Issues with genome indexing with bowtie2-build

Question

[Elisa]

Hi everyone,

I'm trying to build the genome indexes with the following comand line (Ubuntu 18.04):

home/bowtie2-2.4.4-linux-x86_64/bowtie2-build ReferenceGenome GrCh38_index

where ReferenceGenome is the GrCh38.fa downloaded from NCBI to which I have added chr1_KI270763v1_alt.fa sequence.

The version of bowtie2 I am using is: version 2.3.4.1.

I'm not able to understand why only 4 files are generated (.rev.1.bt2 and .rev.2.bt2 files are not generated); moreover, the .2.bt2 is 0 bytes and the other 3 files are too small.

Can someone help me solving this issue?

Thanks in advance

[Sej Modha]

Any specific reasons why you would like to build indexes yourself? Prebuilt indexes are available from bowtie2 webpages for GRCh38 which could save you time and computational power.

http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml

[Elisa]

Because I've had to add to the reference genome GRCh38 the sequence chr1_KI270763v1_alt.fa; as a consequence I have to build my own indexes as the pre-build ones do not have the sequence I've added. Am I wrong?

[ATpoint]

Any error messages? Please add the log file. How much memory is available?

[Sej Modha]

Sorry, I missed that part. That makes sense. Are you getting any errors or the build process was completed successfully?

It is advisable to post any errors that were printed on the terminal during the build step along with your question so we can help you with it.