[2024-01-24 12:36:57,131] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:36:57,133] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:36:57,133] [INFO] DQC Reference Directory: /var/lib/cwl/stg29d66bc3-83d0-4eb0-9366-bd182faf7e24/dqc_reference
[2024-01-24 12:36:58,502] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:36:58,503] [INFO] Task started: Prodigal
[2024-01-24 12:36:58,504] [INFO] Running command: gunzip -c /var/lib/cwl/stgebb197ea-e879-47ed-a124-a439cfedd1fc/GCF_014201515.1_ASM1420151v1_genomic.fna.gz | prodigal -d GCF_014201515.1_ASM1420151v1_genomic.fna/cds.fna -a GCF_014201515.1_ASM1420151v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:05,532] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:05,532] [INFO] Task started: HMMsearch
[2024-01-24 12:37:05,532] [INFO] Running command: hmmsearch --tblout GCF_014201515.1_ASM1420151v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg29d66bc3-83d0-4eb0-9366-bd182faf7e24/dqc_reference/reference_markers.hmm GCF_014201515.1_ASM1420151v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:05,883] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:05,884] [INFO] Found 6/6 markers.
[2024-01-24 12:37:05,910] [INFO] Query marker FASTA was written to GCF_014201515.1_ASM1420151v1_genomic.fna/markers.fasta
[2024-01-24 12:37:05,911] [INFO] Task started: Blastn
[2024-01-24 12:37:05,911] [INFO] Running command: blastn -query GCF_014201515.1_ASM1420151v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg29d66bc3-83d0-4eb0-9366-bd182faf7e24/dqc_reference/reference_markers.fasta -out GCF_014201515.1_ASM1420151v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:06,589] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:06,592] [INFO] Selected 11 target genomes.
[2024-01-24 12:37:06,592] [INFO] Target genome list was writen to GCF_014201515.1_ASM1420151v1_genomic.fna/target_genomes.txt
[2024-01-24 12:37:06,606] [INFO] Task started: fastANI
[2024-01-24 12:37:06,606] [INFO] Running command: fastANI --query /var/lib/cwl/stgebb197ea-e879-47ed-a124-a439cfedd1fc/GCF_014201515.1_ASM1420151v1_genomic.fna.gz --refList GCF_014201515.1_ASM1420151v1_genomic.fna/target_genomes.txt --output GCF_014201515.1_ASM1420151v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:37:14,135] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:14,136] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg29d66bc3-83d0-4eb0-9366-bd182faf7e24/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:37:14,136] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg29d66bc3-83d0-4eb0-9366-bd182faf7e24/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:37:14,148] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:37:14,148] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:37:14,148] [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 mongoliensis	strain=DSM 19169	GCA_014201515.1	452565	452565	type	True	100.0	857	858	95	conclusive
Anoxybacillus suryakundensis	strain=DSM 27374	GCA_001517225.1	1325335	1325335	type	True	94.263	767	858	95	below_threshold
Anoxybacillus suryakundensis	strain=DSM 27374	GCA_001418025.1	1325335	1325335	type	True	94.2419	768	858	95	below_threshold
Anoxybacillus tengchongensis	strain=DSM 23211	GCA_014201585.1	576944	576944	type	True	94.0274	777	858	95	below_threshold
Anoxybacillus kestanbolensis	strain=NCIMB 13971	GCA_023653015.1	227476	227476	type	True	89.678	714	858	95	below_threshold
Anoxybacillus karvacharensis	strain=K1	GCA_001996285.1	1919277	1919277	type	True	89.3223	725	858	95	below_threshold
Anoxybacillus thermarum	strain=AF/04	GCA_000836725.1	404937	404937	type	True	87.5287	704	858	95	below_threshold
Bacillus kexueae	strain=KCTC 33881	GCA_022809095.1	2078952	2078952	type	True	76.8109	94	858	95	below_threshold
Pseudoneobacillus rhizosphaerae	strain=CIP 111885	GCA_917563885.1	2880968	2880968	type	True	76.5194	55	858	95	below_threshold
Neobacillus kokaensis	strain=LOB 377	GCA_014656545.1	2759023	2759023	type	True	76.1059	55	858	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:37:14,150] [INFO] DFAST Taxonomy check result was written to GCF_014201515.1_ASM1420151v1_genomic.fna/tc_result.tsv
[2024-01-24 12:37:14,150] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:37:14,151] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:37:14,151] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg29d66bc3-83d0-4eb0-9366-bd182faf7e24/dqc_reference/checkm_data
[2024-01-24 12:37:14,152] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:37:14,191] [INFO] Task started: CheckM
[2024-01-24 12:37:14,192] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014201515.1_ASM1420151v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014201515.1_ASM1420151v1_genomic.fna/checkm_input GCF_014201515.1_ASM1420151v1_genomic.fna/checkm_result
[2024-01-24 12:37:41,331] [INFO] Task succeeded: CheckM
[2024-01-24 12:37:41,333] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:37:41,352] [INFO] ===== Completeness check finished =====
[2024-01-24 12:37:41,352] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:37:41,353] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014201515.1_ASM1420151v1_genomic.fna/markers.fasta)
[2024-01-24 12:37:41,353] [INFO] Task started: Blastn
[2024-01-24 12:37:41,353] [INFO] Running command: blastn -query GCF_014201515.1_ASM1420151v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg29d66bc3-83d0-4eb0-9366-bd182faf7e24/dqc_reference/reference_markers_gtdb.fasta -out GCF_014201515.1_ASM1420151v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:42,401] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:42,405] [INFO] Selected 6 target genomes.
[2024-01-24 12:37:42,405] [INFO] Target genome list was writen to GCF_014201515.1_ASM1420151v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:37:42,416] [INFO] Task started: fastANI
[2024-01-24 12:37:42,417] [INFO] Running command: fastANI --query /var/lib/cwl/stgebb197ea-e879-47ed-a124-a439cfedd1fc/GCF_014201515.1_ASM1420151v1_genomic.fna.gz --refList GCF_014201515.1_ASM1420151v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014201515.1_ASM1420151v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:37:46,745] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:46,752] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:37:46,752] [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_014201515.1	s__Anoxybacillus mongoliensis	100.0	857	858	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014201585.1	s__Anoxybacillus tengchongensis	94.0182	778	858	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus	95.0	96.46	96.29	0.90	0.87	4	-
GCF_002742685.1	s__Anoxybacillus flavithermus_E	91.2616	742	858	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	89.3958	760	858	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus	95.0	96.37	95.30	0.87	0.86	4	-
GCF_002197485.1	s__Anoxybacillus flavithermus_G	88.4517	692	858	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus	95.0	98.60	95.08	0.91	0.76	28	-
GCF_000836725.1	s__Anoxybacillus thermarum	87.5287	704	858	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:37:46,754] [INFO] GTDB search result was written to GCF_014201515.1_ASM1420151v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:37:46,754] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:37:46,757] [INFO] DFAST_QC result json was written to GCF_014201515.1_ASM1420151v1_genomic.fna/dqc_result.json
[2024-01-24 12:37:46,758] [INFO] DFAST_QC completed!
[2024-01-24 12:37:46,758] [INFO] Total running time: 0h0m50s