Salmon indexing directory missing files?

Question

[bioinfo_cat]

Hi,

I am new to salmon and am trying to build an index. My samples are from Black Sea Bass. My first attempt at building the index I think was successful but it gave me only a 2.4% mapping rate, I know this is bad but one of the things that was suggested to me to try to troubleshoot was to use a transcript from a different organism. Originally I was using zebrafish but now I am trying European seabags.

This time when I build the index the final directory that is created is missing a lot of files that the directory from the zebrafish indexing had.

The zebra fish index directory has these: command.1.txt* duplicate_clusters.tsv header.json quasi_index.log rsd.bin txpInfo.bin zebrafish_index.e8742769.1 zebrafish_index.pe8742769.1 zebrafish_index.sh commands.txt hash.bin indexing.log refInfo.json sa.bin versionInfo.json zebrafish_index.o8742769.1 zebrafish_index.po8742769.1

But the new directory has only these: command.1.txt* commands.txt seabass_index_dups.e8760153.1 seabass_index_dups.o8760153.1 seabass_index_dups.pe8760153.1 seabass_index_dups.po8760153.1 seabass_index_dups.sh

Does anyone know what could possibly be wrong?

Thanks in advance!

[Fabio Marroni]

The files

seabass_index_dups.e8760153.1
seabass_index_dups.o8760153.1
seabass_index_dups.pe8760153.1 
seabass_index_dups.po8760153.1

are the log files form your queuing system. Read them and see if there is an error. The missing files are probably due to the fact that the indexing didn't complete properly.