[2024-01-24 13:49:44,222] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:44,224] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:44,224] [INFO] DQC Reference Directory: /var/lib/cwl/stg73093926-3a44-4c35-a7ae-e3a32551211c/dqc_reference
[2024-01-24 13:49:45,639] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:45,640] [INFO] Task started: Prodigal
[2024-01-24 13:49:45,641] [INFO] Running command: gunzip -c /var/lib/cwl/stgedb2a784-7228-4a69-a45f-df6c020cd9be/GCF_900445355.1_43024_D01_genomic.fna.gz | prodigal -d GCF_900445355.1_43024_D01_genomic.fna/cds.fna -a GCF_900445355.1_43024_D01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:56,362] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:56,363] [INFO] Task started: HMMsearch
[2024-01-24 13:49:56,363] [INFO] Running command: hmmsearch --tblout GCF_900445355.1_43024_D01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg73093926-3a44-4c35-a7ae-e3a32551211c/dqc_reference/reference_markers.hmm GCF_900445355.1_43024_D01_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:56,681] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:56,682] [INFO] Found 6/6 markers.
[2024-01-24 13:49:56,728] [INFO] Query marker FASTA was written to GCF_900445355.1_43024_D01_genomic.fna/markers.fasta
[2024-01-24 13:49:56,729] [INFO] Task started: Blastn
[2024-01-24 13:49:56,729] [INFO] Running command: blastn -query GCF_900445355.1_43024_D01_genomic.fna/markers.fasta -db /var/lib/cwl/stg73093926-3a44-4c35-a7ae-e3a32551211c/dqc_reference/reference_markers.fasta -out GCF_900445355.1_43024_D01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:57,394] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:57,397] [INFO] Selected 11 target genomes.
[2024-01-24 13:49:57,397] [INFO] Target genome list was writen to GCF_900445355.1_43024_D01_genomic.fna/target_genomes.txt
[2024-01-24 13:49:57,401] [INFO] Task started: fastANI
[2024-01-24 13:49:57,401] [INFO] Running command: fastANI --query /var/lib/cwl/stgedb2a784-7228-4a69-a45f-df6c020cd9be/GCF_900445355.1_43024_D01_genomic.fna.gz --refList GCF_900445355.1_43024_D01_genomic.fna/target_genomes.txt --output GCF_900445355.1_43024_D01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:12,921] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:12,922] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg73093926-3a44-4c35-a7ae-e3a32551211c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:12,922] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg73093926-3a44-4c35-a7ae-e3a32551211c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:12,937] [WARNING] Following organisms are indistinguishable with ANI. [Bacillus anthracis(1392), Bacillus cereus(1396), Bacillus thuringiensis(1428)]
[2024-01-24 13:50:12,938] [INFO] Found 11 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 13:50:12,938] [INFO] The taxonomy check result is classified as 'indistinguishable'.
[2024-01-24 13:50:12,938] [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
Bacillus cereus	strain=NCTC2599	GCA_900445355.1	1396	1396	suspected-type	True	100.0	1795	1797	95	indistinguishable
Bacillus cereus	strain=ATCC 14579	GCA_006094295.1	1396	1396	suspected-type	True	99.9959	1789	1797	95	indistinguishable
Bacillus cereus	strain=ATCC 14579	GCA_000007825.1	1396	1396	suspected-type	True	99.9628	1790	1797	95	indistinguishable
Bacillus cereus	strain=FSL M8-0473	GCA_002014665.1	1396	1396	suspected-type	True	99.8986	1658	1797	95	indistinguishable
Bacillus thuringiensis	strain=ATCC 10792	GCA_002119445.1	1428	1428	suspected-type	True	96.731	1601	1797	95	indistinguishable
Bacillus anthracis	strain=Vollum	GCA_022221345.1	1392	1392	type	True	91.7626	1496	1797	95	below_threshold
Bacillus toyonensis	strain=BCT-7112	GCA_000496285.1	155322	155322	type	True	91.7299	1434	1797	95	below_threshold
Bacillus sanguinis	strain=BML-BC004	GCA_018332475.1	2817476	2817476	type	True	91.447	1293	1797	95	below_threshold
Bacillus mycoides	strain=DSM 2048	GCA_022630575.1	1405	1405	type	True	89.6027	1471	1797	95	below_threshold
Neobacillus mesonae	strain=FJAT-13985	GCA_001636315.1	1193713	1193713	type	True	79.5388	97	1797	95	below_threshold
Metabacillus bambusae	strain=BG109	GCA_017497975.1	2795218	2795218	type	True	76.9191	119	1797	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:12,940] [INFO] DFAST Taxonomy check result was written to GCF_900445355.1_43024_D01_genomic.fna/tc_result.tsv
[2024-01-24 13:50:12,940] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:12,940] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:12,940] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg73093926-3a44-4c35-a7ae-e3a32551211c/dqc_reference/checkm_data
[2024-01-24 13:50:12,942] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:12,992] [INFO] Task started: CheckM
[2024-01-24 13:50:12,992] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900445355.1_43024_D01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900445355.1_43024_D01_genomic.fna/checkm_input GCF_900445355.1_43024_D01_genomic.fna/checkm_result
[2024-01-24 13:50:48,630] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:48,631] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 13.89%
Strain heterogeneity: 25.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:48,655] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:48,655] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:48,656] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900445355.1_43024_D01_genomic.fna/markers.fasta)
[2024-01-24 13:50:48,656] [INFO] Task started: Blastn
[2024-01-24 13:50:48,656] [INFO] Running command: blastn -query GCF_900445355.1_43024_D01_genomic.fna/markers.fasta -db /var/lib/cwl/stg73093926-3a44-4c35-a7ae-e3a32551211c/dqc_reference/reference_markers_gtdb.fasta -out GCF_900445355.1_43024_D01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:49,435] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:49,440] [INFO] Selected 10 target genomes.
[2024-01-24 13:50:49,440] [INFO] Target genome list was writen to GCF_900445355.1_43024_D01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:49,460] [INFO] Task started: fastANI
[2024-01-24 13:50:49,460] [INFO] Running command: fastANI --query /var/lib/cwl/stgedb2a784-7228-4a69-a45f-df6c020cd9be/GCF_900445355.1_43024_D01_genomic.fna.gz --refList GCF_900445355.1_43024_D01_genomic.fna/target_genomes_gtdb.txt --output GCF_900445355.1_43024_D01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:04,367] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:04,379] [INFO] Found 10 fastANI hits (3 hits with ANI > circumscription radius)
[2024-01-24 13:51:04,380] [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_000007825.1	s__Bacillus_A cereus	99.9628	1789	1797	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	97.0513	98.55	97.64	0.91	0.84	235	inconclusive
GCF_006384875.1	s__Bacillus_A bombysepticus	97.0623	1617	1797	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	97.0513	98.50	97.53	0.88	0.81	586	inconclusive
GCF_002200015.1	s__Bacillus_A cereus_AZ	96.9163	1509	1797	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	96.9563	N/A	N/A	N/A	N/A	1	-
GCF_002119445.1	s__Bacillus_A thuringiensis	96.7311	1601	1797	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	96.7077	98.15	96.83	0.88	0.79	267	inconclusive
GCF_001595725.1	s__Bacillus_A thuringiensis_K	96.5486	1612	1797	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	96.827	99.05	98.75	0.91	0.78	20	-
GCF_000021305.1	s__Bacillus_A thuringiensis_S	96.0486	1591	1797	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	96.4134	98.69	97.04	0.88	0.75	230	-
GCF_002567495.1	s__Bacillus_A cereus_AQ	94.2071	1528	1797	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	98.10	96.80	0.92	0.88	3	-
GCF_006494425.1	s__Bacillus_A sp006494425	91.7775	1503	1797	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000742895.1	s__Bacillus_A anthracis	91.7618	1520	1797	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.2518	99.29	95.34	0.96	0.83	417	-
GCF_001884235.1	s__Bacillus_A paramycoides	88.8812	1361	1797	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	97.72	97.18	0.88	0.85	10	-
--------------------------------------------------------------------------------
[2024-01-24 13:51:04,381] [INFO] GTDB search result was written to GCF_900445355.1_43024_D01_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:04,382] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:04,386] [INFO] DFAST_QC result json was written to GCF_900445355.1_43024_D01_genomic.fna/dqc_result.json
[2024-01-24 13:51:04,386] [INFO] DFAST_QC completed!
[2024-01-24 13:51:04,386] [INFO] Total running time: 0h1m20s