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chaolinzhanglab / mCross

A computational tool for de novo RBP motif discovery
https://zhanglab.c2b2.columbia.edu/index.php/MCross
MIT License
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Error: PatternMatch: not found when running mCross.pl #1

Open Srimeenakshis opened 1 month ago

Srimeenakshis commented 1 month ago

I am trying to use mCross to detect RNA motifs for an RBP using the alternative approach that skips the top n-mer detection step. I provide FASTA sequences for background and peak signals directly. However, I receive the following error when running the mCross.pl script:

h: 1: PatternMatch: not found CMD=PatternMatch -l ./mCross.pl_1722868127_0.260478057972254/consensus.txt /home/user/peak_sites_all_101nt_mCross.fa > ./mCross.pl_1722868127_0.260478057972254/site.bed failed:32512 at /home/user/miniconda3/envs/mCross_env/lib/mcross/mCross.pl line 322. main::refineMotif(ARRAY(0xecd240), 1, 1, "/home/user/bg_sites_all"..., 10, 100, "./mCross.pl_1722868127_0.260478057972254") called at /home/user/miniconda3/envs/mCross_env/lib/mcross/mCross.pl line 258.

Run mCross using the alternative method with the following command

mCross.pl -l 10 -p 2 -N 10 -m 1 --bg /path/to/background.fasta --prefix mR1--score-method sqrt /path/to/peak_signal.fasta /path/to/output

Could you kindly provide guidance on how to resolve this issue? If there are additional steps or configurations needed, please let me know.

zhangchaolin commented 1 month ago

Could you clarify if you installed mCross as follows?

conda install chaolinzhanglab::mcross

Thanks, Chaolin

On Aug 5, 2024, at 10:45 AM, Srimeenakshi.S @.***> wrote:

I am trying to use mCross to detect RNA motifs for an RBP using the alternative approach that skips the top n-mer detection step. I provide FASTA sequences for background and peak signals directly. However, I receive the following error when running the mCross.pl script:

h: 1: PatternMatch: not found CMD=PatternMatch -l ./mCross.pl_1722868127_0.260478057972254/consensus.txt /home/user/peak_sites_all_101nt_mCross.fa > ./mCross.pl_1722868127_0.260478057972254/site.bed failed:32512 at /home/user/miniconda3/envs/mCross_env/lib/mcross/mCross.pl line 322. main::refineMotif(ARRAY(0xecd240), 1, 1, "/home/user/bg_sites_all"..., 10, 100, "./mCross.pl_1722868127_0.260478057972254") called at /home/user/miniconda3/envs/mCross_env/lib/mcross/mCross.pl line 258.

Run mCross using the alternative method with the following command

mCross.pl -l 10 -p 2 -N 10 -m 1 --bg /path/to/background.fasta --prefix mR1--score-method sqrt /path/to/peak_signal.fasta /path/to/output

Could you kindly provide guidance on how to resolve this issue? If there are additional steps or configurations needed, please let me know.

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Srimeenakshis commented 1 month ago

Hi, thanks for the reply. I installed as mentioned in the MCross documentation, as follows conda install -y -c chaolinzhanglab/noarch mcross

wydai07 commented 1 month ago

maybe check if you can call the command directly? $PatternMatch Usage: PatternMatch [-biv?] [-c|--motif-consensus=STRING] [-m|--number-of-mismatches=INT]
[-l|--motif-list-file=STRING] [-b|--both-strands] [-i|--ignore-repeat] [-v|--verbose]
[-o|--output-file=STRING] [-?|--help] [--usage] fasta-file(.gz)

Srimeenakshis commented 1 month ago

Thank you for the suggestion. I attempted to run the PatternMatch command directly, but it resulted in a "command not found" error. It appears that PatternMatch is either not installed or not available in my system's PATH.. Could you please guide where to find and install PatternMatch, or if it's part of another tool or package? Any additional instructions or alternative solutions would be greatly appreciated!! :)

zhangchaolin commented 1 month ago

That’s because PatternMatch was not compiled or not the path was not set properly.

Chaolin

On Aug 5, 2024, at 3:30 PM, Srimeenakshi.S @.***> wrote:

Thank you for the suggestion. I attempted to run the PatternMatch command directly, but it resulted in a "command not found" error. It appears that PatternMatch is either not installed or not available in my system's PATH.. Could you please guide where to find and install PatternMatch, or if it's part of another tool or package? Any additional instructions or alternative solutions would be greatly appreciated!! :)

— Reply to this email directly, view it on GitHub https://github.com/chaolinzhanglab/mCross/issues/1#issuecomment-2269765412, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEJPO7JIN2QK6CCLYQASZ23ZP7HFZAVCNFSM6AAAAABMAOUKZSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDENRZG43DKNBRGI. You are receiving this because you commented.

Srimeenakshis commented 1 month ago

Hi @zhangchaolin and @wydai07,

Thank you so much for your responses and help.

I reinstalled mCross using conda install chaolinzhanglab::mcross and again attempted the motif search analysis. I successfully ran the step to find the list of top-nmers before executing the mCross.pl script. However, I encountered the same PatternMatch error when running the mCross.pl script. Despite reinstalling mCross, I am still unable to locate the PatternMatch command.

Could you provide further guidance on how to resolve this issue? Is PatternMatch a separate tool that needs to be installed independently, or should it be included with mCross? Thanks so much in advance :)