[2024-01-24 13:31:57,680] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:57,683] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:57,683] [INFO] DQC Reference Directory: /var/lib/cwl/stg99fc5ded-7d3c-4123-8ef4-37a6e9b03a44/dqc_reference
[2024-01-24 13:31:59,107] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:59,108] [INFO] Task started: Prodigal
[2024-01-24 13:31:59,108] [INFO] Running command: gunzip -c /var/lib/cwl/stg13adcbc0-94b3-41dc-8c17-b1b5c38a6a23/GCF_016908975.1_ASM1690897v1_genomic.fna.gz | prodigal -d GCF_016908975.1_ASM1690897v1_genomic.fna/cds.fna -a GCF_016908975.1_ASM1690897v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:12,019] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:12,020] [INFO] Task started: HMMsearch
[2024-01-24 13:32:12,020] [INFO] Running command: hmmsearch --tblout GCF_016908975.1_ASM1690897v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg99fc5ded-7d3c-4123-8ef4-37a6e9b03a44/dqc_reference/reference_markers.hmm GCF_016908975.1_ASM1690897v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:12,316] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:12,318] [INFO] Found 6/6 markers.
[2024-01-24 13:32:12,366] [INFO] Query marker FASTA was written to GCF_016908975.1_ASM1690897v1_genomic.fna/markers.fasta
[2024-01-24 13:32:12,367] [INFO] Task started: Blastn
[2024-01-24 13:32:12,367] [INFO] Running command: blastn -query GCF_016908975.1_ASM1690897v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg99fc5ded-7d3c-4123-8ef4-37a6e9b03a44/dqc_reference/reference_markers.fasta -out GCF_016908975.1_ASM1690897v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:12,939] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:12,943] [INFO] Selected 20 target genomes.
[2024-01-24 13:32:12,943] [INFO] Target genome list was writen to GCF_016908975.1_ASM1690897v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:12,949] [INFO] Task started: fastANI
[2024-01-24 13:32:12,949] [INFO] Running command: fastANI --query /var/lib/cwl/stg13adcbc0-94b3-41dc-8c17-b1b5c38a6a23/GCF_016908975.1_ASM1690897v1_genomic.fna.gz --refList GCF_016908975.1_ASM1690897v1_genomic.fna/target_genomes.txt --output GCF_016908975.1_ASM1690897v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:33,459] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:33,460] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg99fc5ded-7d3c-4123-8ef4-37a6e9b03a44/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:33,460] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg99fc5ded-7d3c-4123-8ef4-37a6e9b03a44/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:33,475] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:32:33,475] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:33,476] [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 cucumis	strain=DSM 101566	GCA_016908975.1	1740721	1740721	type	True	100.0	1972	1978	95	conclusive
Neobacillus bataviensis	strain=LMG 21833	GCA_000307875.1	220685	220685	type	True	79.0131	500	1978	95	below_threshold
Neobacillus vireti	strain=DSM 15602	GCA_001026695.1	220686	220686	type	True	78.8608	467	1978	95	below_threshold
Neobacillus drentensis	strain=FJAT-10044	GCA_001636415.1	220684	220684	type	True	78.799	510	1978	95	below_threshold
Neobacillus novalis	strain=FJAT-14227	GCA_001636395.1	220687	220687	type	True	78.7331	501	1978	95	below_threshold
Neobacillus vireti	strain=LMG 21834	GCA_000508325.2	220686	220686	type	True	78.7019	443	1978	95	below_threshold
Neobacillus drentensis	strain=NBRC 102427	GCA_001591445.1	220684	220684	type	True	78.6477	489	1978	95	below_threshold
Neobacillus rhizophilus	strain=FJAT-49825	GCA_018343535.1	2833579	2833579	type	True	78.6217	423	1978	95	below_threshold
Neobacillus novalis	strain=NBRC 102450	GCA_001591805.1	220687	220687	type	True	78.5728	492	1978	95	below_threshold
Neobacillus soli	strain=DSM 15604	GCA_002335815.1	220688	220688	type	True	78.5414	492	1978	95	below_threshold
Neobacillus soli	strain=NBRC 102451	GCA_001591665.1	220688	220688	type	True	78.4082	468	1978	95	below_threshold
Neobacillus citreus	strain=FJAT-50051	GCA_018343545.2	2833578	2833578	type	True	78.4074	388	1978	95	below_threshold
Neobacillus mesonae	strain=FJAT-13985	GCA_001636315.1	1193713	1193713	type	True	78.4059	348	1978	95	below_threshold
Neobacillus kokaensis	strain=LOB 377	GCA_014656545.1	2759023	2759023	type	True	78.0863	370	1978	95	below_threshold
Neobacillus sedimentimangrovi	strain=FJAT-2464	GCA_010614825.1	2699460	2699460	type	True	77.9855	260	1978	95	below_threshold
Metabacillus endolithicus	strain=KCTC 33579	GCA_023078335.1	1535204	1535204	type	True	77.2285	111	1978	95	below_threshold
Lederbergia citrisecundus	strain=FJAT-49732	GCA_018343695.1	2833583	2833583	type	True	76.7746	106	1978	95	below_threshold
Lederbergia wuyishanensis	strain=CGMCC 1.12709	GCA_022900255.1	1347903	1347903	type	True	76.613	87	1978	95	below_threshold
Bacillus mycoides	strain=DSM 2048	GCA_000003925.1	1405	1405	type	True	76.5712	100	1978	95	below_threshold
Bacillus mycoides	strain=ATCC 6462	GCA_000832605.1	1405	1405	type	True	76.5043	98	1978	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:33,583] [INFO] DFAST Taxonomy check result was written to GCF_016908975.1_ASM1690897v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:33,583] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:33,583] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:33,584] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg99fc5ded-7d3c-4123-8ef4-37a6e9b03a44/dqc_reference/checkm_data
[2024-01-24 13:32:33,585] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:33,640] [INFO] Task started: CheckM
[2024-01-24 13:32:33,640] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016908975.1_ASM1690897v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016908975.1_ASM1690897v1_genomic.fna/checkm_input GCF_016908975.1_ASM1690897v1_genomic.fna/checkm_result
[2024-01-24 13:33:15,880] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:15,884] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:15,940] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:15,940] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:15,941] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016908975.1_ASM1690897v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:15,941] [INFO] Task started: Blastn
[2024-01-24 13:33:15,941] [INFO] Running command: blastn -query GCF_016908975.1_ASM1690897v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg99fc5ded-7d3c-4123-8ef4-37a6e9b03a44/dqc_reference/reference_markers_gtdb.fasta -out GCF_016908975.1_ASM1690897v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:16,840] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:16,844] [INFO] Selected 8 target genomes.
[2024-01-24 13:33:16,844] [INFO] Target genome list was writen to GCF_016908975.1_ASM1690897v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:16,857] [INFO] Task started: fastANI
[2024-01-24 13:33:16,857] [INFO] Running command: fastANI --query /var/lib/cwl/stg13adcbc0-94b3-41dc-8c17-b1b5c38a6a23/GCF_016908975.1_ASM1690897v1_genomic.fna.gz --refList GCF_016908975.1_ASM1690897v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016908975.1_ASM1690897v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:29,109] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:29,117] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:29,117] [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_016908975.1	s__Neobacillus cucumis	100.0	1972	1978	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	conclusive
GCF_002585305.1	s__Neobacillus sp002585305	83.3058	1217	1978	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	97.64	95.53	0.90	0.84	3	-
GCF_002860255.1	s__Neobacillus cucumis_A	82.4709	1095	1978	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_018613415.1	s__Neobacillus sp018613415	82.2422	1115	1978	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_009928415.1	s__Neobacillus sp009928415	81.8055	1022	1978	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_900177675.1	s__Neobacillus sp900177675	79.319	617	1978	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	79.2362	574	1978	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_000307875.1	s__Neobacillus bataviensis	79.0059	501	1978	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 13:33:29,119] [INFO] GTDB search result was written to GCF_016908975.1_ASM1690897v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:29,120] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:29,123] [INFO] DFAST_QC result json was written to GCF_016908975.1_ASM1690897v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:29,124] [INFO] DFAST_QC completed!
[2024-01-24 13:33:29,124] [INFO] Total running time: 0h1m31s