[2023-06-28 16:31:46,160] [INFO] DFAST_QC pipeline started.
[2023-06-28 16:31:46,164] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 16:31:46,165] [INFO] DQC Reference Directory: /var/lib/cwl/stga896e4d7-2cfd-4f8a-bdeb-fa5c0768f0d4/dqc_reference
[2023-06-28 16:31:47,375] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 16:31:47,376] [INFO] Task started: Prodigal
[2023-06-28 16:31:47,377] [INFO] Running command: gunzip -c /var/lib/cwl/stgd45b7d13-7338-4fcf-8d1e-9542d30d7d78/GCA_944342125.1_BRZ_QA_bin59_genomic.fna.gz | prodigal -d GCA_944342125.1_BRZ_QA_bin59_genomic.fna/cds.fna -a GCA_944342125.1_BRZ_QA_bin59_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 16:31:49,182] [INFO] Task succeeded: Prodigal
[2023-06-28 16:31:49,183] [INFO] Task started: HMMsearch
[2023-06-28 16:31:49,183] [INFO] Running command: hmmsearch --tblout GCA_944342125.1_BRZ_QA_bin59_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga896e4d7-2cfd-4f8a-bdeb-fa5c0768f0d4/dqc_reference/reference_markers.hmm GCA_944342125.1_BRZ_QA_bin59_genomic.fna/protein.faa > /dev/null
[2023-06-28 16:31:49,436] [INFO] Task succeeded: HMMsearch
[2023-06-28 16:31:49,437] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd45b7d13-7338-4fcf-8d1e-9542d30d7d78/GCA_944342125.1_BRZ_QA_bin59_genomic.fna.gz]
[2023-06-28 16:31:49,461] [INFO] Query marker FASTA was written to GCA_944342125.1_BRZ_QA_bin59_genomic.fna/markers.fasta
[2023-06-28 16:31:49,462] [INFO] Task started: Blastn
[2023-06-28 16:31:49,462] [INFO] Running command: blastn -query GCA_944342125.1_BRZ_QA_bin59_genomic.fna/markers.fasta -db /var/lib/cwl/stga896e4d7-2cfd-4f8a-bdeb-fa5c0768f0d4/dqc_reference/reference_markers.fasta -out GCA_944342125.1_BRZ_QA_bin59_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 16:31:50,092] [INFO] Task succeeded: Blastn
[2023-06-28 16:31:50,096] [INFO] Selected 14 target genomes.
[2023-06-28 16:31:50,097] [INFO] Target genome list was writen to GCA_944342125.1_BRZ_QA_bin59_genomic.fna/target_genomes.txt
[2023-06-28 16:31:50,102] [INFO] Task started: fastANI
[2023-06-28 16:31:50,102] [INFO] Running command: fastANI --query /var/lib/cwl/stgd45b7d13-7338-4fcf-8d1e-9542d30d7d78/GCA_944342125.1_BRZ_QA_bin59_genomic.fna.gz --refList GCA_944342125.1_BRZ_QA_bin59_genomic.fna/target_genomes.txt --output GCA_944342125.1_BRZ_QA_bin59_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 16:31:55,465] [INFO] Task succeeded: fastANI
[2023-06-28 16:31:55,465] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga896e4d7-2cfd-4f8a-bdeb-fa5c0768f0d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 16:31:55,466] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga896e4d7-2cfd-4f8a-bdeb-fa5c0768f0d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 16:31:55,468] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 16:31:55,468] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 16:31:55,468] [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
--------------------------------------------------------------------------------
[2023-06-28 16:31:55,470] [INFO] DFAST Taxonomy check result was written to GCA_944342125.1_BRZ_QA_bin59_genomic.fna/tc_result.tsv
[2023-06-28 16:31:55,471] [INFO] ===== Taxonomy check completed =====
[2023-06-28 16:31:55,471] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 16:31:55,471] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga896e4d7-2cfd-4f8a-bdeb-fa5c0768f0d4/dqc_reference/checkm_data
[2023-06-28 16:31:55,474] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 16:31:55,496] [INFO] Task started: CheckM
[2023-06-28 16:31:55,497] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944342125.1_BRZ_QA_bin59_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944342125.1_BRZ_QA_bin59_genomic.fna/checkm_input GCA_944342125.1_BRZ_QA_bin59_genomic.fna/checkm_result
[2023-06-28 16:32:10,034] [INFO] Task succeeded: CheckM
[2023-06-28 16:32:10,036] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-28 16:32:10,058] [INFO] ===== Completeness check finished =====
[2023-06-28 16:32:10,059] [INFO] ===== Start GTDB Search =====
[2023-06-28 16:32:10,059] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944342125.1_BRZ_QA_bin59_genomic.fna/markers.fasta)
[2023-06-28 16:32:10,059] [INFO] Task started: Blastn
[2023-06-28 16:32:10,059] [INFO] Running command: blastn -query GCA_944342125.1_BRZ_QA_bin59_genomic.fna/markers.fasta -db /var/lib/cwl/stga896e4d7-2cfd-4f8a-bdeb-fa5c0768f0d4/dqc_reference/reference_markers_gtdb.fasta -out GCA_944342125.1_BRZ_QA_bin59_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 16:32:11,012] [INFO] Task succeeded: Blastn
[2023-06-28 16:32:11,018] [INFO] Selected 19 target genomes.
[2023-06-28 16:32:11,018] [INFO] Target genome list was writen to GCA_944342125.1_BRZ_QA_bin59_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 16:32:11,030] [INFO] Task started: fastANI
[2023-06-28 16:32:11,030] [INFO] Running command: fastANI --query /var/lib/cwl/stgd45b7d13-7338-4fcf-8d1e-9542d30d7d78/GCA_944342125.1_BRZ_QA_bin59_genomic.fna.gz --refList GCA_944342125.1_BRZ_QA_bin59_genomic.fna/target_genomes_gtdb.txt --output GCA_944342125.1_BRZ_QA_bin59_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 16:32:16,150] [INFO] Task succeeded: fastANI
[2023-06-28 16:32:16,157] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 16:32:16,157] [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_905197045.1	s__Onthovivens sp905197045	79.9661	169	347	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-826;g__Onthovivens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900540395.1	s__Onthovivens sp900540395	79.2368	175	347	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-826;g__Onthovivens	95.0	95.91	95.71	0.83	0.80	3	-
GCA_900545015.1	s__Onthovivens sp900545015	77.4844	93	347	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-826;g__Onthovivens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017470115.1	s__Onthovivens sp017470115	77.4697	57	347	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-826;g__Onthovivens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900540365.1	s__Onthovivens sp900540365	76.8745	59	347	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-826;g__Onthovivens	95.0	98.93	97.87	0.89	0.80	3	-
GCA_002438785.1	s__Onthovivens sp002438785	76.835	50	347	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-826;g__Onthovivens	95.0	99.26	99.24	0.93	0.93	3	-
--------------------------------------------------------------------------------
[2023-06-28 16:32:16,159] [INFO] GTDB search result was written to GCA_944342125.1_BRZ_QA_bin59_genomic.fna/result_gtdb.tsv
[2023-06-28 16:32:16,160] [INFO] ===== GTDB Search completed =====
[2023-06-28 16:32:16,163] [INFO] DFAST_QC result json was written to GCA_944342125.1_BRZ_QA_bin59_genomic.fna/dqc_result.json
[2023-06-28 16:32:16,163] [INFO] DFAST_QC completed!
[2023-06-28 16:32:16,163] [INFO] Total running time: 0h0m30s