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CNVboy

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Join Date: Jun 2011

Posts: 27
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#1

Pindel problem

11-19-2011, 04:39 PM

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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KaiYe

Senior Member

Join Date: Jun 2009

Posts: 133
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#2

03-06-2012, 01:33 PM

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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