In case anyone might be able to help, i have explored this further by using a few chromosomes concatenated together that span the location between chromosomes E2 and E3, and this smaller set of chromosomes will index with no problems and the files file does not give a -1 value for chromosome E3. This suggests it is not specific formatting of the chromosome files.

I could really use some help!

Thanks, Peter

It looks very much like 32-bit integer overflow -- the maximum signed 32 bit integer value is 2147483647, which is just above the last number before -1 printed above. In the short term it looks like you'll get around this by using a 64-bit platform; both linux & mac worked for me. I used the Bioconductor docker container to do this on my mac; maybe similar steps could work on Windows?

On my mac I created a little directory hierarchy

/Users/maXXX$ tree tmp/cats
tmp/cats
├── data
│   └── GCF_000181335.3_Felis_catus_9.0_genomic.fna.gz
└── libraries

(maXXX is my user account, obfuscated) I then ran docker following the instructions at http://bioconductor.org/help/docker/, especially the 'Mounting Additional Volumes' section. Specifically I ran the command

docker run -it \
       -v /Users/maXXX/tmp/cats/libraries:/usr/local/lib/R/host-site-library \
       -v /Users/maXXX/tmp/cats/data:/home/rstudio/data \
       -e PASSWORD=meow \
       -p 8787:8787 \
       bioconductor/bioconductor_docker:RELEASE_3_10

The first -v says make my mac's directory tmp/cats/libraries available as the 'local' library where R will install new packages The second -v says to share the place where I want my analysis data to be made available with the docker container under the rstudio account. The -e and -p commands set up the environment in which the docker container's RStudio will run.

After running the command, I can go to my web browser and visit http://127.0.0.1:8787. I'm asked for user name (rstudio) and password (meow, as above!) and then I'm in RStudio. I changed into the data directory

setwd("/home/rstudio/data")

install RSubread

BiocManager::install("Rsubread")

and then went about the business of building the index.

Maybe a little intimidating at first, and maybe some challenges on Windows that I don't have any experience with, but actually not too bad once you get the hang of it.

> download.file("https://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Felis_catus/latest_assembly_versions/GCF_000181335.3_Felis_catus_9.0/GCF_000181335.3_Felis_catus_9.0_genomic.fna.gz","cat.fna.gz")
> buildindex("whatevs/cat", "cat.fna.gz", gappedIndex = TRUE)
<SNIP>
       Rsubread 2.0.1

//================================= setting ==================================\\
||                                                                            ||
||                Index name : cat                                            ||
||               Index space : base space                                     ||
||               Index split : no-split                                       ||
||          Repeat threshold : 100 repeats                                    ||
||              Gapped index : yes                                            ||
||                                                                            ||
||       Free / total memory : 12.2GB / 15.9GB                                ||
||                                                                            ||
||               Input files : 1 file in total                                ||
||                             o cat.fna.gz                                   ||
||                                                                            ||
\\============================================================================//

//================================= Running ==================================\\
||                                                                            ||
|| Check the integrity of provided reference sequences ...                    ||
|| No format issues were found                                                ||
|| Scan uninformative subreads in reference sequences ...                     ||
|| 139772 uninformative subreads were found.                                  ||
|| These subreads were excluded from index building.                          ||
|| Estimate the index size...                                                 ||
||    8%,   0 mins elapsed, rate=6912.7k bps/s                                ||
||   16%,   0 mins elapsed, rate=7346.8k bps/s                                ||
||   24%,   1 mins elapsed, rate=7454.2k bps/s                                ||
<SNIP>
||   91%,   4 mins elapsed, rate=7739.3k bps/s                                ||
|| 5.2 GB of memory is needed for index building.                             ||
|| Build the index...                                                         ||
||    8%,   0 mins elapsed, rate=4409.5k bps/s                                ||
||   16%,   1 mins elapsed, rate=4595.6k bps/s                                ||
<SNIP>
||   91%,   8 mins elapsed, rate=4759.9k bps/s                                ||
|| Save current index block...                                                ||
||  [ 0.0% finished ]                                                         ||
||  [ 10.0% finished ]                                                        ||
||  [ 20.0% finished ]                                                        ||
<SNIP>
||  [ 100.0% finished ]                                                       ||
||                                                                            ||
||                     Total running time: 24.5 minutes.                      ||
||     Index C:\Users\jmacdon\Desktop\whatevs\cat was successfully built!     ||
||                                                                            ||
\\============================================================================//

> system("ls -lah whatevs")
total 4.9G
drwxr-xr-x 1 jmacdon None    0 Mar 16 14:55 .
drwxr-xr-x 1 jmacdon None    0 Mar 16 14:55 ..
-rw-r--r-- 1 jmacdon None 604M Mar 16 14:55 cat.00.b.array
-rw-r--r-- 1 jmacdon None 4.3G Mar 16 14:55 cat.00.b.tab
-rw-r--r-- 1 jmacdon None 240K Mar 16 14:53 cat.files
-rw-r--r-- 1 jmacdon None    0 Mar 16 14:31 cat.log
-rw-r--r-- 1 jmacdon None 115K Mar 16 14:55 cat.reads
[1] 0

Had to use gappedIndex because my crappy little desktop only has 16 Gb RAM, but otherwise seems fine?