User: leandro.ishi.lima
leandro.ishi.lima • 90
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Posts by leandro.ishi.lima
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... Hello,
happy to hear it worked out for you!
Kind regards. ...
written 14 months ago by
leandro.ishi.lima • 90
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... Dear Erica,
The log shows that KisSplice failed when building the de Bruijn graph. Such errors are usually memory-related, but since this is the first time we have this specific error, we can't be sure. Your output also shows that KisSplice used 47.3 Gb of RAM before crashing. KisSplice failing wit ...
written 15 months ago by
leandro.ishi.lima • 90
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... Dear Erica,
to check if it is a memory error, could you please paste the output of the following commands.
To retrieve the amount of memory in your machine:
free -h
To get the maximum resident set size used by a command:
/usr/bin/time --verbose
Where `` is your KisSplice command.
Afte ...
written 15 months ago by
leandro.ishi.lima • 90
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... Dear pauloneill27,
Thanks for the confirmation! Please don't hesitate on contacting us in case of any doubt!
Kind regards. ...
written 16 months ago by
leandro.ishi.lima • 90
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... Dear pauloneill27,
Just to confirm, there are no problems here then?
Thanks for the report.
Kind regards. ...
written 16 months ago by
leandro.ishi.lima • 90
1
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Answer:
A: Error in running KisSplice
... Dear 963786304,
The error probably indicates that KisSplice was not able to locate your input file.
It is possible that you were not located in the directory which contained your data when you launched KisSplice.
I suggest you change directory and retry, or use the full path to your data file in th ...
written 17 months ago by
leandro.ishi.lima • 90
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Answer:
A: error while Kissplice run
... Dear KG,
I am redirecting your doubt to the other maintainers, but could you give us more details on the pipeline you are using to call SNPs from transcriptome data, if possible with the command lines?
We also propose the following pipeline: http://kissplice.prabi.fr/TWAS/ for SNP calling from RNA ...
written 18 months ago by
leandro.ishi.lima • 90
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... Dear Bilal Sarwar,
If KisSplice is taking too much time to run, you could try running the experimental algorithm by adding `--experimental` to your command line. It can be faster, at the cost of using more RAM.
Note also that by using `-s 1` you will get only the Type0a-SNPs, which are single SNP ...
written 19 months ago by
leandro.ishi.lima • 90
0
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3
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538
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... Dear Bilal Sarwar,
If KisSplice is taking too much time to run, you could try running the experimental algorithm by adding `--experimental` to your command line. It can be faster, at the cost of using more RAM.
Note also that by using `-s 1` you will get only the Type0a-SNPs, which are single SNP ...
written 19 months ago by
leandro.ishi.lima • 90
1
vote
1
answer
449
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1
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... Dear Archie,
I guess it was a downtime on the FTP server, since now it seems to be working. I was able to download KisSplice2RefTranscriptome version 1.3.2 when writing this message. Could you please retry and check if it is working for you now?
Kind regards. ...
written 23 months ago by
leandro.ishi.lima • 90
Latest awards to leandro.ishi.lima
Scholar
23 months ago,
created an answer that has been accepted.
For A: Error in running KisSplice_ks_debruijn4
Scholar
3.6 years ago,
created an answer that has been accepted.
For A: Error in running KisSplice_ks_debruijn4
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