Dear CT2 team,
Thanks for such amzing work.
My issue is that there is no taxonomic assignment rank infomation (eg: "Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; unclassified Podoviridae; crAss-like viruses; environmental samples") compare normal output (see as below "blastx.out (correct)"), and the error output is "*blastx.out (something error)", when I run CT2 on "testcontig_DNA.fasta", and so threre
is no correct taxnonmic name for contig 4 / 5 in " DNA_CONTIG_SUMMARY.tsv", which it should be "crAass-like phage".
I check the "err.log", but find nothing. Looking forward your reply. Thanks a lot.
@@@@@@@@@@@@@@@@@@@@@@@@@
Your specified arguments:
original contigs: ../testcontigs_DNA_ct2.fasta
forward reads: /mnt/data/share/software/Cenote-Taker2/test/no_reads
reverse reads: /mnt/data/share/software/Cenote-Taker2/test/no_reads
title of this run: DNA
Isolate source: unknown
collection date: unknown
metagenome_type: unknown
SRA run number: unknown
SRA experiment number: unknown
SRA sample number: unknown
Bioproject number: unknown
template file: /mnt/data/share/software/Cenote-Taker2/dummy_template.sbt
minimum circular contig length: 1000
minimum linear contig length: 1
virus domain database: standard
min. viral hallmarks for linear: 0
min. viral hallmarks for circular: 0
handle known seqs: do_not_check_knowns
contig assembler: unknown_assembler
DNA or RNA: DNA
HHsuite tool: hhblits
original or TPA: original
Do BLASTP?: no_blastp
Do Prophage Pruning?: True
Filter out plasmids?: True
Run BLASTN against nt? none
Location of Cenote scripts: /mnt/data/share/software/Cenote-Taker2
Location of scratch directory: none
GB of memory: 500
number of CPUs available for run: 100
Annotation mode? True
@@@@@@@@@@@@@@@@@@@@@@@@@
scratch space will not be used in this run
HHsuite database locations:
/mnt/data/share/software/Cenote-Taker2/NCBI_CD/NCBI_CD
/mnt/data/share/software/Cenote-Taker2/pfam_32_db/pfam
/mnt/data/share/software/Cenote-Taker2/pdb70/pdb70
/mnt/data/share/software/Cenote-Taker2/test/../testcontigs_DNA_ct2.fasta
no CRISPR file given
Prophage pruning requires --lin_minimum_hallmark_genes >= 1. changing to:
--lin_minimum_hallmark_genes 1
time update: locating inputs: 11-16-21---10:25:35
/mnt/data/share/software/Cenote-Taker2/test/../testcontigs_DNA_ct2.fasta
File with .fasta extension detected, attempting to keep contigs over 1 nt and find circular sequences with apc.pl
No circular contigs detected.
no reads provided or reads not found
No circular fasta files detected.
time update: running IRF for ITRs in non-circular contigs 11-16-21---10:25:35
time update: running prodigal on linear contigs 11-16-21---10:25:35
time update: running linear contigs with hmmscan against virus hallmark gene database: standard 11-16-21---10:25:37
Starting pruning of non-DTR/circular contigs with viral domains
pruning script opened
fna files found
./DNA1.fna is too short to prune chromosomal regions
./DNA2.fna is too short to prune chromosomal regions
./DNA3.fna is too short to prune chromosomal regions
mv: cannot stat './DNA5.AA.sorted.fasta': No such file or directory
./DNA5.fna is too short to prune chromosomal regions
time update: HMMSCAN of common viral domains beginning 11-16-21---10:25:38
time update: making tables for hmmscan and rpsblast outputs 11-16-21---10:25:39
time update: running RPSBLAST on each sequence 11-16-21---10:25:39
/mnt/data/share/software/Cenote-Taker2/test/DNA/no_end_contigs_with_viral_domain/COMBINED_RESULTS_PRUNE.AA.rpsblast.out
time update: parsing tables into virus_signal.seq files for hmmscan and rpsblast outputs 11-16-21---10:25:40
time update: Identifying virus chunks, chromosomal junctions, and pruning contigs as necessary 11-16-21---10:25:41
Running file: DNA4.virus_signal.seq
Window +/- to the right ... Chunk_end Window midpoint
0 1 + ... none 2500
0 1 + ... none 2500
[2 rows x 6 columns]
time update: Making prophage table 11-16-21---10:25:43
cat: DNA5.AA.hmmscan.sort.out: No such file or directory
cut: DNA5.AA.hmmscan.sort.out: No such file or directory
cut: DNA5.AA.hmmscan.sort.out: No such file or directory
FINISHED PRUNING CONTIGS WITH AT LEAST 1 VIRAL DOMAIN(S)
Grabbing ORFs wihout RPS-BLAST hits and separating them into individual files for HHsearch
time update: running HHsearch or HHblits 11-16-21---10:25:43
Combining tbl files from all search results AND fix overlapping ORF module
No ITR contigs with minimum hallmark genes found.
Annotating linear contigs
time update: running BLASTX, annotate linear contigs 11-16-21---10:25:43
time update: running PHANOTATE, annotate linear contigs 11-16-21---10:26:18
time update: running Prodigal, annotate linear contigs 11-16-21---10:26:23
time update: running hmmscan1, annotating linear contigs 11-16-21---10:26:24
time update: running hmmscan2, annotating linear contigs 11-16-21---10:26:25
time update: running RPSBLAST, annotating linear contigs 11-16-21---10:26:27
/mnt/data/share/software/Cenote-Taker2/test/DNA/no_end_contigs_with_viral_domain/COMBINED_RESULTS.rotate.AA.rpsblast.out
time update: running tRNAscan-SE 11-16-21---10:26:28
Grabbing ORFs wihout RPS-BLAST hits and separating them into individual files for HHsearch
time update: running HHsearch or HHblits 11-16-21---10:26:31
Combining tbl files from all search results AND fix overlapping ORF module, linear contigs
finalizing taxonomy for linear contigs
DNA2_vs01 is a CRESS virus of some kind
No suitable ORF for taxonomy found for DNA5_vs01, using BLASTX result.
time update: finished annotating linear contigs 11-16-21---10:26:51
time update: running tbl2asn 11-16-21---10:26:53
[real-tbl2asn] Replaced ' ' with '#'
[real-tbl2asn] Replaced ' ' with '#'
[real-tbl2asn] Flatfile DNA1_vs01
[real-tbl2asn] Validating DNA1_vs01
[real-tbl2asn] Replaced ' ' with '#'
[real-tbl2asn] Replaced ' ' with '#'
[real-tbl2asn] Flatfile DNA2_vs01
[real-tbl2asn] Validating DNA2_vs01
[real-tbl2asn] Replaced ' ' with '#'
[real-tbl2asn] Replaced ' ' with '#'
[real-tbl2asn] Flatfile DNA3_vs01
[real-tbl2asn] Validating DNA3_vs01
[real-tbl2asn] Replaced ' ' with '#'
[real-tbl2asn] Replaced ' ' with '#'
[real-tbl2asn] Flatfile DNA4_vs01
[real-tbl2asn] Validating DNA4_vs01
[real-tbl2asn] Replaced ' ' with '#'
[real-tbl2asn] Replaced ' ' with '#'
[real-tbl2asn] Flatfile DNA5_vs01
[real-tbl2asn] Validating DNA5_vs01
[tbl2asn-forever] WARNING: .gbf|.sqn files have incorrect date (01-JAN-2019) and will need to be corrected.
Making gtf tables from final feature tables
time update: Finishing 11-16-21---10:26:55
Virus prediction summary:
5 virus contigs were detected/predicted. 0 contigs had DTRs/circularity. 0 contigs had ITRs. 5 were linear/had no end features
Prophage pruning summary:
1 linear contigs > 10 kb were run through pruning module, and 0 virus sub-contigs (putative prophages/proviruses) were extracted from these. 1 virus contigs were kept intact.
removing ancillary files
output directory: DNA
CENOTE-TAKER 2 HAS FINISHED TAKING CENOTES<<<<<<
/mnt/data/share/software/Cenote-Taker2
prodigal found
BWA found
samtools found
mummer found
circlator found
blastp found
blastn found
blastx found
rpsblast found
bioawk found
efetch found
ktClassifyBLAST found
hmmscan found
bowtie2 found
tRNAscan-SE found
pileup.sh found
tbl2asn found
getorf found
transeq found
bedtools found
Dear CT2 team, Thanks for such amzing work. My issue is that there is no taxonomic assignment rank infomation (eg: "Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; unclassified Podoviridae; crAss-like viruses; environmental samples") compare normal output (see as below "blastx.out (correct)"), and the error output is "*blastx.out (something error)", when I run CT2 on "testcontig_DNA.fasta", and so threre is no correct taxnonmic name for contig 4 / 5 in " DNA_CONTIG_SUMMARY.tsv", which it should be "crAass-like phage".
I check the "err.log", but find nothing. Looking forward your reply. Thanks a lot.
DNA_CONTIG_SUMMARY.tsv
blastx.out (something error)
==> no_end_contigs_with_viral_domain/DNA2_vs01.tax_guide.blastx.out <== DNA2_vs01 gi|289163351|ref|YP_003422530.1| replicase [Porcine circovirus type 1/2a] 99.359 0.0312
==> no_end_contigs_with_viral_domain/DNA3_vs01.tax_guide.blastx.out <== DNA3_vs01_8 gi|1464309244|ref|YP_009507580.1| major capsid protein [Heterosigma akashiwo virus 01] 46.154 9.20e-122 442
==> no_end_contigs_with_viral_domain/DNA4_vs01.tax_guide.blastx.out <== DNA4_vs01_12 gi|674660398|ref|YP_009052554.1| putative Terminase large subunit [uncultured crAssphage] 100.000 0.0 751
==> no_end_contigs_with_viral_domain/DNA5_vs01.tax_guide.blastx.out <== DNA5_vs01 gi|674660359|ref|YP_009052511.1| putative Protein of unknown function (DUF932) [uncultured crAssphage] 100.000 0.0 343
Version 2.1.3
@@@@@@@@@@@@@@@@@@@@@@@@@ Your specified arguments: original contigs: ../testcontigs_DNA_ct2.fasta forward reads: /mnt/data/share/software/Cenote-Taker2/test/no_reads reverse reads: /mnt/data/share/software/Cenote-Taker2/test/no_reads title of this run: DNA Isolate source: unknown collection date: unknown metagenome_type: unknown SRA run number: unknown SRA experiment number: unknown SRA sample number: unknown Bioproject number: unknown template file: /mnt/data/share/software/Cenote-Taker2/dummy_template.sbt minimum circular contig length: 1000 minimum linear contig length: 1 virus domain database: standard min. viral hallmarks for linear: 0 min. viral hallmarks for circular: 0 handle known seqs: do_not_check_knowns contig assembler: unknown_assembler DNA or RNA: DNA HHsuite tool: hhblits original or TPA: original Do BLASTP?: no_blastp Do Prophage Pruning?: True Filter out plasmids?: True Run BLASTN against nt? none Location of Cenote scripts: /mnt/data/share/software/Cenote-Taker2 Location of scratch directory: none GB of memory: 500 number of CPUs available for run: 100 Annotation mode? True @@@@@@@@@@@@@@@@@@@@@@@@@ scratch space will not be used in this run HHsuite database locations: /mnt/data/share/software/Cenote-Taker2/NCBI_CD/NCBI_CD /mnt/data/share/software/Cenote-Taker2/pfam_32_db/pfam /mnt/data/share/software/Cenote-Taker2/pdb70/pdb70 /mnt/data/share/software/Cenote-Taker2/test/../testcontigs_DNA_ct2.fasta no CRISPR file given Prophage pruning requires --lin_minimum_hallmark_genes >= 1. changing to: --lin_minimum_hallmark_genes 1 time update: locating inputs: 11-16-21---10:25:35 /mnt/data/share/software/Cenote-Taker2/test/../testcontigs_DNA_ct2.fasta File with .fasta extension detected, attempting to keep contigs over 1 nt and find circular sequences with apc.pl No circular contigs detected. no reads provided or reads not found No circular fasta files detected. time update: running IRF for ITRs in non-circular contigs 11-16-21---10:25:35 time update: running prodigal on linear contigs 11-16-21---10:25:35 time update: running linear contigs with hmmscan against virus hallmark gene database: standard 11-16-21---10:25:37 Starting pruning of non-DTR/circular contigs with viral domains pruning script opened fna files found ./DNA1.fna is too short to prune chromosomal regions ./DNA2.fna is too short to prune chromosomal regions ./DNA3.fna is too short to prune chromosomal regions mv: cannot stat './DNA5.AA.sorted.fasta': No such file or directory ./DNA5.fna is too short to prune chromosomal regions time update: HMMSCAN of common viral domains beginning 11-16-21---10:25:38 time update: making tables for hmmscan and rpsblast outputs 11-16-21---10:25:39 time update: running RPSBLAST on each sequence 11-16-21---10:25:39 /mnt/data/share/software/Cenote-Taker2/test/DNA/no_end_contigs_with_viral_domain/COMBINED_RESULTS_PRUNE.AA.rpsblast.out time update: parsing tables into virus_signal.seq files for hmmscan and rpsblast outputs 11-16-21---10:25:40 time update: Identifying virus chunks, chromosomal junctions, and pruning contigs as necessary 11-16-21---10:25:41 Running file: DNA4.virus_signal.seq Window +/- to the right ... Chunk_end Window midpoint 0 1 + ... none 2500 0 1 + ... none 2500
[2 rows x 6 columns] time update: Making prophage table 11-16-21---10:25:43 cat: DNA5.AA.hmmscan.sort.out: No such file or directory cut: DNA5.AA.hmmscan.sort.out: No such file or directory cut: DNA5.AA.hmmscan.sort.out: No such file or directory FINISHED PRUNING CONTIGS WITH AT LEAST 1 VIRAL DOMAIN(S) Grabbing ORFs wihout RPS-BLAST hits and separating them into individual files for HHsearch time update: running HHsearch or HHblits 11-16-21---10:25:43 Combining tbl files from all search results AND fix overlapping ORF module No ITR contigs with minimum hallmark genes found. Annotating linear contigs time update: running BLASTX, annotate linear contigs 11-16-21---10:25:43 time update: running PHANOTATE, annotate linear contigs 11-16-21---10:26:18 time update: running Prodigal, annotate linear contigs 11-16-21---10:26:23 time update: running hmmscan1, annotating linear contigs 11-16-21---10:26:24 time update: running hmmscan2, annotating linear contigs 11-16-21---10:26:25 time update: running RPSBLAST, annotating linear contigs 11-16-21---10:26:27 /mnt/data/share/software/Cenote-Taker2/test/DNA/no_end_contigs_with_viral_domain/COMBINED_RESULTS.rotate.AA.rpsblast.out time update: running tRNAscan-SE 11-16-21---10:26:28 Grabbing ORFs wihout RPS-BLAST hits and separating them into individual files for HHsearch time update: running HHsearch or HHblits 11-16-21---10:26:31 Combining tbl files from all search results AND fix overlapping ORF module, linear contigs finalizing taxonomy for linear contigs DNA2_vs01 is a CRESS virus of some kind No suitable ORF for taxonomy found for DNA5_vs01, using BLASTX result. time update: finished annotating linear contigs 11-16-21---10:26:51 time update: running tbl2asn 11-16-21---10:26:53 [real-tbl2asn] Replaced ' ' with '#' [real-tbl2asn] Replaced ' ' with '#' [real-tbl2asn] Flatfile DNA1_vs01
[real-tbl2asn] Validating DNA1_vs01
[real-tbl2asn] Replaced ' ' with '#' [real-tbl2asn] Replaced ' ' with '#' [real-tbl2asn] Flatfile DNA2_vs01
[real-tbl2asn] Validating DNA2_vs01
[real-tbl2asn] Replaced ' ' with '#' [real-tbl2asn] Replaced ' ' with '#' [real-tbl2asn] Flatfile DNA3_vs01
[real-tbl2asn] Validating DNA3_vs01
[real-tbl2asn] Replaced ' ' with '#' [real-tbl2asn] Replaced ' ' with '#' [real-tbl2asn] Flatfile DNA4_vs01
[real-tbl2asn] Validating DNA4_vs01
[real-tbl2asn] Replaced ' ' with '#' [real-tbl2asn] Replaced ' ' with '#' [real-tbl2asn] Flatfile DNA5_vs01
[real-tbl2asn] Validating DNA5_vs01
[tbl2asn-forever] WARNING: .gbf|.sqn files have incorrect date (01-JAN-2019) and will need to be corrected. Making gtf tables from final feature tables
time update: Finishing 11-16-21---10:26:55 Virus prediction summary: 5 virus contigs were detected/predicted. 0 contigs had DTRs/circularity. 0 contigs had ITRs. 5 were linear/had no end features Prophage pruning summary: 1 linear contigs > 10 kb were run through pruning module, and 0 virus sub-contigs (putative prophages/proviruses) were extracted from these. 1 virus contigs were kept intact. removing ancillary files output directory: DNA