[2023-06-16 19:20:02,010] [INFO] DFAST_QC pipeline started.
[2023-06-16 19:20:02,028] [INFO] DFAST_QC version: 0.5.7
[2023-06-16 19:20:02,028] [INFO] DQC Reference Directory: /var/lib/cwl/stg9dc6c078-c519-407d-8325-c602f6963a5e/dqc_reference
[2023-06-16 19:20:03,230] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-16 19:20:03,230] [INFO] Task started: Prodigal
[2023-06-16 19:20:03,231] [INFO] Running command: gunzip -c /var/lib/cwl/stg6befeb4f-8754-4f2f-80b1-cf8345215bae/GCA_003166315.1_20110700_S2D_genomic.fna.gz | prodigal -d GCA_003166315.1_20110700_S2D_genomic.fna/cds.fna -a GCA_003166315.1_20110700_S2D_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-16 19:20:09,191] [INFO] Task succeeded: Prodigal
[2023-06-16 19:20:09,191] [INFO] Task started: HMMsearch
[2023-06-16 19:20:09,191] [INFO] Running command: hmmsearch --tblout GCA_003166315.1_20110700_S2D_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9dc6c078-c519-407d-8325-c602f6963a5e/dqc_reference/reference_markers.hmm GCA_003166315.1_20110700_S2D_genomic.fna/protein.faa > /dev/null
[2023-06-16 19:20:09,368] [INFO] Task succeeded: HMMsearch
[2023-06-16 19:20:09,369] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg6befeb4f-8754-4f2f-80b1-cf8345215bae/GCA_003166315.1_20110700_S2D_genomic.fna.gz]
[2023-06-16 19:20:09,410] [INFO] Query marker FASTA was written to GCA_003166315.1_20110700_S2D_genomic.fna/markers.fasta
[2023-06-16 19:20:09,410] [INFO] Task started: Blastn
[2023-06-16 19:20:09,410] [INFO] Running command: blastn -query GCA_003166315.1_20110700_S2D_genomic.fna/markers.fasta -db /var/lib/cwl/stg9dc6c078-c519-407d-8325-c602f6963a5e/dqc_reference/reference_markers.fasta -out GCA_003166315.1_20110700_S2D_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 19:20:10,002] [INFO] Task succeeded: Blastn
[2023-06-16 19:20:10,005] [INFO] Selected 19 target genomes.
[2023-06-16 19:20:10,006] [INFO] Target genome list was writen to GCA_003166315.1_20110700_S2D_genomic.fna/target_genomes.txt
[2023-06-16 19:20:10,010] [INFO] Task started: fastANI
[2023-06-16 19:20:10,010] [INFO] Running command: fastANI --query /var/lib/cwl/stg6befeb4f-8754-4f2f-80b1-cf8345215bae/GCA_003166315.1_20110700_S2D_genomic.fna.gz --refList GCA_003166315.1_20110700_S2D_genomic.fna/target_genomes.txt --output GCA_003166315.1_20110700_S2D_genomic.fna/fastani_result.tsv --threads 1
[2023-06-16 19:20:20,200] [INFO] Task succeeded: fastANI
[2023-06-16 19:20:20,200] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9dc6c078-c519-407d-8325-c602f6963a5e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-16 19:20:20,200] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9dc6c078-c519-407d-8325-c602f6963a5e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-16 19:20:20,202] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-16 19:20:20,202] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-16 19:20:20,202] [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
--------------------------------------------------------------------------------
[2023-06-16 19:20:20,204] [INFO] DFAST Taxonomy check result was written to GCA_003166315.1_20110700_S2D_genomic.fna/tc_result.tsv
[2023-06-16 19:20:20,205] [INFO] ===== Taxonomy check completed =====
[2023-06-16 19:20:20,205] [INFO] ===== Start completeness check using CheckM =====
[2023-06-16 19:20:20,205] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9dc6c078-c519-407d-8325-c602f6963a5e/dqc_reference/checkm_data
[2023-06-16 19:20:20,208] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-16 19:20:20,234] [INFO] Task started: CheckM
[2023-06-16 19:20:20,234] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_003166315.1_20110700_S2D_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_003166315.1_20110700_S2D_genomic.fna/checkm_input GCA_003166315.1_20110700_S2D_genomic.fna/checkm_result
[2023-06-16 19:20:44,264] [INFO] Task succeeded: CheckM
[2023-06-16 19:20:44,265] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 1.85%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-16 19:20:44,288] [INFO] ===== Completeness check finished =====
[2023-06-16 19:20:44,288] [INFO] ===== Start GTDB Search =====
[2023-06-16 19:20:44,289] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_003166315.1_20110700_S2D_genomic.fna/markers.fasta)
[2023-06-16 19:20:44,289] [INFO] Task started: Blastn
[2023-06-16 19:20:44,289] [INFO] Running command: blastn -query GCA_003166315.1_20110700_S2D_genomic.fna/markers.fasta -db /var/lib/cwl/stg9dc6c078-c519-407d-8325-c602f6963a5e/dqc_reference/reference_markers_gtdb.fasta -out GCA_003166315.1_20110700_S2D_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 19:20:45,108] [INFO] Task succeeded: Blastn
[2023-06-16 19:20:45,116] [INFO] Selected 18 target genomes.
[2023-06-16 19:20:45,116] [INFO] Target genome list was writen to GCA_003166315.1_20110700_S2D_genomic.fna/target_genomes_gtdb.txt
[2023-06-16 19:20:45,130] [INFO] Task started: fastANI
[2023-06-16 19:20:45,131] [INFO] Running command: fastANI --query /var/lib/cwl/stg6befeb4f-8754-4f2f-80b1-cf8345215bae/GCA_003166315.1_20110700_S2D_genomic.fna.gz --refList GCA_003166315.1_20110700_S2D_genomic.fna/target_genomes_gtdb.txt --output GCA_003166315.1_20110700_S2D_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-16 19:20:53,311] [INFO] Task succeeded: fastANI
[2023-06-16 19:20:53,319] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-16 19:20:53,319] [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_003160265.1	s__Palsa-1188 sp003160265	98.3098	443	724	d__Bacteria;p__Firmicutes_B;c__Moorellia;o__Thermacetogeniales;f__Thermacetogeniaceae;g__Palsa-1188	95.0	98.52	98.46	0.80	0.80	3	conclusive
GCA_003132605.1	s__Palsa-1188 sp003132605	91.8856	336	724	d__Bacteria;p__Firmicutes_B;c__Moorellia;o__Thermacetogeniales;f__Thermacetogeniaceae;g__Palsa-1188	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902812385.1	s__DULK01 sp902812385	76.6563	68	724	d__Bacteria;p__Firmicutes_B;c__Moorellia;o__Thermacetogeniales;f__Thermacetogeniaceae;g__DULK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902812435.1	s__DULK01 sp902812435	76.6548	53	724	d__Bacteria;p__Firmicutes_B;c__Moorellia;o__Thermacetogeniales;f__Thermacetogeniaceae;g__DULK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012840385.1	s__DULK01 sp012840385	76.604	69	724	d__Bacteria;p__Firmicutes_B;c__Moorellia;o__Thermacetogeniales;f__Thermacetogeniaceae;g__DULK01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-16 19:20:53,321] [INFO] GTDB search result was written to GCA_003166315.1_20110700_S2D_genomic.fna/result_gtdb.tsv
[2023-06-16 19:20:53,322] [INFO] ===== GTDB Search completed =====
[2023-06-16 19:20:53,324] [INFO] DFAST_QC result json was written to GCA_003166315.1_20110700_S2D_genomic.fna/dqc_result.json
[2023-06-16 19:20:53,325] [INFO] DFAST_QC completed!
[2023-06-16 19:20:53,325] [INFO] Total running time: 0h0m51s