How to pass --tempdir parameter to MACS2 from CallPeaks?

[ajynair]

I am trying Signac pbmc tutorial in Ubuntu and getting errors while using CallPeaks().

peaks <- CallPeaks(pbmc, macs2.path = "/home/user1/anaconda3/envs/signac/bin/macs2")
..
INFO @ Tue, 18 Apr 2023 15:07:21: #3 Call peaks...
INFO @ Tue, 18 Apr 2023 15:07:21: #3 Pre-compute pvalue-qvalue table...
INFO @ Tue, 18 Apr 2023 15:10:11: #3 Call peaks for each chromosome...
ValueError: cannot resize this array: it does not own its data
Exception ignored in: 'MACS2.IO.CallPeakUnit.clean_up_ndarray'
ValueError: cannot resize this array: it does not own its data
ValueError: cannot resize this array: it does not own its data
Exception ignored in: 'MACS2.IO.CallPeakUnit.clean_up_ndarray'
ValueError: cannot resize this array: it does not own its data
ValueError: cannot resize this array: it does not own its data
Exception ignored in: 'MACS2.IO.CallPeakUnit.clean_up_ndarray'
ValueError: cannot resize this array: it does not own its data
IINFO @ Tue, 18 Apr 2023 12:52:53: #4 Write output xls file... /tmp/RtmpW3I1Ts/SeuratProject_peaks.xls
INFO @ Tue, 18 Apr 2023 12:52:53: #4 Write peak in narrowPeak format file... /tmp/RtmpW3I1Ts/SeuratProject_peaks.narrowPeak
INFO @ Tue, 18 Apr 2023 12:52:53: #4 Write summits bed file... /tmp/RtmpW3I1Ts/SeuratProject_summits.bed
INFO @ Tue, 18 Apr 2023 12:52:53: Done!

I am seeing low disk space warning in root disk. First, is this a serious error? Second, I was thinking if MACS2 is working in my /home/user1/tmp (there is space in that disk) this error will go. Can I pass "--tempdir /home/user1/tmp" to the MACS2 from CallPeaks()?

[timoast]

By default Signac puts the temporary files in the directory defined by tempdir() in R (usually /tmp/Rxxxxxxxx). I think the outdir parameter in CallPeaks() is what you want to change here (there's no --tempdir parameter for MACS2 https://github.com/macs3-project/MACS/blob/master/docs/callpeak.md)

Further documentation for CallPeaks() is available here: https://stuartlab.org/signac/reference/callpeaks (or run ?CallPeaks in R)

[ajynair]

There is probably some version of MACS2 with a --tempdir (macs3-project/MACS#148) but looks like the one I have installed does not. Anyway, the problem I was facing was MACS2 was writing temporary files to root disk which had space limitations (Signac was writing the temporary files in the tempdir() folder in the user disk so there weren't any issues) and so the number of peaks detected were very low. This was probably due to truncated output from MACS2 due to space limitation. I re-partitioned my root disk to give it more space and the issue is solved. Thanks Tim!