Transcriptome index

[mtxellrb]

Hi,

I ran mantee without specifying a transcriptome index, the program is supposed to create its own index but outputs the next message and dies instead:

"The provided transcriptome index does not exist or is incorrect. If the parameter t_index is left blank, Manatee will create the transcriptome index based on the provided annotation."

Is there anything I'm missing? Thanks in advanced!

Best,

Meritxell

[jehandzlik]

Hi,

Thanks for the comment. If you are using config file, make sure the t_index parameter is indeed left blank. Even a space would be recognized as a character and prompt the error message you see.

Best,

Joanna

[ramostapiai]

Hello,

I have the same problem. but there is no way that I won't get an error with t_index. I put a blank, a period, an enter, but it always fails and says: The provided transcriptome index does not exist or is incorrect. and If the parameter t_index is left blank, Manatee will create the transcriptome index based on the provided annotation.

This a try to lunch.

perl manatee \ -i ${i}.Unmapped.cut.fastq \ -o $output \ -index $index_dir/Sn \ -genome $index_dir/GCF_000007045.1_ASM704v1_genomic.fna \ -annotation $index_dir/GCA_000007045.1_ASM704v1_genomic.gtf \ -cores 20 \ -t_index

[jehandzlik]

Hello,

I couldn't reproduce your error. Including -t_index in the command like without any trailing spaces or characters didn't give me the error message your are describing. You could possibly try avoiding writing the -t_index parameter in your command.

Best,

Joanna

[kamaloxfordpathology]

Hi Joanna, Hope you are doing well. Could you kindly help me with the error. I am also getting the error "The provided transcriptome index does not exist or is incorrect. If the parameter t_index is left blank, Manatee will create the transcriptome index based on the provided annotation.". Here is my code

!/bin/bash

module load MANATEE index_path="/Genomes/BOWTIE/grch38_human" genome_path="/Genomes/FASTA/Human/GRCh38.primary_assembly.genome.fa" annotation_path="/Genomes/GTF/Human/smallRNA-Seq/Manatee_RNA_types_combined.gtf" mkdir manatee_ouput for filename in ./*.fastq.gz do echo $filename manatee -i $filename -o ./manatee_output -index $index_path -genome $genome_path -annotation $annotation_path done