[2023-06-14 00:42:33,108] [INFO] DFAST_QC pipeline started.
[2023-06-14 00:42:33,110] [INFO] DFAST_QC version: 0.5.7
[2023-06-14 00:42:33,110] [INFO] DQC Reference Directory: /var/lib/cwl/stg249b0831-2843-4b75-be16-bcd191ca2be8/dqc_reference
[2023-06-14 00:42:34,417] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-14 00:42:34,418] [INFO] Task started: Prodigal
[2023-06-14 00:42:34,418] [INFO] Running command: gunzip -c /var/lib/cwl/stg77bf39d3-318f-4907-b276-b87ea150792a/GCA_022797775.1_ASM2279777v1_genomic.fna.gz | prodigal -d GCA_022797775.1_ASM2279777v1_genomic.fna/cds.fna -a GCA_022797775.1_ASM2279777v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-14 00:42:40,727] [INFO] Task succeeded: Prodigal
[2023-06-14 00:42:40,728] [INFO] Task started: HMMsearch
[2023-06-14 00:42:40,728] [INFO] Running command: hmmsearch --tblout GCA_022797775.1_ASM2279777v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg249b0831-2843-4b75-be16-bcd191ca2be8/dqc_reference/reference_markers.hmm GCA_022797775.1_ASM2279777v1_genomic.fna/protein.faa > /dev/null
[2023-06-14 00:42:40,982] [INFO] Task succeeded: HMMsearch
[2023-06-14 00:42:40,983] [INFO] Found 6/6 markers.
[2023-06-14 00:42:41,014] [INFO] Query marker FASTA was written to GCA_022797775.1_ASM2279777v1_genomic.fna/markers.fasta
[2023-06-14 00:42:41,014] [INFO] Task started: Blastn
[2023-06-14 00:42:41,014] [INFO] Running command: blastn -query GCA_022797775.1_ASM2279777v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg249b0831-2843-4b75-be16-bcd191ca2be8/dqc_reference/reference_markers.fasta -out GCA_022797775.1_ASM2279777v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-14 00:42:41,702] [INFO] Task succeeded: Blastn
[2023-06-14 00:42:41,708] [INFO] Selected 13 target genomes.
[2023-06-14 00:42:41,708] [INFO] Target genome list was writen to GCA_022797775.1_ASM2279777v1_genomic.fna/target_genomes.txt
[2023-06-14 00:42:41,709] [INFO] Task started: fastANI
[2023-06-14 00:42:41,709] [INFO] Running command: fastANI --query /var/lib/cwl/stg77bf39d3-318f-4907-b276-b87ea150792a/GCA_022797775.1_ASM2279777v1_genomic.fna.gz --refList GCA_022797775.1_ASM2279777v1_genomic.fna/target_genomes.txt --output GCA_022797775.1_ASM2279777v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-14 00:42:47,995] [INFO] Task succeeded: fastANI
[2023-06-14 00:42:47,996] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg249b0831-2843-4b75-be16-bcd191ca2be8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-14 00:42:47,997] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg249b0831-2843-4b75-be16-bcd191ca2be8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-14 00:42:48,007] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-06-14 00:42:48,008] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-14 00:42:48,008] [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
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	80.4879	366	766	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	78.899	216	766	95	below_threshold
Pusillibacter faecalis	strain=MM59	GCA_018408705.1	2714358	2714358	type	True	78.631	245	766	95	below_threshold
Clostridium phoceensis	strain=GD3	GCA_001244495.1	1650661	1650661	type	True	77.9876	170	766	95	below_threshold
Oscillibacter ruminantium	strain=GH1	GCA_000307265.1	1263547	1263547	type	True	77.9429	197	766	95	below_threshold
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	77.9103	186	766	95	below_threshold
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	77.8744	200	766	95	below_threshold
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	77.857	153	766	95	below_threshold
Vescimonas coprocola	strain=MM50	GCA_018408575.1	2714355	2714355	type	True	77.7923	154	766	95	below_threshold
Vescimonas fastidiosa	strain=MM35	GCA_018326305.1	2714353	2714353	type	True	77.6832	136	766	95	below_threshold
Faecalibacterium gallinarum	strain=JCM 17207	GCA_022180365.1	2903556	2903556	type	True	76.7701	90	766	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-14 00:42:48,010] [INFO] DFAST Taxonomy check result was written to GCA_022797775.1_ASM2279777v1_genomic.fna/tc_result.tsv
[2023-06-14 00:42:48,011] [INFO] ===== Taxonomy check completed =====
[2023-06-14 00:42:48,011] [INFO] ===== Start completeness check using CheckM =====
[2023-06-14 00:42:48,012] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg249b0831-2843-4b75-be16-bcd191ca2be8/dqc_reference/checkm_data
[2023-06-14 00:42:48,014] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-14 00:42:48,046] [INFO] Task started: CheckM
[2023-06-14 00:42:48,046] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022797775.1_ASM2279777v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022797775.1_ASM2279777v1_genomic.fna/checkm_input GCA_022797775.1_ASM2279777v1_genomic.fna/checkm_result
[2023-06-14 00:43:12,302] [INFO] Task succeeded: CheckM
[2023-06-14 00:43:12,304] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-14 00:43:12,327] [INFO] ===== Completeness check finished =====
[2023-06-14 00:43:12,328] [INFO] ===== Start GTDB Search =====
[2023-06-14 00:43:12,329] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022797775.1_ASM2279777v1_genomic.fna/markers.fasta)
[2023-06-14 00:43:12,329] [INFO] Task started: Blastn
[2023-06-14 00:43:12,329] [INFO] Running command: blastn -query GCA_022797775.1_ASM2279777v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg249b0831-2843-4b75-be16-bcd191ca2be8/dqc_reference/reference_markers_gtdb.fasta -out GCA_022797775.1_ASM2279777v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-14 00:43:13,601] [INFO] Task succeeded: Blastn
[2023-06-14 00:43:13,608] [INFO] Selected 11 target genomes.
[2023-06-14 00:43:13,608] [INFO] Target genome list was writen to GCA_022797775.1_ASM2279777v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-14 00:43:13,611] [INFO] Task started: fastANI
[2023-06-14 00:43:13,611] [INFO] Running command: fastANI --query /var/lib/cwl/stg77bf39d3-318f-4907-b276-b87ea150792a/GCA_022797775.1_ASM2279777v1_genomic.fna.gz --refList GCA_022797775.1_ASM2279777v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022797775.1_ASM2279777v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-14 00:43:20,945] [INFO] Task succeeded: fastANI
[2023-06-14 00:43:20,955] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-14 00:43:20,956] [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_910574635.1	s__Dysosmobacter sp009774015	97.5229	681	766	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	96.89	96.54	0.80	0.71	5	conclusive
GCA_009773995.1	s__Dysosmobacter sp009773995	90.9292	527	766	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	99.84	99.84	0.82	0.82	2	-
GCA_910587705.1	s__Dysosmobacter sp910587705	90.4793	609	766	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910579435.1	s__Dysosmobacter sp910579435	89.9048	565	766	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910583785.1	s__Dysosmobacter sp910583785	89.8483	607	766	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910587875.1	s__Dysosmobacter sp910587875	89.3428	554	766	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910583695.1	s__Dysosmobacter sp910583695	88.831	584	766	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910576865.1	s__Dysosmobacter sp910576865	88.6591	567	766	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910588175.1	s__Dysosmobacter sp910588175	88.4354	532	766	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910585245.1	s__Dysosmobacter sp910585245	86.1589	568	766	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910587525.1	s__Dysosmobacter sp910587525	81.0983	351	766	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-14 00:43:20,958] [INFO] GTDB search result was written to GCA_022797775.1_ASM2279777v1_genomic.fna/result_gtdb.tsv
[2023-06-14 00:43:20,958] [INFO] ===== GTDB Search completed =====
[2023-06-14 00:43:20,965] [INFO] DFAST_QC result json was written to GCA_022797775.1_ASM2279777v1_genomic.fna/dqc_result.json
[2023-06-14 00:43:20,966] [INFO] DFAST_QC completed!
[2023-06-14 00:43:20,966] [INFO] Total running time: 0h0m48s