[2023-06-28 21:36:10,367] [INFO] DFAST_QC pipeline started.
[2023-06-28 21:36:10,372] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 21:36:10,372] [INFO] DQC Reference Directory: /var/lib/cwl/stgf63ddc92-55c8-4546-8815-be17a9a68a22/dqc_reference
[2023-06-28 21:36:11,780] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 21:36:11,781] [INFO] Task started: Prodigal
[2023-06-28 21:36:11,782] [INFO] Running command: gunzip -c /var/lib/cwl/stg68d39694-e7f6-4d8c-a658-95cd97be7732/GCA_944363545.1_BRZ_D_bin87_genomic.fna.gz | prodigal -d GCA_944363545.1_BRZ_D_bin87_genomic.fna/cds.fna -a GCA_944363545.1_BRZ_D_bin87_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 21:36:13,555] [INFO] Task succeeded: Prodigal
[2023-06-28 21:36:13,556] [INFO] Task started: HMMsearch
[2023-06-28 21:36:13,556] [INFO] Running command: hmmsearch --tblout GCA_944363545.1_BRZ_D_bin87_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf63ddc92-55c8-4546-8815-be17a9a68a22/dqc_reference/reference_markers.hmm GCA_944363545.1_BRZ_D_bin87_genomic.fna/protein.faa > /dev/null
[2023-06-28 21:36:13,808] [INFO] Task succeeded: HMMsearch
[2023-06-28 21:36:13,809] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg68d39694-e7f6-4d8c-a658-95cd97be7732/GCA_944363545.1_BRZ_D_bin87_genomic.fna.gz]
[2023-06-28 21:36:13,827] [INFO] Query marker FASTA was written to GCA_944363545.1_BRZ_D_bin87_genomic.fna/markers.fasta
[2023-06-28 21:36:13,828] [INFO] Task started: Blastn
[2023-06-28 21:36:13,828] [INFO] Running command: blastn -query GCA_944363545.1_BRZ_D_bin87_genomic.fna/markers.fasta -db /var/lib/cwl/stgf63ddc92-55c8-4546-8815-be17a9a68a22/dqc_reference/reference_markers.fasta -out GCA_944363545.1_BRZ_D_bin87_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 21:36:15,349] [INFO] Task succeeded: Blastn
[2023-06-28 21:36:15,353] [INFO] Selected 16 target genomes.
[2023-06-28 21:36:15,353] [INFO] Target genome list was writen to GCA_944363545.1_BRZ_D_bin87_genomic.fna/target_genomes.txt
[2023-06-28 21:36:15,366] [INFO] Task started: fastANI
[2023-06-28 21:36:15,366] [INFO] Running command: fastANI --query /var/lib/cwl/stg68d39694-e7f6-4d8c-a658-95cd97be7732/GCA_944363545.1_BRZ_D_bin87_genomic.fna.gz --refList GCA_944363545.1_BRZ_D_bin87_genomic.fna/target_genomes.txt --output GCA_944363545.1_BRZ_D_bin87_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 21:36:21,249] [INFO] Task succeeded: fastANI
[2023-06-28 21:36:21,250] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf63ddc92-55c8-4546-8815-be17a9a68a22/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 21:36:21,250] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf63ddc92-55c8-4546-8815-be17a9a68a22/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 21:36:21,253] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 21:36:21,253] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 21:36:21,253] [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 21:36:21,255] [INFO] DFAST Taxonomy check result was written to GCA_944363545.1_BRZ_D_bin87_genomic.fna/tc_result.tsv
[2023-06-28 21:36:21,256] [INFO] ===== Taxonomy check completed =====
[2023-06-28 21:36:21,256] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 21:36:21,257] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf63ddc92-55c8-4546-8815-be17a9a68a22/dqc_reference/checkm_data
[2023-06-28 21:36:21,261] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 21:36:21,279] [INFO] Task started: CheckM
[2023-06-28 21:36:21,279] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944363545.1_BRZ_D_bin87_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944363545.1_BRZ_D_bin87_genomic.fna/checkm_input GCA_944363545.1_BRZ_D_bin87_genomic.fna/checkm_result
[2023-06-28 21:36:35,718] [INFO] Task succeeded: CheckM
[2023-06-28 21:36:35,719] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 21:36:35,745] [INFO] ===== Completeness check finished =====
[2023-06-28 21:36:35,745] [INFO] ===== Start GTDB Search =====
[2023-06-28 21:36:35,746] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944363545.1_BRZ_D_bin87_genomic.fna/markers.fasta)
[2023-06-28 21:36:35,746] [INFO] Task started: Blastn
[2023-06-28 21:36:35,746] [INFO] Running command: blastn -query GCA_944363545.1_BRZ_D_bin87_genomic.fna/markers.fasta -db /var/lib/cwl/stgf63ddc92-55c8-4546-8815-be17a9a68a22/dqc_reference/reference_markers_gtdb.fasta -out GCA_944363545.1_BRZ_D_bin87_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 21:36:36,570] [INFO] Task succeeded: Blastn
[2023-06-28 21:36:36,579] [INFO] Selected 8 target genomes.
[2023-06-28 21:36:36,579] [INFO] Target genome list was writen to GCA_944363545.1_BRZ_D_bin87_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 21:36:36,613] [INFO] Task started: fastANI
[2023-06-28 21:36:36,614] [INFO] Running command: fastANI --query /var/lib/cwl/stg68d39694-e7f6-4d8c-a658-95cd97be7732/GCA_944363545.1_BRZ_D_bin87_genomic.fna.gz --refList GCA_944363545.1_BRZ_D_bin87_genomic.fna/target_genomes_gtdb.txt --output GCA_944363545.1_BRZ_D_bin87_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 21:36:38,570] [INFO] Task succeeded: fastANI
[2023-06-28 21:36:38,578] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 21:36:38,578] [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_900540365.1	s__Onthovivens sp900540365	97.264	358	406	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-826;g__Onthovivens	95.0	98.93	97.87	0.89	0.80	3	conclusive
GCA_017477255.1	s__Onthovivens sp017477255	78.5323	76	406	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_002438785.1	s__Onthovivens sp002438785	78.0445	119	406	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-826;g__Onthovivens	95.0	99.26	99.24	0.93	0.93	3	-
GCA_905197045.1	s__Onthovivens sp905197045	77.8258	91	406	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	77.5836	96	406	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	77.3106	88	406	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_016302065.1	s__Onthovivens sp016302065	77.1998	73	406	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_002451465.1	s__Onthovivens sp002451465	77.1513	76	406	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-826;g__Onthovivens	95.0	99.55	99.46	0.95	0.89	6	-
--------------------------------------------------------------------------------
[2023-06-28 21:36:38,580] [INFO] GTDB search result was written to GCA_944363545.1_BRZ_D_bin87_genomic.fna/result_gtdb.tsv
[2023-06-28 21:36:38,581] [INFO] ===== GTDB Search completed =====
[2023-06-28 21:36:38,584] [INFO] DFAST_QC result json was written to GCA_944363545.1_BRZ_D_bin87_genomic.fna/dqc_result.json
[2023-06-28 21:36:38,584] [INFO] DFAST_QC completed!
[2023-06-28 21:36:38,584] [INFO] Total running time: 0h0m28s