Error running IGGPIPE test data: jellyfish::compacted_hash::ErrorReading

[dipsaha]

I have installed IGGPIPE in Ubuntu 14.04 lts workstation following the guides of IGGPIPE instructions. While running test data, it throws error. Following is the log file:

getSeqInfo file(s) for genome(s) ALL are up to date.

getKmers file(s) for genome(s) ALL are up to date.

*** getKmers PARAMS=allParameters.test GENOME=1 ***
Extracting unique 11-mers from testFASTA/ITAG2.4_test.fasta into binary file outTestHP11/Kmers/Kmers_1.kmers
(time
jellyfish count -C -m 11 -s 80M -U 1 -o outTestHP11/Kmers/Kmers_1.kmers testFASTA/ITAG2.4_test.fasta ) 2>&1 ### getKmers_1
1.12user 0.02system 0:01.14elapsed 100%CPU (0avgtext+0avgdata 45772maxresident)k
0inputs+3744outputs (0major+8060minor)pagefaults 0swaps
Finished.

*** kmersToText PARAMS=allParameters.test GENOME=1 ***
Converting 11-mers from binary file outTestHP11/Kmers/Kmers_1.kmers into text format in file outTestHP11/Kmers/Kmers_1.kmers.txt
(time
jellyfish dump -c -o outTestHP11/Kmers/Kmers_1.kmers.txt outTestHP11/Kmers/Kmers_1.kmers ) 2>&1 ### jellydump_1
terminate called after throwing an instance of 'jellyfish::compacted_hash::ErrorReading'
what(): 'outTestHP11/Kmers/Kmers_1.kmers': File truncated
Command terminated by signal 6
0.00user 0.00system 0:00.13elapsed 1%CPU (0avgtext+0avgdata 1696maxresident)k
0inputs+0outputs (0major+493minor)pagefaults 0swaps

Can you please troubleshoot this for me. I am not an expert Bioinformatics guy hence, I may require detailed advices to make the program work. Please help.

[tedtoal]

Hi dipsaha,

Well, congratulations. You are the first and only person I’ve heard from about IGGPIPE since my paper was published!

It’s been quite a while and I’m not surprised there would be some problems with installation by now. Things keep changing.

I’ll try to help you, although it may take me a while, I'll have to try to remember things and study this and see if I can understand what’s going on.

It says: "what(): 'outTestHP11/Kmers/Kmers_1.kmers': File truncated"

That file was just created (successfully, apparently) in the previous step.

Can you do an 'ls -l' on that file and see what the file size is? I just checked that file on my machine, I actually still have it. It's size is 1914732. I think yours should be the same.

I did a search for this error and found someone else with the same thing. In their case I think the .kmers file size was 0. At any rate, in the end what fixed the problem for them was to update to the latest version of Jellyfish. I think you should give that a try. But before doing it, delete the outTestHP11/Kmers/Kmers_1.kmers file and rerun the make and see if there are any different errors at all.

I'll try to stick with you on this until we get it working for you. Can you tell me what you're using it for, out of curiosity?

Ted Toal

[dipsaha]

Hi ted,

Many thanks for your response. I could troubleshoot the problem. It was because of the lower version of jellyfish. The latest version fixed the problem and I was able to run the test data successfully. I am not sure about the file size (couldn't ascertain it from the 'ls -l' command.

You said not many people used this pipeline; may I know why? For your information, I am interested to look into InDels between (i) 2-3 genomes of Corchorus and (ii) 4 genomes of Linum; both separate analysis. I have completed run of the first one. A quick look into the Primer designing files, I could find majority of the primers are showing product size below 100 bp. I am not sure, if I may need to reset the all parameters and primer3settings file. Will try that in next week.

Thanks for your suggestions

Best regards
Dip

[tedtoal]

I don't know why no one seemed to use the pipeline. For all I know, many did, and simply never needed to contact me. My speculation has been that most experiments these days are using high-throughput sequencing and not PCR, and there is little demand for the kind of PCR primers the pipeline creates.

Hmm, product size below 100 bp sounds like you DO have the parameters set that way.

Let me know how well it works out for you. You can contact me also at twtoal@ucdavis.edu

Ted