[2023-06-04 17:47:40,461] [INFO] DFAST_QC pipeline started.
[2023-06-04 17:47:40,463] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 17:47:40,463] [INFO] DQC Reference Directory: /var/lib/cwl/stga72f5211-e20d-46c4-8edb-b3d154c187b7/dqc_reference
[2023-06-04 17:47:42,508] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 17:47:42,509] [INFO] Task started: Prodigal
[2023-06-04 17:47:42,510] [INFO] Running command: gunzip -c /var/lib/cwl/stg14b184e2-6e27-4c58-9201-f08da8642a64/GCA_004552245.1_ASM455224v1_genomic.fna.gz | prodigal -d GCA_004552245.1_ASM455224v1_genomic.fna/cds.fna -a GCA_004552245.1_ASM455224v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 17:47:46,422] [INFO] Task succeeded: Prodigal
[2023-06-04 17:47:46,422] [INFO] Task started: HMMsearch
[2023-06-04 17:47:46,422] [INFO] Running command: hmmsearch --tblout GCA_004552245.1_ASM455224v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga72f5211-e20d-46c4-8edb-b3d154c187b7/dqc_reference/reference_markers.hmm GCA_004552245.1_ASM455224v1_genomic.fna/protein.faa > /dev/null
[2023-06-04 17:47:46,648] [INFO] Task succeeded: HMMsearch
[2023-06-04 17:47:46,650] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg14b184e2-6e27-4c58-9201-f08da8642a64/GCA_004552245.1_ASM455224v1_genomic.fna.gz]
[2023-06-04 17:47:46,676] [INFO] Query marker FASTA was written to GCA_004552245.1_ASM455224v1_genomic.fna/markers.fasta
[2023-06-04 17:47:46,676] [INFO] Task started: Blastn
[2023-06-04 17:47:46,676] [INFO] Running command: blastn -query GCA_004552245.1_ASM455224v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga72f5211-e20d-46c4-8edb-b3d154c187b7/dqc_reference/reference_markers.fasta -out GCA_004552245.1_ASM455224v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 17:47:47,422] [INFO] Task succeeded: Blastn
[2023-06-04 17:47:47,427] [INFO] Selected 17 target genomes.
[2023-06-04 17:47:47,428] [INFO] Target genome list was writen to GCA_004552245.1_ASM455224v1_genomic.fna/target_genomes.txt
[2023-06-04 17:47:47,827] [INFO] Task started: fastANI
[2023-06-04 17:47:47,827] [INFO] Running command: fastANI --query /var/lib/cwl/stg14b184e2-6e27-4c58-9201-f08da8642a64/GCA_004552245.1_ASM455224v1_genomic.fna.gz --refList GCA_004552245.1_ASM455224v1_genomic.fna/target_genomes.txt --output GCA_004552245.1_ASM455224v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 17:47:55,923] [INFO] Task succeeded: fastANI
[2023-06-04 17:47:55,924] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga72f5211-e20d-46c4-8edb-b3d154c187b7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 17:47:55,925] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga72f5211-e20d-46c4-8edb-b3d154c187b7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 17:47:55,943] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 17:47:55,944] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-04 17:47:55,944] [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
Butyricicoccus pullicaecorum	strain=DSM 23266	GCA_900167005.1	501571	501571	type	True	80.3856	254	472	95	below_threshold
Intestinibacillus massiliensis	strain=type strain: Marseille-P3216	GCA_900155735.1	1871029	1871029	type	True	79.2546	175	472	95	below_threshold
Butyricicoccus faecihominis	strain=JCM 31056	GCA_014648015.1	1712515	1712515	type	True	78.5318	149	472	95	below_threshold
Butyricicoccus faecihominis	strain=JCM 31056	GCA_016586375.1	1712515	1712515	type	True	78.5094	148	472	95	below_threshold
Agathobaculum desmolans	strain=ATCC 43058	GCA_000701665.1	39484	39484	type	True	78.2617	121	472	95	below_threshold
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	77.1069	63	472	95	below_threshold
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	76.8433	63	472	95	below_threshold
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	76.7749	60	472	95	below_threshold
Feifania hominis	strain=BX7	GCA_014384765.1	2763660	2763660	type	True	75.8072	53	472	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-04 17:47:55,947] [INFO] DFAST Taxonomy check result was written to GCA_004552245.1_ASM455224v1_genomic.fna/tc_result.tsv
[2023-06-04 17:47:55,948] [INFO] ===== Taxonomy check completed =====
[2023-06-04 17:47:55,948] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 17:47:55,948] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga72f5211-e20d-46c4-8edb-b3d154c187b7/dqc_reference/checkm_data
[2023-06-04 17:47:55,950] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 17:47:55,970] [INFO] Task started: CheckM
[2023-06-04 17:47:55,970] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_004552245.1_ASM455224v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_004552245.1_ASM455224v1_genomic.fna/checkm_input GCA_004552245.1_ASM455224v1_genomic.fna/checkm_result
[2023-06-04 17:48:14,359] [INFO] Task succeeded: CheckM
[2023-06-04 17:48:14,361] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 68.23%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-04 17:48:14,382] [INFO] ===== Completeness check finished =====
[2023-06-04 17:48:14,383] [INFO] ===== Start GTDB Search =====
[2023-06-04 17:48:14,383] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_004552245.1_ASM455224v1_genomic.fna/markers.fasta)
[2023-06-04 17:48:14,383] [INFO] Task started: Blastn
[2023-06-04 17:48:14,384] [INFO] Running command: blastn -query GCA_004552245.1_ASM455224v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga72f5211-e20d-46c4-8edb-b3d154c187b7/dqc_reference/reference_markers_gtdb.fasta -out GCA_004552245.1_ASM455224v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 17:48:15,586] [INFO] Task succeeded: Blastn
[2023-06-04 17:48:15,591] [INFO] Selected 13 target genomes.
[2023-06-04 17:48:15,591] [INFO] Target genome list was writen to GCA_004552245.1_ASM455224v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 17:48:15,890] [INFO] Task started: fastANI
[2023-06-04 17:48:15,890] [INFO] Running command: fastANI --query /var/lib/cwl/stg14b184e2-6e27-4c58-9201-f08da8642a64/GCA_004552245.1_ASM455224v1_genomic.fna.gz --refList GCA_004552245.1_ASM455224v1_genomic.fna/target_genomes_gtdb.txt --output GCA_004552245.1_ASM455224v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 17:48:21,618] [INFO] Task succeeded: fastANI
[2023-06-04 17:48:21,635] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 17:48:21,635] [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_004552245.1	s__Butyricicoccus sp004552245	100.0	466	472	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Butyricicoccus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_019119435.1	s__Butyricicoccus avicola	80.7869	242	472	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Butyricicoccus	95.0	98.92	98.91	0.91	0.91	3	-
GCF_900167005.1	s__Butyricicoccus pullicaecorum	80.3723	255	472	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Butyricicoccus	95.0	98.10	95.60	0.92	0.80	7	-
GCF_003481705.1	s__Agathobaculum sp003481705	79.3256	183	472	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum	95.0	98.33	96.26	0.92	0.82	8	-
GCF_900155735.1	s__Intestinibacillus massiliensis	79.2546	175	472	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Intestinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900625105.1	s__Agathobaculum sp900625105	79.1641	200	472	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900604335.1	s__Butyricicoccus sp900604335	78.9863	157	472	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Butyricicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900547195.1	s__Butyricicoccus sp900547195	78.938	164	472	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Butyricicoccus	95.0	97.99	97.22	0.87	0.84	3	-
GCA_019115615.1	s__Agathobaculum merdavium	78.7801	163	472	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019113065.1	s__Agathobaculum stercoravium	78.7456	183	472	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum	95.0	98.25	98.25	0.89	0.89	2	-
GCA_018366195.1	s__Butyricicoccus pullicaecorum_C	78.1523	69	472	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Butyricicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_904420185.1	s__Butyricicoccus sp904420185	78.0719	132	472	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Butyricicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018366035.1	s__Butyricicoccus pullicaecorum_A	77.6907	64	472	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Butyricicoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-04 17:48:21,638] [INFO] GTDB search result was written to GCA_004552245.1_ASM455224v1_genomic.fna/result_gtdb.tsv
[2023-06-04 17:48:21,639] [INFO] ===== GTDB Search completed =====
[2023-06-04 17:48:21,644] [INFO] DFAST_QC result json was written to GCA_004552245.1_ASM455224v1_genomic.fna/dqc_result.json
[2023-06-04 17:48:21,645] [INFO] DFAST_QC completed!
[2023-06-04 17:48:21,645] [INFO] Total running time: 0h0m41s