[2023-06-07 23:15:53,615] [INFO] DFAST_QC pipeline started.
[2023-06-07 23:15:53,618] [INFO] DFAST_QC version: 0.5.7
[2023-06-07 23:15:53,618] [INFO] DQC Reference Directory: /var/lib/cwl/stg44e910d2-4ac8-410b-bbf6-75aa60947b93/dqc_reference
[2023-06-07 23:15:54,886] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-07 23:15:54,887] [INFO] Task started: Prodigal
[2023-06-07 23:15:54,887] [INFO] Running command: gunzip -c /var/lib/cwl/stgb75d627e-aa60-4b26-b997-0e6595e7ea72/GCA_945831715.1_SRR5976187_bin.38_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945831715.1_SRR5976187_bin.38_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945831715.1_SRR5976187_bin.38_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-07 23:16:05,294] [INFO] Task succeeded: Prodigal
[2023-06-07 23:16:05,295] [INFO] Task started: HMMsearch
[2023-06-07 23:16:05,295] [INFO] Running command: hmmsearch --tblout GCA_945831715.1_SRR5976187_bin.38_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg44e910d2-4ac8-410b-bbf6-75aa60947b93/dqc_reference/reference_markers.hmm GCA_945831715.1_SRR5976187_bin.38_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-07 23:16:05,508] [INFO] Task succeeded: HMMsearch
[2023-06-07 23:16:05,510] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgb75d627e-aa60-4b26-b997-0e6595e7ea72/GCA_945831715.1_SRR5976187_bin.38_metaWRAP_v1.3_MAG_genomic.fna.gz]
[2023-06-07 23:16:05,531] [INFO] Query marker FASTA was written to GCA_945831715.1_SRR5976187_bin.38_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-07 23:16:05,532] [INFO] Task started: Blastn
[2023-06-07 23:16:05,532] [INFO] Running command: blastn -query GCA_945831715.1_SRR5976187_bin.38_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg44e910d2-4ac8-410b-bbf6-75aa60947b93/dqc_reference/reference_markers.fasta -out GCA_945831715.1_SRR5976187_bin.38_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 23:16:06,128] [INFO] Task succeeded: Blastn
[2023-06-07 23:16:06,134] [INFO] Selected 20 target genomes.
[2023-06-07 23:16:06,135] [INFO] Target genome list was writen to GCA_945831715.1_SRR5976187_bin.38_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-07 23:16:06,136] [INFO] Task started: fastANI
[2023-06-07 23:16:06,137] [INFO] Running command: fastANI --query /var/lib/cwl/stgb75d627e-aa60-4b26-b997-0e6595e7ea72/GCA_945831715.1_SRR5976187_bin.38_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945831715.1_SRR5976187_bin.38_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945831715.1_SRR5976187_bin.38_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-07 23:16:18,464] [INFO] Task succeeded: fastANI
[2023-06-07 23:16:18,464] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg44e910d2-4ac8-410b-bbf6-75aa60947b93/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-07 23:16:18,465] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg44e910d2-4ac8-410b-bbf6-75aa60947b93/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-07 23:16:18,468] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-07 23:16:18,468] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-07 23:16:18,468] [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
Prevotellamassilia timonensis	strain=Marseille-P2831	GCA_900106785.1	1852370	1852370	type	True	76.4403	52	436	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-07 23:16:18,470] [INFO] DFAST Taxonomy check result was written to GCA_945831715.1_SRR5976187_bin.38_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-07 23:16:18,471] [INFO] ===== Taxonomy check completed =====
[2023-06-07 23:16:18,471] [INFO] ===== Start completeness check using CheckM =====
[2023-06-07 23:16:18,472] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg44e910d2-4ac8-410b-bbf6-75aa60947b93/dqc_reference/checkm_data
[2023-06-07 23:16:18,474] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-07 23:16:18,567] [INFO] Task started: CheckM
[2023-06-07 23:16:18,568] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945831715.1_SRR5976187_bin.38_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945831715.1_SRR5976187_bin.38_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945831715.1_SRR5976187_bin.38_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-07 23:16:53,055] [INFO] Task succeeded: CheckM
[2023-06-07 23:16:53,057] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.39%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-07 23:16:53,078] [INFO] ===== Completeness check finished =====
[2023-06-07 23:16:53,078] [INFO] ===== Start GTDB Search =====
[2023-06-07 23:16:53,078] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945831715.1_SRR5976187_bin.38_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-07 23:16:53,079] [INFO] Task started: Blastn
[2023-06-07 23:16:53,079] [INFO] Running command: blastn -query GCA_945831715.1_SRR5976187_bin.38_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg44e910d2-4ac8-410b-bbf6-75aa60947b93/dqc_reference/reference_markers_gtdb.fasta -out GCA_945831715.1_SRR5976187_bin.38_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 23:16:53,865] [INFO] Task succeeded: Blastn
[2023-06-07 23:16:53,878] [INFO] Selected 21 target genomes.
[2023-06-07 23:16:53,878] [INFO] Target genome list was writen to GCA_945831715.1_SRR5976187_bin.38_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-07 23:16:53,881] [INFO] Task started: fastANI
[2023-06-07 23:16:53,881] [INFO] Running command: fastANI --query /var/lib/cwl/stgb75d627e-aa60-4b26-b997-0e6595e7ea72/GCA_945831715.1_SRR5976187_bin.38_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945831715.1_SRR5976187_bin.38_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945831715.1_SRR5976187_bin.38_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-07 23:17:01,424] [INFO] Task succeeded: fastANI
[2023-06-07 23:17:01,438] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-07 23:17:01,439] [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_004552865.1	s__Alloprevotella sp004552865	97.2717	298	436	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Alloprevotella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_004557185.1	s__Alloprevotella sp004557185	77.5379	108	436	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Alloprevotella	95.0	98.58	98.39	0.90	0.87	3	-
GCA_004552195.1	s__Alloprevotella sp004552195	77.4094	83	436	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Alloprevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900768625.1	s__Alloprevotella sp900768625	77.2222	69	436	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Alloprevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004562975.1	s__Alloprevotella sp004562975	77.0019	73	436	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Alloprevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004552155.1	s__Alloprevotella sp004552155	76.8641	85	436	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Alloprevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004555425.1	s__Alloprevotella sp004555425	76.6141	62	436	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Alloprevotella	95.0	98.00	97.95	0.85	0.83	3	-
GCA_905216095.1	s__Alloprevotella sp905216095	76.533	55	436	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Alloprevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900772575.1	s__Alloprevotella sp900772575	76.3591	53	436	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Alloprevotella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-07 23:17:01,441] [INFO] GTDB search result was written to GCA_945831715.1_SRR5976187_bin.38_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-07 23:17:01,441] [INFO] ===== GTDB Search completed =====
[2023-06-07 23:17:01,444] [INFO] DFAST_QC result json was written to GCA_945831715.1_SRR5976187_bin.38_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-07 23:17:01,444] [INFO] DFAST_QC completed!
[2023-06-07 23:17:01,444] [INFO] Total running time: 0h1m8s