[2024-01-25 18:47:35,697] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:47:35,703] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:47:35,703] [INFO] DQC Reference Directory: /var/lib/cwl/stg46d49248-e1e4-40d7-b033-bce425f1d72b/dqc_reference
[2024-01-25 18:47:36,914] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:47:36,915] [INFO] Task started: Prodigal
[2024-01-25 18:47:36,915] [INFO] Running command: gunzip -c /var/lib/cwl/stgc0393a6f-dd00-4a58-88d7-06b4d40acc0d/GCF_000770375.1_ASM77037v1_genomic.fna.gz | prodigal -d GCF_000770375.1_ASM77037v1_genomic.fna/cds.fna -a GCF_000770375.1_ASM77037v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:47:43,209] [INFO] Task succeeded: Prodigal
[2024-01-25 18:47:43,209] [INFO] Task started: HMMsearch
[2024-01-25 18:47:43,209] [INFO] Running command: hmmsearch --tblout GCF_000770375.1_ASM77037v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg46d49248-e1e4-40d7-b033-bce425f1d72b/dqc_reference/reference_markers.hmm GCF_000770375.1_ASM77037v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:47:43,430] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:47:43,431] [INFO] Found 6/6 markers.
[2024-01-25 18:47:43,460] [INFO] Query marker FASTA was written to GCF_000770375.1_ASM77037v1_genomic.fna/markers.fasta
[2024-01-25 18:47:43,461] [INFO] Task started: Blastn
[2024-01-25 18:47:43,461] [INFO] Running command: blastn -query GCF_000770375.1_ASM77037v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg46d49248-e1e4-40d7-b033-bce425f1d72b/dqc_reference/reference_markers.fasta -out GCF_000770375.1_ASM77037v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:47:44,048] [INFO] Task succeeded: Blastn
[2024-01-25 18:47:44,052] [INFO] Selected 12 target genomes.
[2024-01-25 18:47:44,052] [INFO] Target genome list was writen to GCF_000770375.1_ASM77037v1_genomic.fna/target_genomes.txt
[2024-01-25 18:47:44,059] [INFO] Task started: fastANI
[2024-01-25 18:47:44,059] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0393a6f-dd00-4a58-88d7-06b4d40acc0d/GCF_000770375.1_ASM77037v1_genomic.fna.gz --refList GCF_000770375.1_ASM77037v1_genomic.fna/target_genomes.txt --output GCF_000770375.1_ASM77037v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:47:51,845] [INFO] Task succeeded: fastANI
[2024-01-25 18:47:51,846] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg46d49248-e1e4-40d7-b033-bce425f1d72b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:47:51,846] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg46d49248-e1e4-40d7-b033-bce425f1d72b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:47:51,852] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:47:51,853] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:47:51,853] [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
Anoxybacillus gonensis	strain=G2	GCA_000770375.1	198467	198467	suspected-type	True	100.0	895	896	95	conclusive
Anoxybacillus gonensis	strain=G2	GCA_001187595.1	198467	198467	suspected-type	True	99.9998	889	896	95	conclusive
Anoxybacillus kamchatkensis	strain=DSM 14988	GCA_013761015.1	196180	196180	type	True	94.6044	730	896	95	below_threshold
Anoxybacillus ayderensis	strain=AB04	GCA_000833605.1	265546	265546	type	True	94.2443	766	896	95	below_threshold
Anoxybacillus thermarum	strain=AF/04	GCA_000836725.1	404937	404937	type	True	93.7187	707	896	95	below_threshold
Anoxybacillus kestanbolensis	strain=NCIMB 13971	GCA_023653015.1	227476	227476	type	True	88.1814	712	896	95	below_threshold
Anoxybacillus karvacharensis	strain=K1	GCA_001996285.1	1919277	1919277	type	True	88.0014	722	896	95	below_threshold
Anoxybacillus voinovskiensis	strain=DSM 17075	GCA_014196205.1	230470	230470	type	True	79.719	366	896	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:47:51,854] [INFO] DFAST Taxonomy check result was written to GCF_000770375.1_ASM77037v1_genomic.fna/tc_result.tsv
[2024-01-25 18:47:51,855] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:47:51,855] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:47:51,855] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg46d49248-e1e4-40d7-b033-bce425f1d72b/dqc_reference/checkm_data
[2024-01-25 18:47:51,856] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:47:51,883] [INFO] Task started: CheckM
[2024-01-25 18:47:51,884] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000770375.1_ASM77037v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000770375.1_ASM77037v1_genomic.fna/checkm_input GCF_000770375.1_ASM77037v1_genomic.fna/checkm_result
[2024-01-25 18:48:15,035] [INFO] Task succeeded: CheckM
[2024-01-25 18:48:15,036] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:48:15,055] [INFO] ===== Completeness check finished =====
[2024-01-25 18:48:15,055] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:48:15,056] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000770375.1_ASM77037v1_genomic.fna/markers.fasta)
[2024-01-25 18:48:15,056] [INFO] Task started: Blastn
[2024-01-25 18:48:15,056] [INFO] Running command: blastn -query GCF_000770375.1_ASM77037v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg46d49248-e1e4-40d7-b033-bce425f1d72b/dqc_reference/reference_markers_gtdb.fasta -out GCF_000770375.1_ASM77037v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:48:15,801] [INFO] Task succeeded: Blastn
[2024-01-25 18:48:15,804] [INFO] Selected 10 target genomes.
[2024-01-25 18:48:15,804] [INFO] Target genome list was writen to GCF_000770375.1_ASM77037v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:48:15,820] [INFO] Task started: fastANI
[2024-01-25 18:48:15,820] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0393a6f-dd00-4a58-88d7-06b4d40acc0d/GCF_000770375.1_ASM77037v1_genomic.fna.gz --refList GCF_000770375.1_ASM77037v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000770375.1_ASM77037v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:48:22,375] [INFO] Task succeeded: fastANI
[2024-01-25 18:48:22,382] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:48:22,382] [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_001187595.1	s__Anoxybacillus gonensis	99.9998	889	896	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus	95.0	98.51	96.49	0.91	0.88	6	conclusive
GCF_000833605.1	s__Anoxybacillus ayderensis	94.2047	768	896	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus	95.0	97.55	97.17	0.91	0.88	8	-
GCF_000836725.1	s__Anoxybacillus thermarum	93.7187	707	896	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002742685.1	s__Anoxybacillus flavithermus_E	90.4893	731	896	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus	95.0	99.92	99.92	0.93	0.93	2	-
GCA_002243705.1	s__Anoxybacillus flavithermus	88.0469	737	896	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus	95.0	96.37	95.30	0.87	0.86	4	-
GCF_014201515.1	s__Anoxybacillus mongoliensis	88.0335	740	896	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014201585.1	s__Anoxybacillus tengchongensis	87.0739	743	896	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus	95.0	96.46	96.29	0.90	0.87	4	-
GCF_002197485.1	s__Anoxybacillus flavithermus_G	86.7764	696	896	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus	95.0	98.60	95.08	0.91	0.76	28	-
GCF_900111795.1	s__Anoxybacillus pushchinoensis	85.8404	668	896	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus	95.0	95.71	95.71	0.84	0.84	2	-
GCF_014196205.1	s__Anoxybacillus_A voinovskiensis	79.719	366	896	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus_A	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:48:22,384] [INFO] GTDB search result was written to GCF_000770375.1_ASM77037v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:48:22,385] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:48:22,387] [INFO] DFAST_QC result json was written to GCF_000770375.1_ASM77037v1_genomic.fna/dqc_result.json
[2024-01-25 18:48:22,387] [INFO] DFAST_QC completed!
[2024-01-25 18:48:22,387] [INFO] Total running time: 0h0m47s