gsnap complains about iit file

[efoss]

I am trying to run gsnap with RNA seq data. It starts to look like it's working, but then it dies with this complaint:

IIT file splice_sites_102311_1.iit appears to have an offset that is too large (offset after sigmas 6929586440, filesize 5395915 ...

Does anyone know what I am doing wrong? The lines in my iit file look like this:


>FBgn0034742_CG4294 2R:18492684..18492683 acceptor
>FBgn0034742_CG4294 2R:18490231..18490230 donor
>FBgn0034742_CG4294 2R:18490174..18490173 acceptor
>FBgn0034742_CG4294 2R:18489794..18489793 donor
>FBgn0034742_CG4294 2R:18489732..18489731 acceptor
>FBgn0034742_CG4294 2R:18489453..18489452 donor
>FBgn0034742_CG4294 2R:18489321..18489320 acceptor
>FBgn0034742_CG4294 2R:18489035..18489034 donor
>FBgn0034742_CG4294 2R:18488876..18488875 acceptor
>FBgn0034742_CG4294 2R:18488718..18488717 donor
>FBgn0034742_CG4294 2R:18488653..18488652 acceptor
>FBgn0034742_CG4294 2R:18488870..18488869 acceptor
>FBgn0034742_CG4294 2R:18488718..18488717 donor
>FBgn0034742_CG4294 2R:18488653..18488652 acceptor
>FBgn0034742_CG4294 2R:18488301..18488300 donor
>FBgn0032640_Sgt 2L:17473468..17473469 acceptor
>FBgn0032640_Sgt 2L:17471852..17471853 donor
>FBgn0032640_Sgt 2L:17473560..17473561 acceptor
>FBgn0259204_CG42308 X:6905441..6905442 donor
>FBgn0259204_CG42308 X:6905526..6905527 acceptor
>FBgn0259204_CG42308 X:6905789..6905790 donor
>FBgn0259204_CG42308 X:6905850..6905851 acceptor
>FBgn0259204_CG42308 X:6905522..6905523 acceptor
>FBgn0259204_CG42308 X:6905789..6905790 donor

Thank you.

Eric

[efoss]

For what it's worth, this was my command:

gsnap --gunzip -d from_Flybase_5p41 -D /home/efoss/gene_databases/GMAP_GSNAP_db -t 10 --format=sam -N 1 -s splice_sites_102311_1.iit D09NJACXX_s8_1_illumina12index_7_SL7776.fastq.gz D09NJACXX_s8_2_illumina12index_7_SL7776.fastq.gz > D09NJACXX_s8_illumina12index_7_SL7776.sam

[geparada]

Hi efoss

I'm having the same error... did you find a solution?

I'm using:

gsnap -d hg19_12k-mer ../SJ.15M.mut -N 1 -B 5 -t 8 -O -m 0.06 -A sam -k 12 -s ~/db/transcriptome/hg19/Gene_models/gencode.v9.annotation.splice_sites_gsnap

I tried to run GSNAP with a smaller iit file, but the result is the same


cheers,

[efoss]

Hi efoss

I'm having the same error... did you find a solution?

I'm using:

gsnap -d hg19_12k-mer ../SJ.15M.mut -N 1 -B 5 -t 8 -O -m 0.06 -A sam -k 12 -s ~/db/transcriptome/hg19/Gene_models/gencode.v9.annotation.splice_sites_gsnap

I tried to run GSNAP with a smaller iit file, but the result is the same


cheers,

Hi Geparada,

Yes - I figured out what I was doing wrong. My iit file was just like I showed above, and that was my mistake. Apparently an iit file is not a text file but rather a binary file. I used gsnap utilities to convert this text file to an iit file like this:

cat splice_sites.txt | iit_store -o splice_sites

Then things worked.

Good luck!

Best wishes,

Eric

[geparada]

I din't know that the iit files are binary.
Now I worked!

Cheers!