GCA_902617595.1_AG-919-N16_genomic.fna/tc_result.tsv
[2023-06-04 17:43:59,368] [INFO] ===== Taxonomy check completed =====
[2023-06-04 17:43:59,368] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 17:43:59,368] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeb97146d-e6d4-4ba3-ab13-cdf2754b9ca8/dqc_reference/checkm_data
[2023-06-04 17:43:59,371] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 17:43:59,410] [INFO] Task started: CheckM
[2023-06-04 17:43:59,410] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902617595.1_AG-919-N16_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902617595.1_AG-919-N16_genomic.fna/checkm_input GCA_902617595.1_AG-919-N16_genomic.fna/checkm_result
[2023-06-04 17:44:16,046] [INFO] Task succeeded: CheckM
[2023-06-04 17:44:16,047] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 45.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 17:44:16,068] [INFO] ===== Completeness check finished =====
[2023-06-04 17:44:16,069] [INFO] ===== Start GTDB Search =====
[2023-06-04 17:44:16,069] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902617595.1_AG-919-N16_genomic.fna/markers.fasta)
[2023-06-04 17:44:16,070] [INFO] Task started: Blastn
[2023-06-04 17:44:16,070] [INFO] Running command: blastn -query GCA_902617595.1_AG-919-N16_genomic.fna/markers.fasta -db /var/lib/cwl/stgeb97146d-e6d4-4ba3-ab13-cdf2754b9ca8/dqc_reference/reference_markers_gtdb.fasta -out GCA_902617595.1_AG-919-N16_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 17:44:16,875] [INFO] Task succeeded: Blastn
[2023-06-04 17:44:16,880] [INFO] Selected 16 target genomes.
[2023-06-04 17:44:16,880] [INFO] Target genome list was writen to GCA_902617595.1_AG-919-N16_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 17:44:17,237] [INFO] Task started: fastANI
[2023-06-04 17:44:17,237] [INFO] Running command: fastANI --query /var/lib/cwl/stg3410b803-ce30-49da-b7fa-731319ac02fa/GCA_902617595.1_AG-919-N16_genomic.fna.gz --refList GCA_902617595.1_AG-919-N16_genomic.fna/target_genomes_gtdb.txt --output GCA_902617595.1_AG-919-N16_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 17:44:21,659] [INFO] Task succeeded: fastANI
[2023-06-04 17:44:21,667] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 17:44:21,667] [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_902612965.1	s__GCA-002684695 sp902612965	96.3842	374	475	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__GCA-002684695;g__GCA-002684695	95.0	96.38	96.38	0.79	0.79	2	conclusive
GCA_902539295.1	s__GCA-002684695 sp902539295	93.2947	327	475	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__GCA-002684695;g__GCA-002684695	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002684695.1	s__GCA-002684695 sp002684695	77.2962	131	475	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__GCA-002684695;g__GCA-002684695	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902532475.1	s__GCA-002684695 sp902532475	77.1353	83	475	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__GCA-002684695;g__GCA-002684695	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-04 17:44:21,669] [INFO] GTDB search result was written to GCA_902617595.1_AG-919-N16_genomic.fna/result_gtdb.tsv
[2023-06-04 17:44:21,670] [INFO] ===== GTDB Search completed =====
[2023-06-04 17:44:21,672] [INFO] DFAST_QC result json was written to GCA_902617595.1_AG-919-N16_genomic.fna/dqc_result.json
[2023-06-04 17:44:21,672] [INFO] DFAST_QC completed!
[2023-06-04 17:44:21,672] [INFO] Total running time: 0h0m35s