Question: GMAP v2017-06-20 error
0
gravatar for bioinfo17
2.9 years ago by
bioinfo1730
bioinfo1730 wrote:

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

alignment gmap software error • 1.3k views
ADD COMMENTlink modified 2.6 years ago by KVC_bioinfo440 • written 2.9 years ago by bioinfo1730

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.

ADD REPLYlink written 2.9 years ago by WouterDeCoster43k

Thanks, will do that.

ADD REPLYlink written 2.9 years ago by bioinfo1730

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

ADD REPLYlink written 2.2 years ago by Gilson 0
0
gravatar for KVC_bioinfo
2.6 years ago by
KVC_bioinfo440
Boston
KVC_bioinfo440 wrote:

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.

ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by KVC_bioinfo440
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