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meme problem [solved] #2
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Hi KQ2012, |
YES, MEME is the problem. This was magically solved by removing the old MEME and using: Unfortunately, there is appeared to be some new issues with R, please see below [info] Doing fimo2.DREME-1.BTTATCW... [info] Doing fimo2.DREME-2.CCCGCCY... I installed the CENTIPEDE and a few more packages in R on my Mac, but it seems a different version is used in this conda env. Any idea? Another error might be related to this or the "make_cut_matrix" script that we discussed: Traceback (most recent call last): Thanks so much! |
Could you check if the path of R ( |
The one I specified was not installed with this package. Good Catch! I will update the config file and re-run it. Thanks! |
Hi, fl
I am creating a new issue here, I was able to bypass the bowtie2 index problem by changing the "hg" to "genome". Unfortunately, still having a little problem with the rest of the code. Please see below which I copied directly from my terminal, as there is no error message, however, I did reach the end telling me that the analysis was successful w/o any files in the fimo folder, my symster is MacOS Mojave version 10.14.6 not sure if this information is helpful. Thanks a lot!
[info] Generating the normalized signal file with BigWig format...
Sun Feb 7 21:47:45 EST 2021
[info] Your bigwig file won't be normalized with spike-in reads
[info] Input file is /Volumes/Backup/CUT-RUNTools-2.0-master/test/GATA1_D7_30min_chr11/peakcalling/macs2.narrow/GATA1_D7_30min_chr11_peaks.narrowPeak
[info] Get randomized [1000] peaks from the top [2000] peaks...
[info] Filtering the blacklist regions for the selected peak files
[info] Getting Fasta sequences
[info] Start MEME analysis for de novo motif finding ...
[info] Up to 10 will be output ...
Log::Log4perl configuration looks suspicious: No loggers defined at /Users/kunhuaqin/miniconda3/envs/meme/lib/site_perl/5.26.2/Log/Log4perl/Config.pm line 325.
Starting getsize: getsize random1000/MEME_GATA1_D7_30min_chr11_shuf/GATA1_D7_30min_chr11_summits_padded.fa 1> $metrics
dyld: Library not loaded: @rpath/libicui18n.58.dylib
Referenced from: /Users/kq2012/miniconda3/envs/meme/bin/getsize
Reason: image not found
getsize process died with signal 6, without coredump
getsize failed me... at /Users/kq2012/miniconda3/envs/meme/bin//meme-chip line 740.
[info] De Novo motifs can be found: random1000/MEME_GATA1_D7_30min_chr11_shuf ...
[info] Loading the De Novo motifs ...
Traceback (most recent call last):
File "/Volumes/Backup/CUT-RUNTools-2.0-master/install/read.meme.py", line 92, in
ss = read_summary(this_dir + "/summary.tsv")
File "/Volumes/Backup/CUT-RUNTools-2.0-master/install/read.meme.py", line 7, in read_summary
f = open(n)
FileNotFoundError: [Errno 2] No such file or directory: 'random1000/MEME_GATA1_D7_30min_chr11_shuf/summary.tsv'
[info] The signficance cutoff of Fimo scaning is 0.0005...
[info] Motif files can be found: random1000/MEME_GATA1_D7_30min_chr11_shuf/motifs
[info] Filtering the blacklist regions for the selected peak files
[info] Getting Fasta sequences
[info] Scaning the De Novo motifs for each peak
ls: random1000/MEME_GATA1_D7_30min_chr11_shuf/motifs: No such file or directory
[info] Output can be found: fimo.result/GATA1_D7_30min_chr11
Congrats! The bulk data analysis is complete!
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