error running EviAnn

[guptapa]

Hi,
I tried to run EviAnn with bam alignments, protein seq, and fastq reads as evidence to annotate a genome but keep getting the following msg:

ls: cannot access 'tissue*.bam': No such file or directory
Detecting and annotating processed pseudogenes
Detection of pseudogenes failed

The command I have using:
EviAnn-1.0.8/bin/eviann.sh -t 24 -g Rc_chr.fa -p rnaSeq.txt -r pep.all.fa -l

location of fastq and bam files in rnaSeq.txt:
/home/leaf_val_1.fq /home/leaf_val_2.fq
/home/root_val_1.fq /home/root_val_2.fq
/home/panicle_val_1.fq /home/panicle_val_2.fq
/home/rnaseq_filtered.bam bam

Thanks,
Parul

[alekseyzimin]

Hello, Do not use -l option unless you are running annotation liftover. -l option is not compatible with RNA-seq data input. --Aleksey

…

On Mon, Jul 15, 2024 at 12:41 PM Parul Gupta ***@***.***> wrote: Hi, I tried to run EviAnn with bam alignments, protein seq, and fastq reads as evidence to annotate a genome but keep getting the following msg: ls: cannot access 'tissue*.bam': No such file or directory Detecting and annotating processed pseudogenes Detection of pseudogenes failed The command I have using: EviAnn-1.0.8/bin/eviann.sh -t 24 -g Rc_chr.fa -p rnaSeq.txt -r pep.all.fa -l location of fastq and bam files in rnaSeq.txt: /home/leaf_val_1.fq /home/leaf_val_2.fq /home/root_val_1.fq /home/root_val_2.fq /home/panicle_val_1.fq /home/panicle_val_2.fq /home/rnaseq_filtered.bam bam Thanks, Parul — Reply to this email directly, view it on GitHub <#7>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AGPXGHOJNCJFTY3RKWVQV4LZMP3RXAVCNFSM6AAAAABK443KMCVHI2DSMVQWIX3LMV43ASLTON2WKOZSGQYDSMJXGQ4TKNA> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

-- Dr. Alexey V. Zimin Associate Research Scientist Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA (301)-437-6260 website http://ccb.jhu.edu/people/alekseyz/ blog http://masurca.blogspot.com

[alekseyzimin]

I will update the usage message to remove "also useful when supplying proteins from a single species". On Wed, Jul 17, 2024 at 9:57 AM Aleksey Zimin ***@***.***> wrote:

…

Hello, Do not use -l option unless you are running annotation liftover. -l option is not compatible with RNA-seq data input. --Aleksey On Mon, Jul 15, 2024 at 12:41 PM Parul Gupta ***@***.***> wrote: > Hi, > I tried to run EviAnn with bam alignments, protein seq, and fastq reads > as evidence to annotate a genome but keep getting the following msg: > > ls: cannot access 'tissue*.bam': No such file or directory > Detecting and annotating processed pseudogenes > Detection of pseudogenes failed > > The command I have using: > EviAnn-1.0.8/bin/eviann.sh -t 24 -g Rc_chr.fa -p rnaSeq.txt -r pep.all.fa > -l > > location of fastq and bam files in rnaSeq.txt: > /home/leaf_val_1.fq /home/leaf_val_2.fq > /home/root_val_1.fq /home/root_val_2.fq > /home/panicle_val_1.fq /home/panicle_val_2.fq > /home/rnaseq_filtered.bam bam > > Thanks, > Parul > > — > Reply to this email directly, view it on GitHub > <#7>, or unsubscribe > <https://github.com/notifications/unsubscribe-auth/AGPXGHOJNCJFTY3RKWVQV4LZMP3RXAVCNFSM6AAAAABK443KMCVHI2DSMVQWIX3LMV43ASLTON2WKOZSGQYDSMJXGQ4TKNA> > . > You are receiving this because you are subscribed to this thread.Message > ID: ***@***.***> > -- Dr. Alexey V. Zimin Associate Research Scientist Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA (301)-437-6260 website http://ccb.jhu.edu/people/alekseyz/ blog http://masurca.blogspot.com

-- Dr. Alexey V. Zimin Associate Research Scientist Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA (301)-437-6260 website http://ccb.jhu.edu/people/alekseyz/ blog http://masurca.blogspot.com