Question: Differences Running Dindel On Different Unix Environments
gravatar for Mark Dunning
8.8 years ago by
Mark Dunning20
Cambridge, Uk
Mark Dunning20 wrote:

Hi all,

I am hoping to try out dindel for indel-calling on my NGS data but coming up against some problems getting it to work on both institute's computing cluster and my desktop machine. On the cluster, I downloaded the source code for the latest version (1.01) and modified the MakeFile to point to the version on samtools, and dindel seemed to compile Ok.

However, I cannot seem to follow the basic usage example in the manual. I keep getting directed to the help page but I cannot see which of of the arguments is missing.

/home/mib-cri/software/dindel-1.01-src/dindel --ref hsa_chr17.fa --bamFile Example.bam --outputFile dindel.test --analysis getCIGARindels

Error parsing input options. Usage:

[Required] : --ref arg fasta reference sequence (should be indexed with .fai file) --outputFile arg file-prefix for output results

[Required] Program option: --analysis arg (=indels) Analysis type: getCIGARindels: Extract indels from CIGARs of mapped reads, and infer libary insert size distributions indels: infer indels realignCandidates: Realign/reposition candidates in candidate file etc....

So I then went and downloaded the same source code onto my desktop and compiled again. By the way, I notice that the file size of the dindel executable is different on the different environments (3.2 MB on my machine, 2.8 Mb on the computing cluster). When I try and run dindel on my desktop, I don't get an error about the arguments, but an error that seems to imply that I've specified multiple bam files

/home/dunnin01/software/dindel-1.01-src/dindel --ref hsa_chr17.fa --bamFile Example.bam --outputFile dindel.test --analysis getCIGARindels

Can extract the full set of indels from only BAM file at a time.

Why does one compiled version of the program not recognise arguments, and the other complain about the arguments that I do give it?

indel • 2.4k views
ADD COMMENTlink written 8.8 years ago by Mark Dunning20

I'm having the second problem you encountered....I followed the example and get the following error: Can extract the full set of indels from only BAM file at a time

did you ever figure out what the problem was?

ADD REPLYlink written 7.3 years ago by 2anamaly0
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