[2023-06-29 19:52:23,662] [INFO] DFAST_QC pipeline started.
[2023-06-29 19:52:24,058] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 19:52:24,059] [INFO] DQC Reference Directory: /var/lib/cwl/stg046a2d86-dc1b-47e4-afc8-e1450c19242c/dqc_reference
[2023-06-29 19:52:26,150] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 19:52:26,151] [INFO] Task started: Prodigal
[2023-06-29 19:52:26,152] [INFO] Running command: gunzip -c /var/lib/cwl/stgd3b9935b-9e0e-412b-9d75-c43dd23dd922/GCA_025543155.1_ASM2554315v1_genomic.fna.gz | prodigal -d GCA_025543155.1_ASM2554315v1_genomic.fna/cds.fna -a GCA_025543155.1_ASM2554315v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 19:52:31,382] [INFO] Task succeeded: Prodigal
[2023-06-29 19:52:31,382] [INFO] Task started: HMMsearch
[2023-06-29 19:52:31,382] [INFO] Running command: hmmsearch --tblout GCA_025543155.1_ASM2554315v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg046a2d86-dc1b-47e4-afc8-e1450c19242c/dqc_reference/reference_markers.hmm GCA_025543155.1_ASM2554315v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 19:52:31,589] [INFO] Task succeeded: HMMsearch
[2023-06-29 19:52:31,590] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd3b9935b-9e0e-412b-9d75-c43dd23dd922/GCA_025543155.1_ASM2554315v1_genomic.fna.gz]
[2023-06-29 19:52:31,619] [INFO] Query marker FASTA was written to GCA_025543155.1_ASM2554315v1_genomic.fna/markers.fasta
[2023-06-29 19:52:31,620] [INFO] Task started: Blastn
[2023-06-29 19:52:31,620] [INFO] Running command: blastn -query GCA_025543155.1_ASM2554315v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg046a2d86-dc1b-47e4-afc8-e1450c19242c/dqc_reference/reference_markers.fasta -out GCA_025543155.1_ASM2554315v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 19:52:32,304] [INFO] Task succeeded: Blastn
[2023-06-29 19:52:32,309] [INFO] Selected 17 target genomes.
[2023-06-29 19:52:32,310] [INFO] Target genome list was writen to GCA_025543155.1_ASM2554315v1_genomic.fna/target_genomes.txt
[2023-06-29 19:52:32,314] [INFO] Task started: fastANI
[2023-06-29 19:52:32,314] [INFO] Running command: fastANI --query /var/lib/cwl/stgd3b9935b-9e0e-412b-9d75-c43dd23dd922/GCA_025543155.1_ASM2554315v1_genomic.fna.gz --refList GCA_025543155.1_ASM2554315v1_genomic.fna/target_genomes.txt --output GCA_025543155.1_ASM2554315v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 19:52:41,995] [INFO] Task succeeded: fastANI
[2023-06-29 19:52:41,996] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg046a2d86-dc1b-47e4-afc8-e1450c19242c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 19:52:41,996] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg046a2d86-dc1b-47e4-afc8-e1450c19242c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 19:52:42,009] [INFO] Found 7 fastANI hits (2 hits with ANI > threshold)
[2023-06-29 19:52:42,010] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-29 19:52:42,010] [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 faecihominis	strain=JCM 31056	GCA_016586375.1	1712515	1712515	type	True	95.7814	512	602	95	conclusive
Butyricicoccus faecihominis	strain=JCM 31056	GCA_014648015.1	1712515	1712515	type	True	95.7673	527	602	95	conclusive
Agathobaculum desmolans	strain=ATCC 43058	GCA_000701665.1	39484	39484	type	True	79.3026	249	602	95	below_threshold
Butyricicoccus pullicaecorum	strain=DSM 23266	GCA_900167005.1	501571	501571	type	True	78.6594	152	602	95	below_threshold
Intestinibacillus massiliensis	strain=type strain: Marseille-P3216	GCA_900155735.1	1871029	1871029	type	True	78.2898	147	602	95	below_threshold
Butyricicoccus intestinisimiae	strain=MSJd-7	GCA_018918345.1	2841509	2841509	type	True	77.9505	105	602	95	below_threshold
Butyricicoccus porcorum	strain=BB10	GCA_002157465.1	1945634	1945634	type	True	77.9364	97	602	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 19:52:42,012] [INFO] DFAST Taxonomy check result was written to GCA_025543155.1_ASM2554315v1_genomic.fna/tc_result.tsv
[2023-06-29 19:52:42,012] [INFO] ===== Taxonomy check completed =====
[2023-06-29 19:52:42,013] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 19:52:42,013] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg046a2d86-dc1b-47e4-afc8-e1450c19242c/dqc_reference/checkm_data
[2023-06-29 19:52:42,014] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 19:52:42,043] [INFO] Task started: CheckM
[2023-06-29 19:52:42,043] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_025543155.1_ASM2554315v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_025543155.1_ASM2554315v1_genomic.fna/checkm_input GCA_025543155.1_ASM2554315v1_genomic.fna/checkm_result
[2023-06-29 19:53:03,832] [INFO] Task succeeded: CheckM
[2023-06-29 19:53:03,833] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 19:53:03,856] [INFO] ===== Completeness check finished =====
[2023-06-29 19:53:03,856] [INFO] ===== Start GTDB Search =====
[2023-06-29 19:53:03,857] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_025543155.1_ASM2554315v1_genomic.fna/markers.fasta)
[2023-06-29 19:53:03,857] [INFO] Task started: Blastn
[2023-06-29 19:53:03,858] [INFO] Running command: blastn -query GCA_025543155.1_ASM2554315v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg046a2d86-dc1b-47e4-afc8-e1450c19242c/dqc_reference/reference_markers_gtdb.fasta -out GCA_025543155.1_ASM2554315v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 19:53:04,948] [INFO] Task succeeded: Blastn
[2023-06-29 19:53:04,952] [INFO] Selected 12 target genomes.
[2023-06-29 19:53:04,953] [INFO] Target genome list was writen to GCA_025543155.1_ASM2554315v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 19:53:04,958] [INFO] Task started: fastANI
[2023-06-29 19:53:04,958] [INFO] Running command: fastANI --query /var/lib/cwl/stgd3b9935b-9e0e-412b-9d75-c43dd23dd922/GCA_025543155.1_ASM2554315v1_genomic.fna.gz --refList GCA_025543155.1_ASM2554315v1_genomic.fna/target_genomes_gtdb.txt --output GCA_025543155.1_ASM2554315v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 19:53:10,963] [INFO] Task succeeded: fastANI
[2023-06-29 19:53:10,979] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 19:53:10,979] [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_003096535.1	s__Agathobaculum butyriciproducens	97.9702	526	602	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum	95.0	96.66	95.68	0.85	0.79	34	conclusive
GCA_900544475.1	s__Agathobaculum sp900544475	83.2697	302	602	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum	95.0	97.90	97.82	0.89	0.86	3	-
GCF_003481705.1	s__Agathobaculum sp003481705	83.2157	388	602	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum	95.0	98.33	96.26	0.92	0.82	8	-
GCA_900555465.1	s__Agathobaculum intestinigallinarum	80.7823	196	602	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum	95.0	97.06	97.06	0.83	0.83	2	-
GCF_900625105.1	s__Agathobaculum sp900625105	80.5692	303	602	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	80.2891	248	602	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_019115615.1	s__Agathobaculum merdavium	80.1598	235	602	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_019115185.1	s__Agathobaculum merdipullorum	79.9297	196	602	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_900557315.1	s__Agathobaculum sp900557315	79.8351	169	602	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum	95.0	100.00	100.00	0.98	0.98	2	-
GCA_019114345.1	s__Agathobaculum pullistercoris	79.7767	239	602	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum	95.0	98.72	98.13	0.86	0.78	4	-
GCA_019115425.1	s__Agathobaculum merdigallinarum	79.6921	226	602	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_000701665.1	s__Agathobaculum desmolans	79.2828	250	602	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum	95.0	98.85	98.85	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2023-06-29 19:53:10,984] [INFO] GTDB search result was written to GCA_025543155.1_ASM2554315v1_genomic.fna/result_gtdb.tsv
[2023-06-29 19:53:10,989] [INFO] ===== GTDB Search completed =====
[2023-06-29 19:53:10,997] [INFO] DFAST_QC result json was written to GCA_025543155.1_ASM2554315v1_genomic.fna/dqc_result.json
[2023-06-29 19:53:10,997] [INFO] DFAST_QC completed!
[2023-06-29 19:53:10,997] [INFO] Total running time: 0h0m47s