Error with hera not finding the index

Question

[biomagician]

Dear all,

I have created a Hera index using:

./output/software/hera/build/hera_build --fasta output/genome/celegans/ref/seq/celegans.fa --gtf output/genome/celegans/ref/annotation/celegans.gtf --outdir output/genome/celegans/ref/index/hera/

This creates 3 files: index, reference.inf, transcripts.fasta

I then use:

./output/software/hera/build/hera quant -i output/genome/celegans/ref/index/hera/  output/reads/illumina/trimmed/pooled/altadena1.fastq

but this creates the following error:

Can not open index file or file is not exist!!!

Can anybody help me, please?

Thanks.

Best,

C.

[phuongthao.12csh]

Hi cristian, I have created a similar working directory as your command and tried to map a fastq read file on c.elegans genome (from ensembl). It turned out to work normally on my system.

./output/software/hera/build/hera_build --fasta output/genome/celegans/ref/seq/Caenorhabditis_elegans.WBcel235.dna_sm.toplevel.fa --gtf output/genome/celegans/ref/annotation/Caenorhabditis_elegans.WBcel235.89.gtf --outdir output/genome/celegans/ref/index/hera/
Scan reference sequence ...
Scan gtf file...
Extract transcript sequence
Hera is a program developed by BioTuring for RNA-Seq analysis.
Please contact [e-mail] if you need further support
Index transcripts in: output/genome/celegans/ref/index/hera/transcripts.fasta
Number of sequence  : 58941
____

ls -lha output/genome/celegans/ref/index/hera/
total 1,1G
drwxrwxr-x 2 thaottp thaottp 4,0K Th07 30 22:42 .
drwxrwxr-x 3 thaottp thaottp 4,0K Th07 30 22:38 ..
-rw-rw-r-- 1 thaottp thaottp 973M Th07 30 22:42 index
-rw-rw-r-- 1 thaottp thaottp 3,9M Th07 30 22:41 reference.inf
-rw-rw-r-- 1 thaottp thaottp  54M Th07 30 22:41 transcripts.fasta
___

./output/software/hera/build/hera quant -i output/genome/celegans/ref/index/hera/ sim/sim1_1.fq 
Hera is a program developed by BioTuring for RNA-Seq analysis.
Please contact [e-mail] if you need further support
Process single-end reads in: sim/sim1_1.fq
Number of aligned readsd: 1692/30000000000      
Mean read lenght    : 75.000000
Finish EM with 50 rounds

Can you give me more details about your system (uname -a) and results from index step (ls -lha output/genome/celegans/ref/index/hera/)?

[WouterDeCoster]

Hi phuongthao.12csh,

Since your reaction is a query for more information and not (yet) an answer to OPs question I have moved your reaction to a comment rather than an answer.

Cheers,
Wouter

[biomagician]

Hi, Thanks.

uname -a
Darwin cr517s-MacBook-Pro.local 16.6.0 Darwin Kernel Version 16.6.0: Fri Apr 14 16:21:16 PDT 2017; root:xnu-3789.60.24~6/RELEASE_X86_64 x86_64

Best, C.

[biomagician]

And,

ls -lha output/genome/celegans/ref/index/hera/ 
total 2109200
drwxr-xr-x  6 cr517  staff   204B 30 Jul 16:22 .
drwxr-xr-x  7 cr517  staff   238B 30 Jul 14:33 ..
-rw-r--r--@ 1 cr517  staff   6.0K 30 Jul 16:22 .DS_Store
-rw-r--r--  1 cr517  staff   973M 30 Jul 16:22 index
-rw-r--r--  1 cr517  staff   3.8M 30 Jul 16:22 reference.inf
-rw-r--r--  1 cr517  staff    53M 30 Jul 16:22 transcripts.fasta

[WouterDeCoster]

Perhaps another recommendation for the developers would be to change that error message from:

Can not open index file or file is not exist!!!

To:

Can not open index file or file does not exist!!!

[sonpham]

Thanks WouterDeCoster. We have fixed the typos but still can't reproduce the error!

[sonpham]

Hi Cristian, Thank you for the bug report and sorry for the error! Can you tell me what is the output of "ls output/genome/celegans/ref/index/hera/"

[biomagician]

Hi,

Here it is.

ls output/genome/celegans/ref/index/hera/
index             reference.inf     transcripts.fasta

Best, C.

[GenoMax]

Have you checked hera help? It looks like you may need to include the basename for the index. Instead of -i output/genome/celegans/ref/index/hera/ e.g. -i output/genome/celegans/ref/index/hera/genome.

[biomagician]

Hi,

I tried your change but it did not work. Why two forward slashes? And why 'genome' in particular? What is the basename?

From what is written here: https://github.com/bioturing/hera I cannot find anything about the basename.

Thanks.

Best,

C.

[GenoMax]

Double-slashes were a typo. Fixed.

Answer 1

[phuongthao.12csh]

Hi cristian,

It seems that the error is due to the difference between Mac and Linux. We have fixed it and committed to Github. Please pull or clone ( https://github.com/bioturing/hera ), and check if it can work now.

Bioturing Algorithm Team.

[biomagician]

Thanks, it works now!