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Old 11-19-2011, 03:39 PM   #1
CNVboy
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Location: boston

Join Date: Jun 2011
Posts: 27
Default Pindel problem

I downloaded the binary code of latest version of Pindel.
And then run the command like below;

./pindel_x86_64 -f /home/xxx/data/human_g1k_v37.fasta -i /home/xxx/scratch/S00005/config.txt -c ALL -o /home/xxx/scratch/S00005/S00005

However I got errors like:
Pindel version 0.2.4d, August 26th 2011.
Looping over all chromosomes.
Processing chromosome: 1
Chromosome Size: 249250621
26926 10000
Looking at chromosome 1 bases 0 to 10000000.
Insertsize in bamreads: 264
[bam_index_load] fail to load BAM index.
pindel_x86_64: reader.cpp:400: bool ReadInBamReads(const char*, const std::string&, std::string*, std::vector<SPLIT_READ, std::allocator<SPLIT_READ> >&, int, std::string, int, int): Assertion `idx' failed.
/sge/default/spool/pem610-002/job_scripts/6258159: line 10: 32451 Aborted (core dumped) .......




I'm just wondering how does binary code know where's my samtools? Because when compling source code, we do provide the location of samtools...
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Old 03-06-2012, 12:33 PM   #2
KaiYe
Senior Member
 
Location: amsterdam

Join Date: Jun 2009
Posts: 133
Default

Quote:
Originally Posted by CNVboy View Post
I downloaded the binary code of latest version of Pindel.
And then run the command like below;

./pindel_x86_64 -f /home/xxx/data/human_g1k_v37.fasta -i /home/xxx/scratch/S00005/config.txt -c ALL -o /home/xxx/scratch/S00005/S00005

However I got errors like:
Pindel version 0.2.4d, August 26th 2011.
Looping over all chromosomes.
Processing chromosome: 1
Chromosome Size: 249250621
26926 10000
Looking at chromosome 1 bases 0 to 10000000.
Insertsize in bamreads: 264
[bam_index_load] fail to load BAM index.
pindel_x86_64: reader.cpp:400: bool ReadInBamReads(const char*, const std::string&, std::string*, std::vector<SPLIT_READ, std::allocator<SPLIT_READ> >&, int, std::string, int, int): Assertion `idx' failed.
/sge/default/spool/pem610-002/job_scripts/6258159: line 10: 32451 Aborted (core dumped) .......




I'm just wondering how does binary code know where's my samtools? Because when compling source code, we do provide the location of samtools...
Please index your sorted BAM.

Kai
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