[2023-06-14 01:06:55,796] [INFO] DFAST_QC pipeline started.
[2023-06-14 01:06:55,801] [INFO] DFAST_QC version: 0.5.7
[2023-06-14 01:06:55,802] [INFO] DQC Reference Directory: /var/lib/cwl/stgb8745848-9e85-4fef-9aeb-c1eb08f08ee0/dqc_reference
[2023-06-14 01:06:57,210] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-14 01:06:57,211] [INFO] Task started: Prodigal
[2023-06-14 01:06:57,211] [INFO] Running command: gunzip -c /var/lib/cwl/stgad3d6f9d-0482-4fef-9a82-34c9b58b5c50/GCA_022716375.1_ASM2271637v1_genomic.fna.gz | prodigal -d GCA_022716375.1_ASM2271637v1_genomic.fna/cds.fna -a GCA_022716375.1_ASM2271637v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-14 01:07:16,582] [INFO] Task succeeded: Prodigal
[2023-06-14 01:07:16,582] [INFO] Task started: HMMsearch
[2023-06-14 01:07:16,583] [INFO] Running command: hmmsearch --tblout GCA_022716375.1_ASM2271637v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb8745848-9e85-4fef-9aeb-c1eb08f08ee0/dqc_reference/reference_markers.hmm GCA_022716375.1_ASM2271637v1_genomic.fna/protein.faa > /dev/null
[2023-06-14 01:07:16,897] [INFO] Task succeeded: HMMsearch
[2023-06-14 01:07:16,899] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgad3d6f9d-0482-4fef-9a82-34c9b58b5c50/GCA_022716375.1_ASM2271637v1_genomic.fna.gz]
[2023-06-14 01:07:16,942] [INFO] Query marker FASTA was written to GCA_022716375.1_ASM2271637v1_genomic.fna/markers.fasta
[2023-06-14 01:07:16,942] [INFO] Task started: Blastn
[2023-06-14 01:07:16,942] [INFO] Running command: blastn -query GCA_022716375.1_ASM2271637v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb8745848-9e85-4fef-9aeb-c1eb08f08ee0/dqc_reference/reference_markers.fasta -out GCA_022716375.1_ASM2271637v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-14 01:07:17,584] [INFO] Task succeeded: Blastn
[2023-06-14 01:07:17,588] [INFO] Selected 25 target genomes.
[2023-06-14 01:07:17,589] [INFO] Target genome list was writen to GCA_022716375.1_ASM2271637v1_genomic.fna/target_genomes.txt
[2023-06-14 01:07:17,600] [INFO] Task started: fastANI
[2023-06-14 01:07:17,600] [INFO] Running command: fastANI --query /var/lib/cwl/stgad3d6f9d-0482-4fef-9a82-34c9b58b5c50/GCA_022716375.1_ASM2271637v1_genomic.fna.gz --refList GCA_022716375.1_ASM2271637v1_genomic.fna/target_genomes.txt --output GCA_022716375.1_ASM2271637v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-14 01:07:35,454] [INFO] Task succeeded: fastANI
[2023-06-14 01:07:35,455] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb8745848-9e85-4fef-9aeb-c1eb08f08ee0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-14 01:07:35,456] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb8745848-9e85-4fef-9aeb-c1eb08f08ee0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-14 01:07:35,463] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2023-06-14 01:07:35,463] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-14 01:07:35,463] [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 intestinihominis	strain=YIT 11860	GCA_000296465.1	487174	487174	type	True	98.4114	445	718	95	conclusive
Barnesiella viscericola	strain=C46, DSM 18177	GCA_000512915.1	397865	397865	type	True	79.4934	149	718	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-14 01:07:35,466] [INFO] DFAST Taxonomy check result was written to GCA_022716375.1_ASM2271637v1_genomic.fna/tc_result.tsv
[2023-06-14 01:07:35,466] [INFO] ===== Taxonomy check completed =====
[2023-06-14 01:07:35,467] [INFO] ===== Start completeness check using CheckM =====
[2023-06-14 01:07:35,467] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb8745848-9e85-4fef-9aeb-c1eb08f08ee0/dqc_reference/checkm_data
[2023-06-14 01:07:35,468] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-14 01:07:35,510] [INFO] Task started: CheckM
[2023-06-14 01:07:35,510] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022716375.1_ASM2271637v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022716375.1_ASM2271637v1_genomic.fna/checkm_input GCA_022716375.1_ASM2271637v1_genomic.fna/checkm_result
[2023-06-14 01:08:31,339] [INFO] Task succeeded: CheckM
[2023-06-14 01:08:31,341] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.15%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-14 01:08:31,368] [INFO] ===== Completeness check finished =====
[2023-06-14 01:08:31,368] [INFO] ===== Start GTDB Search =====
[2023-06-14 01:08:31,368] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022716375.1_ASM2271637v1_genomic.fna/markers.fasta)
[2023-06-14 01:08:31,369] [INFO] Task started: Blastn
[2023-06-14 01:08:31,369] [INFO] Running command: blastn -query GCA_022716375.1_ASM2271637v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb8745848-9e85-4fef-9aeb-c1eb08f08ee0/dqc_reference/reference_markers_gtdb.fasta -out GCA_022716375.1_ASM2271637v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-14 01:08:32,161] [INFO] Task succeeded: Blastn
[2023-06-14 01:08:32,166] [INFO] Selected 25 target genomes.
[2023-06-14 01:08:32,166] [INFO] Target genome list was writen to GCA_022716375.1_ASM2271637v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-14 01:08:32,180] [INFO] Task started: fastANI
[2023-06-14 01:08:32,180] [INFO] Running command: fastANI --query /var/lib/cwl/stgad3d6f9d-0482-4fef-9a82-34c9b58b5c50/GCA_022716375.1_ASM2271637v1_genomic.fna.gz --refList GCA_022716375.1_ASM2271637v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022716375.1_ASM2271637v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-14 01:08:43,911] [INFO] Task succeeded: fastANI
[2023-06-14 01:08:43,920] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-14 01:08:43,920] [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_000296465.1	s__Barnesiella intestinihominis	98.3727	446	718	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Barnesiellaceae;g__Barnesiella	95.0	98.49	98.18	0.93	0.86	27	conclusive
GCF_002159975.1	s__Barnesiella merdigallinarum	79.7878	141	718	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Barnesiellaceae;g__Barnesiella	95.0	97.77	95.24	0.93	0.91	5	-
GCF_000512915.1	s__Barnesiella viscericola	79.5436	149	718	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Barnesiellaceae;g__Barnesiella	95.0	97.37	97.37	0.91	0.91	2	-
GCA_019114445.1	s__Barnesiella excrementigallinarum	79.3353	194	718	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Barnesiellaceae;g__Barnesiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019115485.1	s__Barnesiella excrementavium	78.6051	136	718	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Barnesiellaceae;g__Barnesiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900538555.1	s__UMGS27 sp900538555	77.1483	51	718	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Barnesiellaceae;g__UMGS27	95.0	99.31	98.62	0.96	0.93	3	-
--------------------------------------------------------------------------------
[2023-06-14 01:08:43,922] [INFO] GTDB search result was written to GCA_022716375.1_ASM2271637v1_genomic.fna/result_gtdb.tsv
[2023-06-14 01:08:43,922] [INFO] ===== GTDB Search completed =====
[2023-06-14 01:08:43,925] [INFO] DFAST_QC result json was written to GCA_022716375.1_ASM2271637v1_genomic.fna/dqc_result.json
[2023-06-14 01:08:43,925] [INFO] DFAST_QC completed!
[2023-06-14 01:08:43,926] [INFO] Total running time: 0h1m48s