[2023-06-13 13:00:25,004] [INFO] DFAST_QC pipeline started.
[2023-06-13 13:00:25,007] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 13:00:25,007] [INFO] DQC Reference Directory: /var/lib/cwl/stg44c351f2-e997-4677-82f5-457594920b28/dqc_reference
[2023-06-13 13:00:26,334] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 13:00:26,334] [INFO] Task started: Prodigal
[2023-06-13 13:00:26,335] [INFO] Running command: gunzip -c /var/lib/cwl/stgccae7a28-4e64-4c15-a884-e0c17f2e3b35/GCA_947097335.1_SRR8786264_bin.8_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947097335.1_SRR8786264_bin.8_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_947097335.1_SRR8786264_bin.8_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 13:00:30,687] [INFO] Task succeeded: Prodigal
[2023-06-13 13:00:30,687] [INFO] Task started: HMMsearch
[2023-06-13 13:00:30,688] [INFO] Running command: hmmsearch --tblout GCA_947097335.1_SRR8786264_bin.8_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg44c351f2-e997-4677-82f5-457594920b28/dqc_reference/reference_markers.hmm GCA_947097335.1_SRR8786264_bin.8_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 13:00:30,955] [INFO] Task succeeded: HMMsearch
[2023-06-13 13:00:30,957] [INFO] Found 6/6 markers.
[2023-06-13 13:00:30,976] [INFO] Query marker FASTA was written to GCA_947097335.1_SRR8786264_bin.8_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-13 13:00:30,976] [INFO] Task started: Blastn
[2023-06-13 13:00:30,976] [INFO] Running command: blastn -query GCA_947097335.1_SRR8786264_bin.8_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg44c351f2-e997-4677-82f5-457594920b28/dqc_reference/reference_markers.fasta -out GCA_947097335.1_SRR8786264_bin.8_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 13:00:31,606] [INFO] Task succeeded: Blastn
[2023-06-13 13:00:31,610] [INFO] Selected 13 target genomes.
[2023-06-13 13:00:31,610] [INFO] Target genome list was writen to GCA_947097335.1_SRR8786264_bin.8_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-13 13:00:31,614] [INFO] Task started: fastANI
[2023-06-13 13:00:31,614] [INFO] Running command: fastANI --query /var/lib/cwl/stgccae7a28-4e64-4c15-a884-e0c17f2e3b35/GCA_947097335.1_SRR8786264_bin.8_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_947097335.1_SRR8786264_bin.8_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947097335.1_SRR8786264_bin.8_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 13:00:38,528] [INFO] Task succeeded: fastANI
[2023-06-13 13:00:38,528] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg44c351f2-e997-4677-82f5-457594920b28/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 13:00:38,528] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg44c351f2-e997-4677-82f5-457594920b28/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 13:00:38,538] [INFO] Found 9 fastANI hits (3 hits with ANI > threshold)
[2023-06-13 13:00:38,538] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-13 13:00:38,538] [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
Aggregatibacter segnis	strain=ATCC 33393	GCA_000185305.1	739	739	type	True	95.336	484	556	95	conclusive
Aggregatibacter segnis	strain=FDAARGOS_987	GCA_016127115.1	739	739	type	True	95.3034	486	556	95	conclusive
Aggregatibacter segnis	strain=NCTC10977	GCA_900476035.1	739	739	type	True	95.2462	489	556	95	conclusive
Aggregatibacter kilianii	strain=PN_528	GCA_003130255.1	2025884	2025884	type	True	85.8057	423	556	95	below_threshold
Aggregatibacter aphrophilus	strain=ATCC 33389	GCA_000226495.3	732	732	type	True	85.6204	410	556	95	below_threshold
Aggregatibacter aphrophilus	strain=NCTC5906	GCA_900636915.1	732	732	type	True	85.4275	421	556	95	below_threshold
Aggregatibacter actinomycetemcomitans	strain=DSM 8324	GCA_000372365.1	714	714	type	True	81.4668	373	556	95	below_threshold
Aggregatibacter actinomycetemcomitans	strain=NCTC_9710	GCA_008085305.1	714	714	type	True	81.4408	377	556	95	below_threshold
Rodentibacter haemolyticus	strain=DSM 111151	GCA_015356115.1	2778911	2778911	type	True	78.2664	173	556	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 13:00:38,540] [INFO] DFAST Taxonomy check result was written to GCA_947097335.1_SRR8786264_bin.8_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-13 13:00:38,541] [INFO] ===== Taxonomy check completed =====
[2023-06-13 13:00:38,541] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 13:00:38,542] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg44c351f2-e997-4677-82f5-457594920b28/dqc_reference/checkm_data
[2023-06-13 13:00:38,543] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 13:00:38,569] [INFO] Task started: CheckM
[2023-06-13 13:00:38,569] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947097335.1_SRR8786264_bin.8_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947097335.1_SRR8786264_bin.8_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_947097335.1_SRR8786264_bin.8_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-13 13:00:59,718] [INFO] Task succeeded: CheckM
[2023-06-13 13:00:59,719] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.62%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 13:00:59,740] [INFO] ===== Completeness check finished =====
[2023-06-13 13:00:59,740] [INFO] ===== Start GTDB Search =====
[2023-06-13 13:00:59,740] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947097335.1_SRR8786264_bin.8_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-13 13:00:59,741] [INFO] Task started: Blastn
[2023-06-13 13:00:59,741] [INFO] Running command: blastn -query GCA_947097335.1_SRR8786264_bin.8_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg44c351f2-e997-4677-82f5-457594920b28/dqc_reference/reference_markers_gtdb.fasta -out GCA_947097335.1_SRR8786264_bin.8_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 13:01:00,645] [INFO] Task succeeded: Blastn
[2023-06-13 13:01:00,650] [INFO] Selected 9 target genomes.
[2023-06-13 13:01:00,650] [INFO] Target genome list was writen to GCA_947097335.1_SRR8786264_bin.8_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 13:01:00,658] [INFO] Task started: fastANI
[2023-06-13 13:01:00,659] [INFO] Running command: fastANI --query /var/lib/cwl/stgccae7a28-4e64-4c15-a884-e0c17f2e3b35/GCA_947097335.1_SRR8786264_bin.8_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_947097335.1_SRR8786264_bin.8_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947097335.1_SRR8786264_bin.8_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 13:01:05,128] [INFO] Task succeeded: fastANI
[2023-06-13 13:01:05,144] [INFO] Found 8 fastANI hits (2 hits with ANI > circumscription radius)
[2023-06-13 13:01:05,145] [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
GCF_000185305.1	s__Aggregatibacter segnis	95.336	484	556	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Aggregatibacter	95.0	97.84	95.38	0.95	0.88	6	inconclusive
GCF_003130075.1	s__Aggregatibacter segnis_A	95.3175	485	556	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Aggregatibacter	95.0	95.43	95.32	0.90	0.88	6	inconclusive
GCF_017798005.1	s__Aggregatibacter sp000466335	89.6583	393	556	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Aggregatibacter	95.0	95.63	95.17	0.92	0.88	4	-
GCF_003130255.1	s__Aggregatibacter kilianii	85.8116	423	556	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Aggregatibacter	95.0	98.97	97.13	0.96	0.90	14	-
GCF_900636915.1	s__Aggregatibacter aphrophilus	85.4275	421	556	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Aggregatibacter	95.0	97.58	96.00	0.94	0.87	19	-
GCF_003129965.1	s__Aggregatibacter kilianii_A	82.416	426	556	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Aggregatibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000372365.1	s__Aggregatibacter actinomycetemcomitans	81.4777	372	556	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Aggregatibacter	95.0	98.51	97.12	0.94	0.88	80	-
GCF_003130205.1	s__Aggregatibacter actinomycetemcomitans_A	81.3766	368	556	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Aggregatibacter	95.0	97.99	96.75	0.93	0.87	15	-
--------------------------------------------------------------------------------
[2023-06-13 13:01:05,147] [INFO] GTDB search result was written to GCA_947097335.1_SRR8786264_bin.8_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 13:01:05,148] [INFO] ===== GTDB Search completed =====
[2023-06-13 13:01:05,151] [INFO] DFAST_QC result json was written to GCA_947097335.1_SRR8786264_bin.8_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-13 13:01:05,151] [INFO] DFAST_QC completed!
[2023-06-13 13:01:05,151] [INFO] Total running time: 0h0m40s