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Old 04-28-2015, 07:34 AM   #1
JonB
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Location: Norway

Join Date: Jan 2010
Posts: 83
Default GMAP problems: stopping at "Finished checking compiler assumptions"

Edit:
Never mind. It was a simple database error. Fixed it, but don't know how to delete post...

I am trying to map around 300 cDNA sequences to a genome using GMAP. I encountered some problems installing GMAP, but eventually I think it worked out. And I also managed to build an index of my genome. But when I run GMAP like this:

Code:
gmap -d My_genome -2 ~/cDNAs.fasta --format=3
The program never progresses through:

Code:
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
Any idea what could be the problem?

Edit:
It seems that the problem must be with some of the options I used for output, because when I run it like this:

Code:
gmap -d My_genome ~/cDNAs.fasta
the program progresses further, but gives me an error:
Code:
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.
  GMAP 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 (58,449,588 bytes, 14270 pages, 0.09 sec)
Pre-loading compressed genome (bits).....,......,...,...,...,...,...done (58,449,600 bytes, 14270 pages, 0.10 sec)
Cannot find genomic index files in either current or old format.  Looking for files containing ref

Last edited by JonB; 04-28-2015 at 08:03 AM.
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Old 12-03-2015, 06:33 PM   #2
pengchy
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Location: China

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Posts: 116
Default

Hi JonB,

Have you resolved this problem? I have encountered the same problem. But I can run the gamp without error on one compute node, but with problem on another compute node. Is this caused by the hard ware or the system configuration?
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Old 12-07-2015, 11:05 PM   #3
JonB
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Location: Norway

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Hi,
No hardware problems. It was simply me who made a silly mistake. Don't remember exactly, but I think it was a problem with some of the input files.
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