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We are analyzing sequencing data while filtering and trimming fastq files encountered following error. Is the following error due to unavailability of core for processing commands?

Error in colnames<-(*tmp*, value = c("cs103_R1_dada.fastq", "cs110_R1_dada.fastq", : attempt to set 'colnames' on an object with less than two dimensions In addition: Warning message: In mclapply(seq_len(n), do_one, mc.preschedule = mc.preschedule, : all scheduled cores encountered errors in user code >

rahul
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  • I have just resolved my similar question "all scheduled cores encountered errors in user code". After a while investigation, I found an error in my `mclapply` function. This error message disappeared after I fix the code error. So, I suggest you check your code carefully. – pengchy Jul 26 '17 at 10:00

4 Answers4

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As pengchy suggested there may be something wrong with function. try the same call by using lapply and error message will be more informative.

f2003596
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To clarify on what @f2003596 and @HelloWorld said: This just means that a crash occurred within the function you called, i.e. while it was executing that function. But this does not necessarily mean that your function is incorrect. For example, you get the same error when a variable has not been found.

MacOS
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Note: If you include an unexpected argument in mclapply you also can get this error message. I put mC.cores instead of mc.cores by mistake and I got it.

vdebuen
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That would mean your R function has a crash.

ABCD
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