[2023-06-28 11:10:06,430] [INFO] DFAST_QC pipeline started.
[2023-06-28 11:10:06,433] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 11:10:06,433] [INFO] DQC Reference Directory: /var/lib/cwl/stgcb392c76-19ca-4ecb-aafd-61aa976ea6c1/dqc_reference
[2023-06-28 11:10:07,745] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 11:10:07,746] [INFO] Task started: Prodigal
[2023-06-28 11:10:07,746] [INFO] Running command: gunzip -c /var/lib/cwl/stg875c1388-82f2-436f-896f-9f48d8eca318/GCA_944319845.1_BRZ_GC_bin34_genomic.fna.gz | prodigal -d GCA_944319845.1_BRZ_GC_bin34_genomic.fna/cds.fna -a GCA_944319845.1_BRZ_GC_bin34_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 11:10:20,881] [INFO] Task succeeded: Prodigal
[2023-06-28 11:10:20,881] [INFO] Task started: HMMsearch
[2023-06-28 11:10:20,881] [INFO] Running command: hmmsearch --tblout GCA_944319845.1_BRZ_GC_bin34_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcb392c76-19ca-4ecb-aafd-61aa976ea6c1/dqc_reference/reference_markers.hmm GCA_944319845.1_BRZ_GC_bin34_genomic.fna/protein.faa > /dev/null
[2023-06-28 11:10:21,173] [INFO] Task succeeded: HMMsearch
[2023-06-28 11:10:21,174] [INFO] Found 6/6 markers.
[2023-06-28 11:10:21,200] [INFO] Query marker FASTA was written to GCA_944319845.1_BRZ_GC_bin34_genomic.fna/markers.fasta
[2023-06-28 11:10:21,200] [INFO] Task started: Blastn
[2023-06-28 11:10:21,200] [INFO] Running command: blastn -query GCA_944319845.1_BRZ_GC_bin34_genomic.fna/markers.fasta -db /var/lib/cwl/stgcb392c76-19ca-4ecb-aafd-61aa976ea6c1/dqc_reference/reference_markers.fasta -out GCA_944319845.1_BRZ_GC_bin34_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 11:10:21,819] [INFO] Task succeeded: Blastn
[2023-06-28 11:10:21,824] [INFO] Selected 23 target genomes.
[2023-06-28 11:10:21,825] [INFO] Target genome list was writen to GCA_944319845.1_BRZ_GC_bin34_genomic.fna/target_genomes.txt
[2023-06-28 11:10:21,827] [INFO] Task started: fastANI
[2023-06-28 11:10:21,827] [INFO] Running command: fastANI --query /var/lib/cwl/stg875c1388-82f2-436f-896f-9f48d8eca318/GCA_944319845.1_BRZ_GC_bin34_genomic.fna.gz --refList GCA_944319845.1_BRZ_GC_bin34_genomic.fna/target_genomes.txt --output GCA_944319845.1_BRZ_GC_bin34_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 11:10:36,039] [INFO] Task succeeded: fastANI
[2023-06-28 11:10:36,040] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcb392c76-19ca-4ecb-aafd-61aa976ea6c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 11:10:36,040] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcb392c76-19ca-4ecb-aafd-61aa976ea6c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 11:10:36,044] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 11:10:36,044] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 11:10:36,044] [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
Barnesiella viscericola	strain=C46, DSM 18177	GCA_000512915.1	397865	397865	type	True	76.4545	77	791	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 11:10:36,048] [INFO] DFAST Taxonomy check result was written to GCA_944319845.1_BRZ_GC_bin34_genomic.fna/tc_result.tsv
[2023-06-28 11:10:36,049] [INFO] ===== Taxonomy check completed =====
[2023-06-28 11:10:36,050] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 11:10:36,050] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcb392c76-19ca-4ecb-aafd-61aa976ea6c1/dqc_reference/checkm_data
[2023-06-28 11:10:36,052] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 11:10:36,080] [INFO] Task started: CheckM
[2023-06-28 11:10:36,080] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944319845.1_BRZ_GC_bin34_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944319845.1_BRZ_GC_bin34_genomic.fna/checkm_input GCA_944319845.1_BRZ_GC_bin34_genomic.fna/checkm_result
[2023-06-28 11:11:16,186] [INFO] Task succeeded: CheckM
[2023-06-28 11:11:16,187] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 11:11:16,206] [INFO] ===== Completeness check finished =====
[2023-06-28 11:11:16,206] [INFO] ===== Start GTDB Search =====
[2023-06-28 11:11:16,207] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944319845.1_BRZ_GC_bin34_genomic.fna/markers.fasta)
[2023-06-28 11:11:16,207] [INFO] Task started: Blastn
[2023-06-28 11:11:16,207] [INFO] Running command: blastn -query GCA_944319845.1_BRZ_GC_bin34_genomic.fna/markers.fasta -db /var/lib/cwl/stgcb392c76-19ca-4ecb-aafd-61aa976ea6c1/dqc_reference/reference_markers_gtdb.fasta -out GCA_944319845.1_BRZ_GC_bin34_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 11:11:16,957] [INFO] Task succeeded: Blastn
[2023-06-28 11:11:16,961] [INFO] Selected 20 target genomes.
[2023-06-28 11:11:16,961] [INFO] Target genome list was writen to GCA_944319845.1_BRZ_GC_bin34_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 11:11:16,972] [INFO] Task started: fastANI
[2023-06-28 11:11:16,972] [INFO] Running command: fastANI --query /var/lib/cwl/stg875c1388-82f2-436f-896f-9f48d8eca318/GCA_944319845.1_BRZ_GC_bin34_genomic.fna.gz --refList GCA_944319845.1_BRZ_GC_bin34_genomic.fna/target_genomes_gtdb.txt --output GCA_944319845.1_BRZ_GC_bin34_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 11:11:27,130] [INFO] Task succeeded: fastANI
[2023-06-28 11:11:27,142] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 11:11:27,142] [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_900538705.1	s__Barnesiella_A sp900538705	98.8521	766	791	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Barnesiellaceae;g__Barnesiella_A	95.0	99.41	98.81	0.98	0.97	3	conclusive
GCA_900542255.1	s__Barnesiella_A excrementipullorum	82.5563	554	791	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Barnesiellaceae;g__Barnesiella_A	95.0	98.75	98.75	0.93	0.93	2	-
GCA_017531985.1	s__Barnesiella_A sp017531985	77.1507	102	791	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Barnesiellaceae;g__Barnesiella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017481745.1	s__Barnesiella_A sp017481745	77.0098	139	791	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Barnesiellaceae;g__Barnesiella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002159975.1	s__Barnesiella merdigallinarum	76.7793	71	791	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Barnesiellaceae;g__Barnesiella	95.0	97.77	95.24	0.93	0.91	5	-
GCA_017935645.1	s__Barnesiella_A sp017935645	76.4981	106	791	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Barnesiellaceae;g__Barnesiella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000512915.1	s__Barnesiella viscericola	76.4299	78	791	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Barnesiellaceae;g__Barnesiella	95.0	97.37	97.37	0.91	0.91	2	-
GCA_900538555.1	s__UMGS27 sp900538555	76.4048	62	791	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Barnesiellaceae;g__UMGS27	95.0	99.31	98.62	0.96	0.93	3	-
GCA_017462265.1	s__UBA11471 sp017462265	75.9489	52	791	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA11471;g__UBA11471	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 11:11:27,144] [INFO] GTDB search result was written to GCA_944319845.1_BRZ_GC_bin34_genomic.fna/result_gtdb.tsv
[2023-06-28 11:11:27,145] [INFO] ===== GTDB Search completed =====
[2023-06-28 11:11:27,175] [INFO] DFAST_QC result json was written to GCA_944319845.1_BRZ_GC_bin34_genomic.fna/dqc_result.json
[2023-06-28 11:11:27,175] [INFO] DFAST_QC completed!
[2023-06-28 11:11:27,175] [INFO] Total running time: 0h1m21s