Pindel problem

CNVboy · 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...

KaiYe · 03-06-2012, 01:33 PM

Quote:

Originally Posted by CNVboy

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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11-19-2011, 04:39 PM	#1
CNVboy Member Location: boston Join Date: Jun 2011 Posts: 27	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...