Comments (8)
Sorry you are having trouble.
How did you edit your settings.txt? Can you share the file here?
Is this only a problem for hg19 or does it happen for hg38 as well?
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I edited it through filezilla. File attached. and yes just tried with hg38 and still having the same problem. Thanks!
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That looks okay. Just to confirm, you ran the chip
route and it worked. The problem was only for chip-pairs-peaks
?
Can you also share the complete log file where the error is?
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Yes! ChIP route worked great. Here are the log files. Also attaching the peaks-macs in case?
slurm-17597688.txt
[slurm-17597690.txt](https://github.c
peaks-macs.txt
om/igordot/sns/files/8967898/slurm-17597690.txt)
slurm-17597689.txt
a
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I also tried to copy your hg19 to the folder im running these analyses in and set that as the genome-dir but that also didn't work
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I didn't notice it earlier, but if you look at the error message, you'll see it spans two lines because there is a line break after hg19.
It looks like the problem is you have non-UNIX line endings. When you edited the file, you probably introduced those. You can check for yourself with cat -A settings.txt
. You should see just $
, not ^M$
, at the end of every line.
To fix, run:
module load dos2unix/7.4.0
dos2unix settings.txt
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that worked great! thanks!
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Great! The samples CSV files get cleaned up by default. The settings.txt does not, but usually it is not edited, so you are less likely to run into any issues. I should fix that.
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Related Issues (14)
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