Error in running KisSplice_ks_debruijn4

Question

[c.evang]

Dear All, I'm running KisSplice-2.4.0, but after minigraph construction I get the following error:

"Problem with /path/to/kissplice/kissplice-2.4.0/libexec/kissplice/ks_debruijn4
<bound method Popen.poll of <subprocess.Popen object at 0x7f79267871d0>>".

Can anyone help me to solve the problem?

Thanks Chiara

Answer 1

[leandro.ishi.lima]

Dear Chiara,

Could you post the full output and the error log (if you redirected the error stream) please? If you ran in verbose mode (-v), it is even better!

Thanks.

[c.evang]

This is the kissplice_log_summary file:

This is KisSplice, version 2.4.0

The command line was: /home/universita/kissplice-2.4.0/bin/kissplice -t 8 -k 25 -r all_reads_EcoB.fastq -o /home/universita/kissplice -d /home/universita/kissplice Using the read files: /home/universita/all_reads_EcoB.fastq Results will be stored in: /home/universita/kissplice Summary log file will be saved in: /home/universita/kissplice/kissplice_log_summary_16-39-53_13-07-2016_977484

[16:39:53 13/07/2016] --> Building de Bruijn graph... Graph will be written in /home/universita/kissplice/graph_all_reads_EcoB_k25.[edges/nodes].

The program stops after minigraph construction with the error already posted above:

Problem with /path/to/kissplice/kissplice-2.4.0/libexec/kissplice/ks_debruijn4 <bound method="" popen.poll="" of="" <subprocess.popen="" object="" at="" 0x7f79267871d0="">>.

The output files that it produces in the output directory are the following (if they can help to understand what happened): all_read_filenames, graph.nodes, graph.debloom, graph.reads_binary, graph.debloom2, graph.solid_kmers_binary, graph.edges, graph.solid_kmers_binary_with_count, graph.false_positive_kmers graph.t2_kmers, graph.linearSeqs.

Thanks.

[leandro.ishi.lima]

Hello,

We have three options to try to narrow down the reasons why KisSplice is failing to process your data: 1) Check if the compilation and installation are fine: you can do this by entering the directory you compiled KisSplice (i.e. the directory that you ran cmake and make) and running "make test". 2) Check if your fastq file is corrupted. You can also send us the file so that we can check it ourselves. Or, if you prefer, get a small subset of your fastq lines that are able to reproduce this problem and send us. 3) If the two previous options do not work, we can send you a pre-release of the next release that uses a new graph construction tool, GATB (http://gatb.inria.fr/).

Thank you for your report.

[c.evang]

Hello,

I downloaded the software version 2.4.0-p1 and now it seems running well.

Thanks

Answer 2

[gao131yuan]

Hello Chiara, I had met the same question with you, then I checked my cmake and I found there was something wrong with my cmake. So I reinstall cmake , when I run "./bootstrap" it said " version `GLIBCXX_3.4.20' not found" .Then I search for solution , and the key factor is libstdc++, you can input this "strings /usr/local/lib64/libstdc++.so.6|grep GLIBCXX" if you found the"GLIBCXX_3.4.20" you could put the link to right address as following: % cp /usr/local/lib64/libstdc++.so.6.0.21 /usr/lib64/ % cd /usr/lib64/ % rm -f libstdc++.so.6 % ln -s libstdc++.so.6.0.21 libstdc++.so.6 maybe you need a root permission, you can try it!

Answer 3

[gao131yuan]

Update: all the "libstdc++.so.6.0.21" should be "libstdc++.so.6.0.20" in the above answer!