access to genome dir?

[lgoehring]

Hello! I'm having a small issue with the ChIP seq peak calling. The first ChIP route worked great. I'm in the same folder and manually edited the samples.pairs.csv with IPs and inputs. I've updated the settings.txt accordingly and I'm still met with :

peaks-macs.sh ERROR: genome dir /gpfs/data/igorlab/ref/hg19
does not exist

I can see I have access to the folder however. Is there a permissions setting? I'm new to this so I'm sure I'm missing something.

Thanks for your time!

[igordot]

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?

[lgoehring]

I edited it through filezilla. File attached. and yes just tried with hg38 and still having the same problem. Thanks!

settings.txt

[igordot]

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?

[lgoehring]

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

[lgoehring]

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

[igordot]

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

[lgoehring]

that worked great! thanks!

[igordot]

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.