Comments (9)
Sorry figured it out.
from macs.
@xiaomimeow Hey can you please tell me how this error got solved beacuse I am also getting same error.
Traceback (most recent call last):
File "./macs2", line 557, in
main()
File "./macs2", line 55, in main
from MACS2.callpeak import run
ImportError: No module named MACS2.callpeak
Thanks a lot
Ankit
from macs.
Can you check if macs2 is in your python path? If not please add the entire path to macs2 into your python path.
from macs.
Thanks a lot for replying! I have checked macs2 is already there in my python path! I have also mentioned the path through:
export PYTHONPATH
export PATH
Thanks
from macs.
Is there any possibility what went wrong in it?
from macs.
Could you share us how you installed MACS, in detail?
Tao
On Feb 17, 2014, at 8:32 AM, dfv [email protected] wrote:
Is there any possibility what went wrong in it?
—
Reply to this email directly or view it on GitHub.
from macs.
Hi Tao,
I have installed python 2.7.2 locally and numpy 1.8.0 in python directory. In accordance to it seperately i have installed macs2 as mentioned in instrutions with help of python setup.py install command. But when i try to run macs2 with the help of below command :
./macs2 callpeak -t abc.bam -c xyz.bam -f BAM -g ce --broad -n test
I get this error
Traceback (most recent call last):
File "./macs2", line 557, in
main()
File "./macs2", line 40, in main
argparser = prepare_argparser()
File "./macs2", line 109, in prepare_argparser
argparser.add_argument("--version", action="version", version="%(prog)s" +MACS_VERSION)
NameError: global name 'MACS_VERSION' is not defined
and after uncommenting MACS_VERSION in script then I get error mentioned below:
Traceback (most recent call last):
File "./macs2", line 557, in
main()
File "./macs2", line 55, in main
from MACS2.callpeak import run
ImportError: No module named MACS2.callpeak
Thanks a lot
from macs.
Hi dfv,
If you install MACS2 using setup script, then I don't understand why you still need to type './macs2' to run it. The executable 'macs2' script should be installed into /usr/local/bin in linux or Mac OSX by default, and the path (e.g. /usr/local/bin) should be in your environment variable 'PATH'. After installation, you should LEAVE the source code directory, and you shouldn't run './macs2' there.
Best,
Tao
On Feb 17, 2014, at 11:36 AM, dfv [email protected] wrote:
Hi Tao,
I have installed python 2.7.2 locally and numpy 1.8.0 in python directory. In accordance to it seperately i have installed macs2 as mentioned in instrutions with help of python setup.py install command. But when i try to run macs2 with the help of below command :./macs2 callpeak -t abc.bam -c xyz.bam -f BAM -g ce --broad -n test
I get this error
Traceback (most recent call last):
File "./macs2", line 557, in
main()
File "./macs2", line 40, in main
argparser = prepare_argparser()
File "./macs2", line 109, in prepare_argparser
argparser.add_argument("--version", action="version", version="%(prog)s" +MACS_VERSION)
NameError: global name 'MACS_VERSION' is not definedand after uncommenting MACS_VERSION in script then I get error mentioned below:
Traceback (most recent call last):
File "./macs2", line 557, in
main()
File "./macs2", line 55, in main
from MACS2.callpeak import run
ImportError: No module named MACS2.callpeakThanks a lot
from macs.
Hi Tao,
Thank you so much it solved!
from macs.
Related Issues (20)
- What is the difference between "absolute peak summit" and "summit position" in narrowPeak format? HOT 1
- Q: conversion of output files to UCSC track hub format? HOT 1
- Feat: Enhanced clarification of the specific definition of BEDPE as used by MACS HOT 1
- Feat: Reduction of memory consumption HOT 3
- Q: HMMRATAC output and options for _summit.bed HOT 1
- Feat: Built-in scoring for HMMRATAC HOT 1
- Q: HMMRATAC producing too many peaks HOT 10
- Bug: undefined symbol: __pow_finite HOT 3
- Q: HMMRATAC reproducibility HOT 2
- Q: how to use MACS3 for ATAC seq with "himmratac" option? HOT 2
- Bug: Callvar throws an error when run on broadPeak file HOT 15
- Q: impact of sequencing throughput on peak calling HOT 4
- Setting cut-off when using logFE bigWig files from bdgcmp
- Q: How to use HMMRATAC to give us a narrow peak file and have signalValue, p and q-value ? HOT 1
- Bug: OverflowError when running hmmratac
- Number of de-duplicated reads indicated by filterdup log does not match number of lines in output BED file.
- Feat: Add --call-summits option in MACS3 bdgpeakcall?
- Q: using macs3 to detect peaks on long-read readings
- MACS3 callpeak does not create UCSC Browser ready peak files HOT 1
- Better cutoff levels control for bdgcallpeak cutoff-analysis HOT 1
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from macs.