[2024-01-25 18:03:05,708] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:03:05,710] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:03:05,711] [INFO] DQC Reference Directory: /var/lib/cwl/stg7b5c671e-6daa-4165-854d-bd1548c9d7d9/dqc_reference
[2024-01-25 18:03:06,891] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:03:06,892] [INFO] Task started: Prodigal
[2024-01-25 18:03:06,892] [INFO] Running command: gunzip -c /var/lib/cwl/stgb8f662d7-63e7-47e9-8704-959354ef2e89/GCF_023653015.1_ASM2365301v1_genomic.fna.gz | prodigal -d GCF_023653015.1_ASM2365301v1_genomic.fna/cds.fna -a GCF_023653015.1_ASM2365301v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:03:12,635] [INFO] Task succeeded: Prodigal
[2024-01-25 18:03:12,635] [INFO] Task started: HMMsearch
[2024-01-25 18:03:12,635] [INFO] Running command: hmmsearch --tblout GCF_023653015.1_ASM2365301v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7b5c671e-6daa-4165-854d-bd1548c9d7d9/dqc_reference/reference_markers.hmm GCF_023653015.1_ASM2365301v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:03:12,865] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:03:12,866] [INFO] Found 6/6 markers.
[2024-01-25 18:03:12,890] [INFO] Query marker FASTA was written to GCF_023653015.1_ASM2365301v1_genomic.fna/markers.fasta
[2024-01-25 18:03:12,890] [INFO] Task started: Blastn
[2024-01-25 18:03:12,890] [INFO] Running command: blastn -query GCF_023653015.1_ASM2365301v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7b5c671e-6daa-4165-854d-bd1548c9d7d9/dqc_reference/reference_markers.fasta -out GCF_023653015.1_ASM2365301v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:03:13,518] [INFO] Task succeeded: Blastn
[2024-01-25 18:03:13,521] [INFO] Selected 12 target genomes.
[2024-01-25 18:03:13,521] [INFO] Target genome list was writen to GCF_023653015.1_ASM2365301v1_genomic.fna/target_genomes.txt
[2024-01-25 18:03:13,527] [INFO] Task started: fastANI
[2024-01-25 18:03:13,527] [INFO] Running command: fastANI --query /var/lib/cwl/stgb8f662d7-63e7-47e9-8704-959354ef2e89/GCF_023653015.1_ASM2365301v1_genomic.fna.gz --refList GCF_023653015.1_ASM2365301v1_genomic.fna/target_genomes.txt --output GCF_023653015.1_ASM2365301v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:03:22,046] [INFO] Task succeeded: fastANI
[2024-01-25 18:03:22,046] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7b5c671e-6daa-4165-854d-bd1548c9d7d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:03:22,047] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7b5c671e-6daa-4165-854d-bd1548c9d7d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:03:22,055] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:03:22,055] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-25 18:03:22,055] [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 kestanbolensis	strain=NCIMB 13971	GCA_023653015.1	227476	227476	type	True	100.0	834	839	95	inconclusive
Anoxybacillus karvacharensis	strain=K1	GCA_001996285.1	1919277	1919277	type	True	97.258	725	839	95	inconclusive
Anoxybacillus mongoliensis	strain=DSM 19169	GCA_014201515.1	452565	452565	type	True	89.695	724	839	95	below_threshold
Anoxybacillus suryakundensis	strain=DSM 27374	GCA_001418025.1	1325335	1325335	type	True	88.7944	708	839	95	below_threshold
Anoxybacillus tengchongensis	strain=DSM 23211	GCA_014201585.1	576944	576944	type	True	88.7925	741	839	95	below_threshold
Anoxybacillus suryakundensis	strain=DSM 27374	GCA_001517225.1	1325335	1325335	type	True	88.7909	709	839	95	below_threshold
Anoxybacillus gonensis	strain=G2	GCA_000770375.1	198467	198467	suspected-type	True	88.2884	712	839	95	below_threshold
Anoxybacillus thermarum	strain=AF/04	GCA_000836725.1	404937	404937	type	True	87.5499	676	839	95	below_threshold
Bacillus mycoides	strain=DSM 2048	GCA_022630575.1	1405	1405	type	True	76.5825	68	839	95	below_threshold
Metabacillus endolithicus	strain=KCTC 33579	GCA_023078335.1	1535204	1535204	type	True	76.5208	76	839	95	below_threshold
Bacillus sanguinis	strain=BML-BC004	GCA_018332475.1	2817476	2817476	type	True	76.2953	78	839	95	below_threshold
Bacillus anthracis	strain=Vollum	GCA_022221345.1	1392	1392	type	True	76.2637	82	839	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:03:22,057] [INFO] DFAST Taxonomy check result was written to GCF_023653015.1_ASM2365301v1_genomic.fna/tc_result.tsv
[2024-01-25 18:03:22,057] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:03:22,057] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:03:22,058] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7b5c671e-6daa-4165-854d-bd1548c9d7d9/dqc_reference/checkm_data
[2024-01-25 18:03:22,058] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:03:22,087] [INFO] Task started: CheckM
[2024-01-25 18:03:22,087] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_023653015.1_ASM2365301v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_023653015.1_ASM2365301v1_genomic.fna/checkm_input GCF_023653015.1_ASM2365301v1_genomic.fna/checkm_result
[2024-01-25 18:03:44,846] [INFO] Task succeeded: CheckM
[2024-01-25 18:03:44,847] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:03:44,870] [INFO] ===== Completeness check finished =====
[2024-01-25 18:03:44,870] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:03:44,871] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_023653015.1_ASM2365301v1_genomic.fna/markers.fasta)
[2024-01-25 18:03:44,871] [INFO] Task started: Blastn
[2024-01-25 18:03:44,871] [INFO] Running command: blastn -query GCF_023653015.1_ASM2365301v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7b5c671e-6daa-4165-854d-bd1548c9d7d9/dqc_reference/reference_markers_gtdb.fasta -out GCF_023653015.1_ASM2365301v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:03:45,835] [INFO] Task succeeded: Blastn
[2024-01-25 18:03:45,838] [INFO] Selected 8 target genomes.
[2024-01-25 18:03:45,838] [INFO] Target genome list was writen to GCF_023653015.1_ASM2365301v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:03:45,845] [INFO] Task started: fastANI
[2024-01-25 18:03:45,845] [INFO] Running command: fastANI --query /var/lib/cwl/stgb8f662d7-63e7-47e9-8704-959354ef2e89/GCF_023653015.1_ASM2365301v1_genomic.fna.gz --refList GCF_023653015.1_ASM2365301v1_genomic.fna/target_genomes_gtdb.txt --output GCF_023653015.1_ASM2365301v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:03:51,548] [INFO] Task succeeded: fastANI
[2024-01-25 18:03:51,554] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:03:51,555] [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_002243705.1	s__Anoxybacillus flavithermus	95.8731	720	839	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus	95.0	96.37	95.30	0.87	0.86	4	conclusive
GCF_002197485.1	s__Anoxybacillus flavithermus_G	93.9477	672	839	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus	95.0	98.60	95.08	0.91	0.76	28	-
GCF_002742685.1	s__Anoxybacillus flavithermus_E	91.0863	702	839	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus	95.0	99.92	99.92	0.93	0.93	2	-
GCF_014201515.1	s__Anoxybacillus mongoliensis	89.695	724	839	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	88.7925	741	839	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus	95.0	96.46	96.29	0.90	0.87	4	-
GCF_001187595.1	s__Anoxybacillus gonensis	88.2567	731	839	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus	95.0	98.51	96.49	0.91	0.88	6	-
GCF_000833605.1	s__Anoxybacillus ayderensis	88.0146	701	839	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	87.5499	676	839	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:03:51,556] [INFO] GTDB search result was written to GCF_023653015.1_ASM2365301v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:03:51,557] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:03:51,560] [INFO] DFAST_QC result json was written to GCF_023653015.1_ASM2365301v1_genomic.fna/dqc_result.json
[2024-01-25 18:03:51,560] [INFO] DFAST_QC completed!
[2024-01-25 18:03:51,560] [INFO] Total running time: 0h0m46s