[2024-01-24 13:31:44,320] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:44,322] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:44,322] [INFO] DQC Reference Directory: /var/lib/cwl/stgede258d7-22ed-4492-a83d-f9f58dc6d3ec/dqc_reference
[2024-01-24 13:31:45,687] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:45,689] [INFO] Task started: Prodigal
[2024-01-24 13:31:45,689] [INFO] Running command: gunzip -c /var/lib/cwl/stg0734b5db-ecc6-4238-a5d3-163ec53235cc/GCF_001026695.1_ASM102669v1_genomic.fna.gz | prodigal -d GCF_001026695.1_ASM102669v1_genomic.fna/cds.fna -a GCF_001026695.1_ASM102669v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:31:57,276] [INFO] Task succeeded: Prodigal
[2024-01-24 13:31:57,277] [INFO] Task started: HMMsearch
[2024-01-24 13:31:57,277] [INFO] Running command: hmmsearch --tblout GCF_001026695.1_ASM102669v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgede258d7-22ed-4492-a83d-f9f58dc6d3ec/dqc_reference/reference_markers.hmm GCF_001026695.1_ASM102669v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:31:57,615] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:31:57,616] [INFO] Found 6/6 markers.
[2024-01-24 13:31:57,691] [INFO] Query marker FASTA was written to GCF_001026695.1_ASM102669v1_genomic.fna/markers.fasta
[2024-01-24 13:31:57,692] [INFO] Task started: Blastn
[2024-01-24 13:31:57,692] [INFO] Running command: blastn -query GCF_001026695.1_ASM102669v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgede258d7-22ed-4492-a83d-f9f58dc6d3ec/dqc_reference/reference_markers.fasta -out GCF_001026695.1_ASM102669v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:58,399] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:58,402] [INFO] Selected 13 target genomes.
[2024-01-24 13:31:58,402] [INFO] Target genome list was writen to GCF_001026695.1_ASM102669v1_genomic.fna/target_genomes.txt
[2024-01-24 13:31:58,418] [INFO] Task started: fastANI
[2024-01-24 13:31:58,419] [INFO] Running command: fastANI --query /var/lib/cwl/stg0734b5db-ecc6-4238-a5d3-163ec53235cc/GCF_001026695.1_ASM102669v1_genomic.fna.gz --refList GCF_001026695.1_ASM102669v1_genomic.fna/target_genomes.txt --output GCF_001026695.1_ASM102669v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:13,791] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:13,792] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgede258d7-22ed-4492-a83d-f9f58dc6d3ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:13,792] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgede258d7-22ed-4492-a83d-f9f58dc6d3ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:13,811] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:32:13,811] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:13,812] [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
Neobacillus vireti	strain=DSM 15602	GCA_001026695.1	220686	220686	type	True	100.0	1755	1756	95	conclusive
Neobacillus vireti	strain=LMG 21834	GCA_000508325.2	220686	220686	type	True	99.9096	1621	1756	95	conclusive
Neobacillus novalis	strain=FJAT-14227	GCA_001636395.1	220687	220687	type	True	90.4495	1321	1756	95	below_threshold
Neobacillus novalis	strain=NBRC 102450	GCA_001591805.1	220687	220687	type	True	90.3757	1316	1756	95	below_threshold
Neobacillus soli	strain=NBRC 102451	GCA_001591665.1	220688	220688	type	True	81.6651	894	1756	95	below_threshold
Neobacillus bataviensis	strain=LMG 21833	GCA_000307875.1	220685	220685	type	True	80.9989	827	1756	95	below_threshold
Neobacillus drentensis	strain=FJAT-10044	GCA_001636415.1	220684	220684	type	True	79.7197	616	1756	95	below_threshold
Neobacillus rhizophilus	strain=FJAT-49825	GCA_018343535.1	2833579	2833579	type	True	78.9362	473	1756	95	below_threshold
Neobacillus mesonae	strain=FJAT-13985	GCA_001636315.1	1193713	1193713	type	True	78.6622	486	1756	95	below_threshold
Neobacillus citreus	strain=FJAT-50051	GCA_018343545.2	2833578	2833578	type	True	78.6315	440	1756	95	below_threshold
Cytobacillus solani	strain=FJAT-18043	GCA_001420595.1	1637975	1637975	type	True	77.795	212	1756	95	below_threshold
Bacillus kexueae	strain=KCTC 33881	GCA_022809095.1	2078952	2078952	type	True	76.9104	66	1756	95	below_threshold
Anoxybacillus calidus	strain=DSM 25220	GCA_013760845.1	575178	575178	type	True	76.7864	84	1756	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:13,814] [INFO] DFAST Taxonomy check result was written to GCF_001026695.1_ASM102669v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:13,814] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:13,815] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:13,815] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgede258d7-22ed-4492-a83d-f9f58dc6d3ec/dqc_reference/checkm_data
[2024-01-24 13:32:13,817] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:13,867] [INFO] Task started: CheckM
[2024-01-24 13:32:13,868] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001026695.1_ASM102669v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001026695.1_ASM102669v1_genomic.fna/checkm_input GCF_001026695.1_ASM102669v1_genomic.fna/checkm_result
[2024-01-24 13:32:53,460] [INFO] Task succeeded: CheckM
[2024-01-24 13:32:53,462] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:32:53,488] [INFO] ===== Completeness check finished =====
[2024-01-24 13:32:53,489] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:32:53,489] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001026695.1_ASM102669v1_genomic.fna/markers.fasta)
[2024-01-24 13:32:53,490] [INFO] Task started: Blastn
[2024-01-24 13:32:53,490] [INFO] Running command: blastn -query GCF_001026695.1_ASM102669v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgede258d7-22ed-4492-a83d-f9f58dc6d3ec/dqc_reference/reference_markers_gtdb.fasta -out GCF_001026695.1_ASM102669v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:54,295] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:54,300] [INFO] Selected 12 target genomes.
[2024-01-24 13:32:54,300] [INFO] Target genome list was writen to GCF_001026695.1_ASM102669v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:32:54,313] [INFO] Task started: fastANI
[2024-01-24 13:32:54,313] [INFO] Running command: fastANI --query /var/lib/cwl/stg0734b5db-ecc6-4238-a5d3-163ec53235cc/GCF_001026695.1_ASM102669v1_genomic.fna.gz --refList GCF_001026695.1_ASM102669v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001026695.1_ASM102669v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:10,164] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:10,180] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:10,180] [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_001026695.1	s__Neobacillus vireti	100.0	1755	1756	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_001591805.1	s__Neobacillus novalis	90.3757	1316	1756	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001591665.1	s__Neobacillus soli	81.6707	894	1756	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000307875.1	s__Neobacillus bataviensis	81.0008	827	1756	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005154805.1	s__Neobacillus sp005154805	80.5596	825	1756	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011250555.1	s__Neobacillus sp011250555	80.1097	709	1756	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	99.98	99.98	0.98	0.98	2	-
GCF_018613065.1	s__Neobacillus sp018613065	79.5541	630	1756	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	95.53	95.32	0.78	0.75	6	-
GCF_001591445.1	s__Neobacillus drentensis	79.5401	597	1756	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900177675.1	s__Neobacillus sp900177675	79.4519	671	1756	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	98.52	98.52	0.84	0.84	2	-
GCA_019219025.1	s__Neobacillus sp019219025	79.4284	602	1756	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002559145.1	s__Neobacillus sp002559145	79.3309	585	1756	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	95.43	95.43	0.81	0.81	2	-
GCF_007678255.1	s__Neobacillus sp007678255	79.2337	565	1756	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:10,182] [INFO] GTDB search result was written to GCF_001026695.1_ASM102669v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:10,183] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:10,188] [INFO] DFAST_QC result json was written to GCF_001026695.1_ASM102669v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:10,188] [INFO] DFAST_QC completed!
[2024-01-24 13:33:10,188] [INFO] Total running time: 0h1m26s