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[ERROR]: FATAL ERROR: parseSeqFiles failed #82
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What version of crass are you using?
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I cloned the git repo and built it. It is in the master branch.
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I just pushed up a new commit. Can you download it again and see if it fixes the problem. |
Cloned the updated repo and rebuilt. Worked this time! Not sure if this is interesting to you, but the numbers are lower now compared to the version before:
Thanks a lot :) |
Hi,
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Hmm, seems like I only fixed a symptom of the problem with the previous commit. What is strange is that when I take just this one read and run it through I don't get the error. Could you try doing the same thing? Is this a public dataset that I could also download and debug on? |
Also can you send me the full log file of the failed run? |
Hi,
Here is what the log file says:
I provide you also one of the datasets that fails (preprocessed metatranscriptomic reads): https://www.dropbox.com/s/sy8ywj1s1uqe3zb/mt.r1.trimmed.rna_filtered.fq?dl=0 Another issue I am facing is that when I git pull, the version remains 1.0.0
Thanks in advance for your help, Best regards, |
Hi Susana, I've downloaded the file you linked on dropbox but on my computer it runs fine without any errors. Did you change any of the command line options from their default? |
Hi,
What do you suggest? |
I don't think that's a problem, I just forgot to update the version number in one of the files so it isn't going to change the results any. Sorry for the confusion. It may be that your operating system uses a slightly different setup to the one I'm using, which may be causing the issue. Can you tell me what operating system you are using and what version of the c++ compiler you have on your system? |
c++ compiler
operating system
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I'm still not able to replicate this error on the file you gave me. I wasn't able to download you exact operating system but I did recompile my copy of the code with the same version of gcc that you are using. I'm really sorry about this but I don't know why it's giving you an error and not me. Perhaps you could try it on another computer. |
Ok, thanks a lot! |
Hi,
I attempted running
crass
on my data. The the command below was issued followed by the STDOUT:Note that I am running
crass
on data from multiple samples. It only shows problems on data from this particular sample. The reads were preprocessed prior to analysis withcrass
. I have a machine with more than enough memory (>100GB RAM). Any Idea why this could happen?Best regards,
Shaman
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