GMAP v2017-06-20 error

Question

[bioinfo17]

Hi all,

I am trying to align the de novo transcriptome (transcripts) against the reference genome via GMAP using the following command below:

1) have build a database of the genome using gmap-build command,
2)

gmapl -D . -d database -2 genome_fasta  trinity_fasta -f samse > trinity_gmap.sam

Checking compiler assumptions for SSE2: 6B8B4567 327B23C6 xor=59F066A1
Checking compiler assumptions for SSE4.1: -103 -58 max=-58 => compiler sign extends
Checking compiler options for SSE4.2: 6B8B4567 __builtin_clz=1 __builtin_ctz=0 _mm_popcnt_u32=17 __builtin_popcount=17
Finished checking compiler assumptions
Signal received: SIGSEGV
Calling Access_emergency_cleanup

Also I have tried without the -2 genome_fasta flag and keep getting error: must use -d, -G, -1, -2 or --cmdline options.

Any advice, please?

Thanks

[WouterDeCoster]

Please use sensible tags for questions. gmap would have been logic! This allows developers to easily find questions about their tools.

It think your best guess is contacting the developer of GMAP - as far as I know, the developer is very responsive.

[bioinfo17]

Thanks, will do that.

[Gilson]

Did you fix the error? I am experiencing the same issue trying to generate a gff file from trinity contigs:

$ gmap -2 -d GENCODE.V27 -t 16 -B 5 -O -f 2 Trinity.fasta > Trinity_9S_FR_gmap.gff Expansion of offsets is now controlled separately by --expand-offsets (default=1). Checking compiler assumptions for SSE2: 6B8B4567 327B23C6 xor=59F066A1 Checking compiler assumptions for SSE4.1: -103 -58 max=198 => compiler zero extends Checking compiler options for SSE4.2: 6B8B4567 __builtin_clz=1 __builtin_ctz=0 _mm_popcnt_u32=17 __builtin_popcount=17 Finished checking compiler assumptions Signal received: SIGSEGV Calling Access_emergency_cleanup

Answer 1

[KVC_bioinfo]

gmapl -D/ path/to/genome/dir -g genome_fasta.name trinity_fasta -f samse -2 > trinity_gmap.sam

I think the command should work now.