[2023-06-28 10:22:07,842] [INFO] DFAST_QC pipeline started.
[2023-06-28 10:22:07,844] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 10:22:07,845] [INFO] DQC Reference Directory: /var/lib/cwl/stg18bf3d42-02dc-4dd5-9549-a649f12b6e7f/dqc_reference
[2023-06-28 10:22:10,425] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 10:22:10,426] [INFO] Task started: Prodigal
[2023-06-28 10:22:10,426] [INFO] Running command: gunzip -c /var/lib/cwl/stg39ed87b0-b851-426e-8149-ca58e6cdcbe2/GCA_944320015.1_BRZ_N_bin151_genomic.fna.gz | prodigal -d GCA_944320015.1_BRZ_N_bin151_genomic.fna/cds.fna -a GCA_944320015.1_BRZ_N_bin151_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 10:22:26,809] [INFO] Task succeeded: Prodigal
[2023-06-28 10:22:26,809] [INFO] Task started: HMMsearch
[2023-06-28 10:22:26,809] [INFO] Running command: hmmsearch --tblout GCA_944320015.1_BRZ_N_bin151_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg18bf3d42-02dc-4dd5-9549-a649f12b6e7f/dqc_reference/reference_markers.hmm GCA_944320015.1_BRZ_N_bin151_genomic.fna/protein.faa > /dev/null
[2023-06-28 10:22:27,103] [INFO] Task succeeded: HMMsearch
[2023-06-28 10:22:27,104] [INFO] Found 6/6 markers.
[2023-06-28 10:22:27,139] [INFO] Query marker FASTA was written to GCA_944320015.1_BRZ_N_bin151_genomic.fna/markers.fasta
[2023-06-28 10:22:27,140] [INFO] Task started: Blastn
[2023-06-28 10:22:27,140] [INFO] Running command: blastn -query GCA_944320015.1_BRZ_N_bin151_genomic.fna/markers.fasta -db /var/lib/cwl/stg18bf3d42-02dc-4dd5-9549-a649f12b6e7f/dqc_reference/reference_markers.fasta -out GCA_944320015.1_BRZ_N_bin151_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 10:22:27,803] [INFO] Task succeeded: Blastn
[2023-06-28 10:22:27,810] [INFO] Selected 22 target genomes.
[2023-06-28 10:22:27,811] [INFO] Target genome list was writen to GCA_944320015.1_BRZ_N_bin151_genomic.fna/target_genomes.txt
[2023-06-28 10:22:27,815] [INFO] Task started: fastANI
[2023-06-28 10:22:27,815] [INFO] Running command: fastANI --query /var/lib/cwl/stg39ed87b0-b851-426e-8149-ca58e6cdcbe2/GCA_944320015.1_BRZ_N_bin151_genomic.fna.gz --refList GCA_944320015.1_BRZ_N_bin151_genomic.fna/target_genomes.txt --output GCA_944320015.1_BRZ_N_bin151_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 10:22:42,309] [INFO] Task succeeded: fastANI
[2023-06-28 10:22:42,310] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg18bf3d42-02dc-4dd5-9549-a649f12b6e7f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 10:22:42,311] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg18bf3d42-02dc-4dd5-9549-a649f12b6e7f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 10:22:42,320] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 10:22:42,320] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 10:22:42,321] [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	80.4281	468	855	95	below_threshold
Barnesiella intestinihominis	strain=YIT 11860	GCA_000296465.1	487174	487174	type	True	79.8749	419	855	95	below_threshold
Coprobacter fastidiosus	strain=NSB1	GCA_003634345.1	1099853	1099853	type	True	76.3811	50	855	95	below_threshold
Coprobacter fastidiosus	strain=NSB1	GCA_000473955.1	1099853	1099853	type	True	76.2469	52	855	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 10:22:42,323] [INFO] DFAST Taxonomy check result was written to GCA_944320015.1_BRZ_N_bin151_genomic.fna/tc_result.tsv
[2023-06-28 10:22:42,324] [INFO] ===== Taxonomy check completed =====
[2023-06-28 10:22:42,324] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 10:22:42,324] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg18bf3d42-02dc-4dd5-9549-a649f12b6e7f/dqc_reference/checkm_data
[2023-06-28 10:22:42,326] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 10:22:42,367] [INFO] Task started: CheckM
[2023-06-28 10:22:42,367] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944320015.1_BRZ_N_bin151_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944320015.1_BRZ_N_bin151_genomic.fna/checkm_input GCA_944320015.1_BRZ_N_bin151_genomic.fna/checkm_result
[2023-06-28 10:23:28,501] [INFO] Task succeeded: CheckM
[2023-06-28 10:23:28,503] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 10:23:28,524] [INFO] ===== Completeness check finished =====
[2023-06-28 10:23:28,525] [INFO] ===== Start GTDB Search =====
[2023-06-28 10:23:28,525] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944320015.1_BRZ_N_bin151_genomic.fna/markers.fasta)
[2023-06-28 10:23:28,526] [INFO] Task started: Blastn
[2023-06-28 10:23:28,526] [INFO] Running command: blastn -query GCA_944320015.1_BRZ_N_bin151_genomic.fna/markers.fasta -db /var/lib/cwl/stg18bf3d42-02dc-4dd5-9549-a649f12b6e7f/dqc_reference/reference_markers_gtdb.fasta -out GCA_944320015.1_BRZ_N_bin151_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 10:23:29,311] [INFO] Task succeeded: Blastn
[2023-06-28 10:23:29,316] [INFO] Selected 10 target genomes.
[2023-06-28 10:23:29,316] [INFO] Target genome list was writen to GCA_944320015.1_BRZ_N_bin151_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 10:23:29,320] [INFO] Task started: fastANI
[2023-06-28 10:23:29,320] [INFO] Running command: fastANI --query /var/lib/cwl/stg39ed87b0-b851-426e-8149-ca58e6cdcbe2/GCA_944320015.1_BRZ_N_bin151_genomic.fna.gz --refList GCA_944320015.1_BRZ_N_bin151_genomic.fna/target_genomes_gtdb.txt --output GCA_944320015.1_BRZ_N_bin151_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 10:23:34,467] [INFO] Task succeeded: fastANI
[2023-06-28 10:23:34,480] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 10:23:34,480] [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_019114445.1	s__Barnesiella excrementigallinarum	81.9447	541	855	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Barnesiellaceae;g__Barnesiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000512915.1	s__Barnesiella viscericola	80.4372	468	855	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Barnesiellaceae;g__Barnesiella	95.0	97.37	97.37	0.91	0.91	2	-
GCA_019115485.1	s__Barnesiella excrementavium	80.2022	442	855	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Barnesiellaceae;g__Barnesiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002159975.1	s__Barnesiella merdigallinarum	80.1987	481	855	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Barnesiellaceae;g__Barnesiella	95.0	97.77	95.24	0.93	0.91	5	-
GCF_002161555.1	s__Barnesiella merdipullorum	80.1626	500	855	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Barnesiellaceae;g__Barnesiella	95.0	99.43	99.43	0.98	0.98	2	-
GCF_000296465.1	s__Barnesiella intestinihominis	79.892	419	855	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Barnesiellaceae;g__Barnesiella	95.0	98.49	98.18	0.93	0.86	27	-
GCA_900538555.1	s__UMGS27 sp900538555	77.1682	140	855	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Barnesiellaceae;g__UMGS27	95.0	99.31	98.62	0.96	0.93	3	-
GCA_900542765.1	s__UBA11471 sp900542765	76.9352	95	855	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA11471;g__UBA11471	95.0	98.30	98.30	0.95	0.95	2	-
GCA_000434215.1	s__UBA11471 sp000434215	76.6997	66	855	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA11471;g__UBA11471	95.0	99.32	98.64	0.92	0.84	6	-
--------------------------------------------------------------------------------
[2023-06-28 10:23:34,482] [INFO] GTDB search result was written to GCA_944320015.1_BRZ_N_bin151_genomic.fna/result_gtdb.tsv
[2023-06-28 10:23:34,483] [INFO] ===== GTDB Search completed =====
[2023-06-28 10:23:34,486] [INFO] DFAST_QC result json was written to GCA_944320015.1_BRZ_N_bin151_genomic.fna/dqc_result.json
[2023-06-28 10:23:34,486] [INFO] DFAST_QC completed!
[2023-06-28 10:23:34,487] [INFO] Total running time: 0h1m27s