[2024-01-24 13:21:59,063] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:21:59,066] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:21:59,067] [INFO] DQC Reference Directory: /var/lib/cwl/stg42355951-4c1f-457a-b451-b223bed2f53e/dqc_reference
[2024-01-24 13:22:00,298] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:00,299] [INFO] Task started: Prodigal
[2024-01-24 13:22:00,299] [INFO] Running command: gunzip -c /var/lib/cwl/stgca0cd30a-49a2-4238-a055-b116e7e1f801/GCF_900445365.1_50681_C01_genomic.fna.gz | prodigal -d GCF_900445365.1_50681_C01_genomic.fna/cds.fna -a GCF_900445365.1_50681_C01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:11,621] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:11,621] [INFO] Task started: HMMsearch
[2024-01-24 13:22:11,621] [INFO] Running command: hmmsearch --tblout GCF_900445365.1_50681_C01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg42355951-4c1f-457a-b451-b223bed2f53e/dqc_reference/reference_markers.hmm GCF_900445365.1_50681_C01_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:11,969] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:11,970] [INFO] Found 6/6 markers.
[2024-01-24 13:22:12,009] [INFO] Query marker FASTA was written to GCF_900445365.1_50681_C01_genomic.fna/markers.fasta
[2024-01-24 13:22:12,010] [INFO] Task started: Blastn
[2024-01-24 13:22:12,010] [INFO] Running command: blastn -query GCF_900445365.1_50681_C01_genomic.fna/markers.fasta -db /var/lib/cwl/stg42355951-4c1f-457a-b451-b223bed2f53e/dqc_reference/reference_markers.fasta -out GCF_900445365.1_50681_C01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:12,625] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:12,629] [INFO] Selected 25 target genomes.
[2024-01-24 13:22:12,630] [INFO] Target genome list was writen to GCF_900445365.1_50681_C01_genomic.fna/target_genomes.txt
[2024-01-24 13:22:12,639] [INFO] Task started: fastANI
[2024-01-24 13:22:12,639] [INFO] Running command: fastANI --query /var/lib/cwl/stgca0cd30a-49a2-4238-a055-b116e7e1f801/GCF_900445365.1_50681_C01_genomic.fna.gz --refList GCF_900445365.1_50681_C01_genomic.fna/target_genomes.txt --output GCF_900445365.1_50681_C01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:36,634] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:36,635] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg42355951-4c1f-457a-b451-b223bed2f53e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:36,635] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg42355951-4c1f-457a-b451-b223bed2f53e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:36,653] [INFO] Found 23 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:22:36,653] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:22:36,653] [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
Cytobacillus firmus	strain=NCTC10335	GCA_900445365.1	1399	1399	suspected-type	True	100.0	1596	1600	95	conclusive
Cytobacillus firmus	strain=NBRC 15306	GCA_001591465.1	1399	1399	suspected-type	True	99.8725	1340	1600	95	conclusive
Bacillus subtilis subsp. subtilis	strain=168	GCA_024917115.1	135461	1423	type	True	79.6963	75	1600	95	below_threshold
Bacillus tequilensis	strain=NCTC13306	GCA_900445435.1	227866	227866	type	True	79.6038	70	1600	95	below_threshold
Neobacillus mesonae	strain=FJAT-13985	GCA_001636315.1	1193713	1193713	type	True	79.059	156	1600	95	below_threshold
Bacillus vallismortis	strain=DV1-F-3	GCA_000245315.1	72361	72361	type	True	78.9762	60	1600	95	below_threshold
Cytobacillus solani	strain=FJAT-18043	GCA_001420595.1	1637975	1637975	type	True	78.8224	278	1600	95	below_threshold
Neobacillus soli	strain=DSM 15604	GCA_002335815.1	220688	220688	type	True	78.8083	161	1600	95	below_threshold
Mesobacillus jeotgali	strain=DSM 18226	GCA_002874535.1	129985	129985	type	True	78.7858	200	1600	95	below_threshold
Bacillus dakarensis	strain=Marseille-P3515	GCA_900156875.1	1926278	1926278	type	True	78.7054	184	1600	95	below_threshold
Metabacillus dongyingensis	strain=BY2G20	GCA_019933155.2	2874282	2874282	type	True	78.5151	133	1600	95	below_threshold
Cytobacillus horneckiae	strain=1P01SC	GCA_002835735.1	549687	549687	type	True	78.349	222	1600	95	below_threshold
Robertmurraya massiliosenegalensis	strain=JC6	GCA_000311725.1	1287657	1287657	type	True	78.09	155	1600	95	below_threshold
Cytobacillus praedii	strain=FJAT-25547	GCA_001439605.1	1742358	1742358	type	True	77.8414	261	1600	95	below_threshold
Neobacillus cucumis	strain=DSM 101566	GCA_016908975.1	1740721	1740721	type	True	77.6462	141	1600	95	below_threshold
Robertmurraya siralis	strain=171544	GCA_005502275.1	77777	77777	type	True	77.6054	133	1600	95	below_threshold
Mesobacillus campisalis	strain=SA2-6	GCA_000986785.1	1408103	1408103	type	True	77.4022	179	1600	95	below_threshold
Neobacillus piezotolerans	strain=YLB-04	GCA_003362805.1	2259171	2259171	type	True	77.3265	103	1600	95	below_threshold
Metabacillus idriensis	strain=DSM-19097	GCA_904423875.1	324768	324768	type	True	77.3208	121	1600	95	below_threshold
Metabacillus idriensis	strain=DSM 19097	GCA_009674765.1	324768	324768	type	True	77.2267	118	1600	95	below_threshold
Neobacillus soli	strain=NBRC 102451	GCA_001591665.1	220688	220688	type	True	77.2196	140	1600	95	below_threshold
Siminovitchia fordii	strain=DSM 16014	GCA_000374565.1	254759	254759	type	True	76.7188	56	1600	95	below_threshold
Lederbergia wuyishanensis	strain=CGMCC 1.12709	GCA_022900255.1	1347903	1347903	type	True	76.6165	55	1600	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:36,655] [INFO] DFAST Taxonomy check result was written to GCF_900445365.1_50681_C01_genomic.fna/tc_result.tsv
[2024-01-24 13:22:36,655] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:36,655] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:36,656] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg42355951-4c1f-457a-b451-b223bed2f53e/dqc_reference/checkm_data
[2024-01-24 13:22:36,657] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:36,705] [INFO] Task started: CheckM
[2024-01-24 13:22:36,705] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900445365.1_50681_C01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900445365.1_50681_C01_genomic.fna/checkm_input GCF_900445365.1_50681_C01_genomic.fna/checkm_result
[2024-01-24 13:23:15,443] [INFO] Task succeeded: CheckM
[2024-01-24 13:23:15,444] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:23:15,463] [INFO] ===== Completeness check finished =====
[2024-01-24 13:23:15,463] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:23:15,464] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900445365.1_50681_C01_genomic.fna/markers.fasta)
[2024-01-24 13:23:15,464] [INFO] Task started: Blastn
[2024-01-24 13:23:15,464] [INFO] Running command: blastn -query GCF_900445365.1_50681_C01_genomic.fna/markers.fasta -db /var/lib/cwl/stg42355951-4c1f-457a-b451-b223bed2f53e/dqc_reference/reference_markers_gtdb.fasta -out GCF_900445365.1_50681_C01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:16,346] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:16,350] [INFO] Selected 7 target genomes.
[2024-01-24 13:23:16,350] [INFO] Target genome list was writen to GCF_900445365.1_50681_C01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:16,357] [INFO] Task started: fastANI
[2024-01-24 13:23:16,358] [INFO] Running command: fastANI --query /var/lib/cwl/stgca0cd30a-49a2-4238-a055-b116e7e1f801/GCF_900445365.1_50681_C01_genomic.fna.gz --refList GCF_900445365.1_50681_C01_genomic.fna/target_genomes_gtdb.txt --output GCF_900445365.1_50681_C01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:25,247] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:25,256] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:23:25,256] [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_001591465.1	s__Cytobacillus firmus	99.8725	1340	1600	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	99.21	98.02	0.95	0.85	11	conclusive
GCF_001038755.1	s__Cytobacillus firmus_B	94.1553	1169	1600	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	97.85	96.97	0.92	0.91	5	-
GCF_000565285.1	s__Cytobacillus firmus_A	93.9513	1240	1600	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001956215.1	s__Cytobacillus sp001956215	93.5316	1254	1600	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002272225.1	s__Cytobacillus sp002272225	92.6853	1099	1600	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009849585.1	s__Cytobacillus sp009849585	90.0029	1198	1600	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000294775.2	s__Cytobacillus oceanisediminis_B	89.1537	1253	1600	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	98.75	98.26	0.86	0.83	6	-
--------------------------------------------------------------------------------
[2024-01-24 13:23:25,258] [INFO] GTDB search result was written to GCF_900445365.1_50681_C01_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:25,259] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:25,262] [INFO] DFAST_QC result json was written to GCF_900445365.1_50681_C01_genomic.fna/dqc_result.json
[2024-01-24 13:23:25,263] [INFO] DFAST_QC completed!
[2024-01-24 13:23:25,263] [INFO] Total running time: 0h1m26s