Pindel stuck?

[casshyr]

I just installed pindel version 0.2.5a4. I'm new to the software. I followed the instruction on http://gmt.genome.wustl.edu/pindel/0.2.4/install.html

When I run the demo run code, the output basically executed until it reached the part where it said on the terminal:

Insertionsize in config: 250

And then nothing else seems to be happening. I can't tell if the software is running or if it's stuck. No new lines were being written to the output. I waited for 15 minutes but nothing else was happening so I terminated the job.

Is this normal? The demo is only a couple of Mbs, so I don't see why it should take so long.

[KaiYe]

can you show me how you run Pindel on the demo data or what you mean "I run the demo run code"? Pindel is realigning reads than processing the alignment result from mapper so that it is expected to take some minutes if your window size (-w) is large and your coverage is high. Can you submit your job to a node and tell me the entire running log?

some steps take a long time and I do not want to write the message from every part of the code as the log file or your console will contain too much information than necessary.

I just installed pindel version 0.2.5a4. I'm new to the software. I followed the instruction on http://gmt.genome.wustl.edu/pindel/0.2.4/install.html

When I run the demo run code, the output basically executed until it reached the part where it said on the terminal:

Insertionsize in config: 250

And then nothing else seems to be happening. I can't tell if the software is running or if it's stuck. No new lines were being written to the output. I waited for 15 minutes but nothing else was happening so I terminated the job.

Is this normal? The demo is only a couple of Mbs, so I don't see why it should take so long.

[casshyr]

can you show me how you run Pindel on the demo data or what you mean "I run the demo run code"? Pindel is realigning reads than processing the alignment result from mapper so that it is expected to take some minutes if your window size (-w) is large and your coverage is high. Can you submit your job to a node and tell me the entire running log?

some steps take a long time and I do not want to write the message from every part of the code as the log file or your console will contain too much information than necessary.

Hi I basically did the exact same instruction as on the Pindel website. From the Pindel folder I did the following:

cd demo
../pindel -f simulated_reference.fa -i simulated_config.txt -o output

I did not change anything in the .fa file nor the config.txt file. I left everything as it came with in the Pindel package.

But I think I realized the problem - I was simply too impatient. I have started a job processing a 30X human WGS with Pindel and it seems to be running fine now. I was just surprised that a demo job would take so long, because usually for most software's demo, I expected only like ~1-5 minutes to run, so when the demo took more than 15 minutes I mistakenly thought it was stuck.

[KaiYe]

Hi I basically did the exact same instruction as on the Pindel website. From the Pindel folder I did the following:

cd demo
../pindel -f simulated_reference.fa -i simulated_config.txt -o output

I did not change anything in the .fa file nor the config.txt file. I left everything as it came with in the Pindel package.

But I think I realized the problem - I was simply too impatient. I have started a job processing a 30X human WGS with Pindel and it seems to be running fine now. I was just surprised that a demo job would take so long, because usually for most software's demo, I expected only like ~1-5 minutes to run, so when the demo took more than 15 minutes I mistakenly thought it was stuck.

can you get the latest version to test again using demo data? There was one read selection step changed recently and it does slow down Pindel dramatically. Now I have modified it. You should be able to get the demo set finished within 30 seconds. Let's me know if this is not the case.