Gsnap error - possibly very basic

[sjuzhet]

When I put in a basic input, it terminates fairly quickly:

gsnap -d hg19 -N 1 InputR1.fq InputR2.fq
GSNAP version 2015-06-12 called with args: gsnap -d hg19 -N 1 InputR1.fq InputR2.fq
Novel splicing (-N) turned on => assume reads are RNA-Seq
Checking compiler assumptions for popcnt: 000041A7 __builtin_clz=17 __builtin_ctz=0 _mm_popcnt_u32=7 __builtin_popcount=7
Checking compiler assumptions for SSE2: 000041A7 10D63AF1 xor=10D67B56
Checking compiler assumptions for SSE4.1: -89 -15 max=241 => compiler zero extends
Finished checking compiler assumptions
Note: >1 sequence detected, so index files are being memory mapped.
GSNAP can run slowly at first while the computer starts to accumulate
pages from the hard disk into its cache. To copy index files into RAM
instead of memory mapping, use -B 3, -B 4, or -B 5, if you have enough RAM.
For more speed, also try multiple threads (-t <int>), if you have multiple processors or cores.
Allocating memory for compressed genome (oligos)...Error with shmget. Error 2: No such file or directory
Signal received: SIGABRT
Calling Access_emergency_cleanup
Unable to retrieve queryseq for request

When I add -B 3, it gets a little farther:

gsnap -d hg19 -N 1 -B 3 InputR1.fq InputR2.fq
GSNAP version 2015-06-12 called with args: gsnap -d hg19 -N 1 -B 3 InputR1.fq InputR2.fq
Novel splicing (-N) turned on => assume reads are RNA-Seq
Checking compiler assumptions for popcnt: 000041A7 __builtin_clz=17 __builtin_ctz=0 _mm_popcnt_u32=7 __builtin_popcount=7
Checking compiler assumptions for SSE2: 000041A7 10D63AF1 xor=10D67B56
Checking compiler assumptions for SSE4.1: -89 -15 max=241 => compiler zero extends
Finished checking compiler assumptions
Note: >1 sequence detected, so index files are being memory mapped.
GSNAP can run slowly at first while the computer starts to accumulate
pages from the hard disk into its cache. To copy index files into RAM
instead of memory mapping, use -B 3, -B 4, or -B 5, if you have enough RAM.
For more speed, also try multiple threads (-t <int>), if you have multiple processors or cores.
Pre-loading compressed genome (oligos)...,..,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,.,.,..,.,..,.,..,.,....,.,..,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,......,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,.,..,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,.,.,.,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,..done (1,093,035,816 bytes, 266855 pages, 0.10 sec)
Pre-loading compressed genome (bits)...,..,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,.,.,..,.,..,.,..,.,....,.,..,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,......,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,.,..,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,.,.,.,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,...,..done (1,093,035,840 bytes, 266855 pages, 0.10 sec)
Allocating memory for indexij ptrs...Error with shmget. Error 2: No such file or directory
Signal received: SIGABRT
Calling Access_emergency_cleanup
Unable to retrieve queryseq for request

I have little idea what's going wrong. I'm going to keep tinkering, but I was hoping someone here would have some idea of what to do.

[GenoMax]

Looks like the program is not able to find/read the input sequence file(s). Can you try providing full paths to InputR1.fq InputR2.fq?

You may also be getting an error (Error with shmget) with memory allocation in the second try.

[elximo]

I just had a similar error using the same version.

gsnap -d mydatabase --gunzip -B 4 -t 20 -m 8 -N 1 --force-single-end ConditionAlpha.fastq.gz

GSNAP version 2015-06-12 called with args: gsnap -d mydatabase --gunzip -B 4 -t 20 -m 8 -N 1 --force-single-end ConditionAlpha.fastq.gz
Novel splicing (-N) turned on => assume reads are RNA-Seq
Checking compiler assumptions for popcnt: 6B8B4567 __builtin_clz=1 __builtin_ctz=0 _mm_popcnt_u32=17 __builtin_popcount=17
Checking compiler assumptions for SSE2: 6B8B4567 327B23C6 xor=59F066A1
Checking compiler assumptions for SSE4.1: -103 -58 max=198 => compiler zero extends
Finished checking compiler assumptions
Note: >1 sequence detected, so index files are being memory mapped.
GSNAP can run slowly at first while the computer starts to accumulate
pages from the hard disk into its cache. To copy index files into RAM
instead of memory mapping, use -B 3, -B 4, or -B 5, if you have enough RAM.
For more speed, also try multiple threads (-t <int>), if you have multiple processors or cores.
Allocating memory for compressed genome (oligos)...Error with shmget. Error 2: No such file or directory
Signal received: SIGABRT
Calling Access_emergency_cleanup


Would this be a configuration or access rights error? I don't have admin rights on that server and it is a local installation.