[2024-01-25 18:58:35,838] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:58:35,839] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:58:35,839] [INFO] DQC Reference Directory: /var/lib/cwl/stg8e08d78d-4dd2-4d76-8d3e-5f083bba6280/dqc_reference
[2024-01-25 18:58:36,996] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:58:36,997] [INFO] Task started: Prodigal
[2024-01-25 18:58:36,997] [INFO] Running command: gunzip -c /var/lib/cwl/stga9587e7b-51b5-4d19-88b0-ec0fa126666e/GCF_025567495.1_ASM2556749v1_genomic.fna.gz | prodigal -d GCF_025567495.1_ASM2556749v1_genomic.fna/cds.fna -a GCF_025567495.1_ASM2556749v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:58:43,106] [INFO] Task succeeded: Prodigal
[2024-01-25 18:58:43,106] [INFO] Task started: HMMsearch
[2024-01-25 18:58:43,106] [INFO] Running command: hmmsearch --tblout GCF_025567495.1_ASM2556749v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8e08d78d-4dd2-4d76-8d3e-5f083bba6280/dqc_reference/reference_markers.hmm GCF_025567495.1_ASM2556749v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:58:43,320] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:58:43,321] [INFO] Found 6/6 markers.
[2024-01-25 18:58:43,347] [INFO] Query marker FASTA was written to GCF_025567495.1_ASM2556749v1_genomic.fna/markers.fasta
[2024-01-25 18:58:43,347] [INFO] Task started: Blastn
[2024-01-25 18:58:43,348] [INFO] Running command: blastn -query GCF_025567495.1_ASM2556749v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8e08d78d-4dd2-4d76-8d3e-5f083bba6280/dqc_reference/reference_markers.fasta -out GCF_025567495.1_ASM2556749v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:58:43,924] [INFO] Task succeeded: Blastn
[2024-01-25 18:58:43,928] [INFO] Selected 8 target genomes.
[2024-01-25 18:58:43,928] [INFO] Target genome list was writen to GCF_025567495.1_ASM2556749v1_genomic.fna/target_genomes.txt
[2024-01-25 18:58:43,932] [INFO] Task started: fastANI
[2024-01-25 18:58:43,932] [INFO] Running command: fastANI --query /var/lib/cwl/stga9587e7b-51b5-4d19-88b0-ec0fa126666e/GCF_025567495.1_ASM2556749v1_genomic.fna.gz --refList GCF_025567495.1_ASM2556749v1_genomic.fna/target_genomes.txt --output GCF_025567495.1_ASM2556749v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:58:47,997] [INFO] Task succeeded: fastANI
[2024-01-25 18:58:47,998] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8e08d78d-4dd2-4d76-8d3e-5f083bba6280/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:58:47,998] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8e08d78d-4dd2-4d76-8d3e-5f083bba6280/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:58:48,002] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:58:48,002] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:58:48,002] [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
Ruminococcus bicirculans	strain=80/3	GCA_000723465.1	1160721	1160721	type	True	97.4653	825	972	95	conclusive
Ruminococcus albus	strain=7	GCA_000179635.2	1264	1264	suspected-type	True	78.0616	147	972	95	below_threshold
Ruminococcus albus	strain=DSM 20455	GCA_000621285.1	1264	1264	suspected-type	True	77.7573	144	972	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:58:48,003] [INFO] DFAST Taxonomy check result was written to GCF_025567495.1_ASM2556749v1_genomic.fna/tc_result.tsv
[2024-01-25 18:58:48,004] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:58:48,004] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:58:48,004] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8e08d78d-4dd2-4d76-8d3e-5f083bba6280/dqc_reference/checkm_data
[2024-01-25 18:58:48,005] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:58:48,036] [INFO] Task started: CheckM
[2024-01-25 18:58:48,036] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025567495.1_ASM2556749v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025567495.1_ASM2556749v1_genomic.fna/checkm_input GCF_025567495.1_ASM2556749v1_genomic.fna/checkm_result
[2024-01-25 18:59:10,635] [INFO] Task succeeded: CheckM
[2024-01-25 18:59:10,636] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:59:10,653] [INFO] ===== Completeness check finished =====
[2024-01-25 18:59:10,653] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:59:10,653] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025567495.1_ASM2556749v1_genomic.fna/markers.fasta)
[2024-01-25 18:59:10,653] [INFO] Task started: Blastn
[2024-01-25 18:59:10,654] [INFO] Running command: blastn -query GCF_025567495.1_ASM2556749v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8e08d78d-4dd2-4d76-8d3e-5f083bba6280/dqc_reference/reference_markers_gtdb.fasta -out GCF_025567495.1_ASM2556749v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:59:11,640] [INFO] Task succeeded: Blastn
[2024-01-25 18:59:11,644] [INFO] Selected 18 target genomes.
[2024-01-25 18:59:11,644] [INFO] Target genome list was writen to GCF_025567495.1_ASM2556749v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:59:11,664] [INFO] Task started: fastANI
[2024-01-25 18:59:11,664] [INFO] Running command: fastANI --query /var/lib/cwl/stga9587e7b-51b5-4d19-88b0-ec0fa126666e/GCF_025567495.1_ASM2556749v1_genomic.fna.gz --refList GCF_025567495.1_ASM2556749v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025567495.1_ASM2556749v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:59:21,399] [INFO] Task succeeded: fastANI
[2024-01-25 18:59:21,409] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:59:21,410] [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_000723465.1	s__Ruminococcus_D bicirculans	97.4653	825	972	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	97.50	96.68	0.89	0.80	66	conclusive
GCA_900539095.1	s__Ruminococcus_D sp900539095	89.6373	590	972	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	97.71	97.55	0.88	0.82	3	-
GCA_900318545.1	s__Ruminococcus_D sp900318545	78.0919	139	972	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	98.38	97.31	0.84	0.77	8	-
GCF_000621805.1	s__Ruminococcus_D sp000621805	78.0879	143	972	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000179635.2	s__Ruminococcus_D albus	78.0717	146	972	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	98.29	97.69	0.91	0.87	8	-
GCF_900112155.1	s__Ruminococcus_D albus_D	78.0187	148	972	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900319075.1	s__Ruminococcus_D sp900319075	77.9963	120	972	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	98.31	96.98	0.90	0.83	16	-
GCA_017626015.1	s__Ruminococcus_D sp017626015	77.9804	161	972	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902800795.1	s__Ruminococcus_D sp902800795	77.9733	155	972	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	97.42	97.23	0.92	0.92	3	-
GCA_017484095.1	s__Ruminococcus_D sp017484095	77.9453	152	972	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900314975.1	s__Ruminococcus_D sp900314975	77.9088	142	972	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	98.52	97.44	0.93	0.89	4	-
GCF_000526775.1	s__Ruminococcus_D albus_A	77.9015	149	972	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	97.64	97.22	0.89	0.80	5	-
GCA_902762735.1	s__Ruminococcus_D sp902762735	77.7454	132	972	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	97.61	97.61	0.90	0.90	2	-
GCA_002391065.1	s__Ruminococcus_D sp002391065	77.6668	149	972	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109655.1	s__Ruminococcus_D albus_B	77.5063	139	972	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	96.54	96.54	0.90	0.90	2	-
GCA_902767035.1	s__Ruminococcus_D sp902767035	77.2402	126	972	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002368715.1	s__Ruminococcus_D sp002368715	76.878	103	972	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:59:21,412] [INFO] GTDB search result was written to GCF_025567495.1_ASM2556749v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:59:21,412] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:59:21,415] [INFO] DFAST_QC result json was written to GCF_025567495.1_ASM2556749v1_genomic.fna/dqc_result.json
[2024-01-25 18:59:21,415] [INFO] DFAST_QC completed!
[2024-01-25 18:59:21,415] [INFO] Total running time: 0h0m46s