JUM_C.sh #56
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Hi, I have the same issue. I tried perl 5, version 32, subversion 1 and perl 5, version 24, subversion 0. Both gave the smartwatch errors. Did you find a solution? Thanks and good luck! |
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Hi, the smartmatch message is ok and not an error. It just reminds users
this is a new command in Perl. But it is working fine and no problem.
…On Tue, Nov 5, 2024 at 6:01 AM Sara ***@***.***> wrote:
Hi,
I was running JUM_C.sh as the following command:
cd FINAL_JUM_OUTPUT_pvalue_0.05/
bash /home/jum-splicing/JUM_3.0.0/JUM_C.sh --Folder /home/jum-splicing/JUM_3.0.0 --Test pvalue --Cutoff 0.05 --TotalCondition1FileNum 20 --TotalCondition2FileNum 21 --REF /home/salidadiani/jum-splicing/refFlat.txt
When it is running, I am getting this message "Smartmatch is experimental
at /home/jum-splicing/JUM_3.0.0/identify_gene_name_for_JUM_output_1.pl line
55." is it ok, or do I miss something and should I adjust something?
done pre-processing!
starting mapping AS events to genes
Smartmatch is experimental at /home/jum-splicing/JUM_3.0.0/identify_gene_name_for_JUM_output_1.pl line 55.
Smartmatch is experimental at /home/jum-splicing/JUM_3.0.0/identify_gene_name_for_JUM_output_1.pl line 55.
Smartmatch is experimental at /home/jum-splicing/JUM_3.0.0/identify_gene_name_for_JUM_output_1.pl line 55.
Smartmatch is experimental at /home/jum-splicing/JUM_3.0.0/identify_gene_name_for_JUM_output_1.pl line 55.
Smartmatch is experimental at /home/jum-splicing/JUM_3.0.0/identify_gene_name_for_JUM_output_1.pl line 55.
Smartmatch is experimental at /home/jum-splicing/JUM_3.0.0/identify_gene_name_for_JUM_output_1.pl line 55.
Smartmatch is experimental at /home/jum-splicing/JUM_3.0.0/identify_gene_name_for_JUM_output_1.pl line 55.
completed mapping
JUM_C.sh core execution finished in 20173 seconds.
Command is:
bash JUM_C.sh --Folder /home/jum-splicing/JUM_3.0.0 --Test pvalue --Cutoff 0.05 --TotalCondition1FileNum 20 --TotalCondition2FileNum 21 --REF /home/salidadiani/jum-splicing/refFlat.txt
I am also attaching some lines of the refFlat.txt file that I used.
Many thanks!
refFlat.txt
<https://github.com/user-attachments/files/17631265/refFlat.txt>
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This is not an error just a message to remind users about this command in
Perl may not be finalized. But it is working fine.
…On Tue, Nov 19, 2024 at 11:06 AM ikirdok ***@***.***> wrote:
Hi, I have the same issue. I tried perl 5, version 32, subversion 1 and
perl 5, version 24, subversion 0. Both gave the smartwatch errors. Did you
find a solution? Thanks and good luck!
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Hi,
Thank you for your reply! Do you know if this is an important issue? Thanks!
Smartmatch is experimental at /net/beegfs/scratch/ikirdok/programs/JUM_3.0.0/identify_gene_name_for_JUM_output_1.pl line 55.
Smartmatch is experimental at /net/beegfs/scratch/ikirdok/programs/JUM_3.0.0/identify_gene_name_for_JUM_output_1.pl line 55.
Smartmatch is experimental at /net/beegfs/scratch/ikirdok/programs/JUM_3.0.0/identify_gene_name_for_JUM_output_1.pl line 55.
Smartmatch is experimental at /net/beegfs/scratch/ikirdok/programs/JUM_3.0.0/identify_gene_name_for_JUM_output_1.pl line 55.
Smartmatch is experimental at /net/beegfs/scratch/ikirdok/programs/JUM_3.0.0/identify_gene_name_for_JUM_output_1.pl line 55.
Smartmatch is experimental at /net/beegfs/scratch/ikirdok/programs/JUM_3.0.0/identify_gene_name_for_JUM_output_1.pl line 55.
Smartmatch is experimental at /net/beegfs/scratch/ikirdok/programs/JUM_3.0.0/identify_gene_name_for_JUM_output_1.pl line 55.
Use of uninitialized value $i in numeric le (<=) at /net/beegfs/scratch/ikirdok/programs/JUM_3.0.0/final_process_MXE_output.pl line 191, <IN1> line 1.
Use of uninitialized value $i in numeric le (<=) at /net/beegfs/scratch/ikirdok/programs/JUM_3.0.0/final_process_MXE_output.pl line 199, <IN1> line 1.
Use of uninitialized value $i in numeric le (<=) at /net/beegfs/scratch/ikirdok/programs/JUM_3.0.0/final_process_MXE_output.pl line 202, <IN1> line 1.
Use of uninitialized value $i in numeric le (<=) at /net/beegfs/scratch/ikirdok/programs/JUM_3.0.0/final_process_MXE_output.pl line 199, <IN1> line 1.
Use of uninitialized value $i in numeric le (<=) at /net/beegfs/scratch/ikirdok/programs/JUM_3.0.0/final_process_MXE_output.pl line 202, <IN1> line 1.
Use of uninitialized value $i in numeric le (<=) at /net/beegfs/scratch/ikirdok/programs/JUM_3.0.0/final_process_MXE_output.pl line 199, <IN1> line 1.
Use of uninitialized value $i in numeric le (<=) at /net/beegfs/scratch/ikirdok/programs/JUM_3.0.0/final_process_MXE_output.pl line 202, <IN1> line 1.
Use of uninitialized value $i in numeric le (<=) at /net/beegfs/scratch/ikirdok/programs/JUM_3.0.0/final_process_MXE_output.pl line 199, <IN1> line 1.
Use of uninitialized value $i in numeric le (<=) at /net/beegfs/scratch/ikirdok/programs/JUM_3.0.0/final_process_MXE_output.pl line 202, <IN1> line 1.
Use of uninitialized value $as in print at /net/beegfs/scratch/ikirdok/programs/JUM_3.0.0/final_process_MXE_output.pl line 221, <IN1> line 1.
Use of uninitialized value $chr in print at /net/beegfs/scratch/ikirdok/programs/JUM_3.0.0/final_process_MXE_output.pl line 222, <IN1> line 1.
Use of uninitialized value $strand in print at /net/beegfs/scratch/ikirdok/programs/JUM_3.0.0/final_process_MXE_output.pl line 222, <IN1> line 1.
Use of uninitialized value in print at /net/beegfs/scratch/ikirdok/programs/JUM_3.0.0/final_process_MXE_output.pl line 222, <IN1> line 1.
Use of uninitialized value in print at /net/beegfs/scratch/ikirdok/programs/JUM_3.0.0/final_process_MXE_output.pl line 226, <IN1> line 1.
Use of uninitialized value $gene in print at /net/beegfs/scratch/ikirdok/programs/JUM_3.0.0/final_process_MXE_output.pl line 228, <IN1> line 1.
Use of uninitialized value $chr in print at /net/beegfs/scratch/ikirdok/programs/JUM_3.0.0/final_process_MXE_output.pl line 228, <IN1> line 1.
Use of uninitialized value $strand in print at /net/beegfs/scratch/ikirdok/programs/JUM_3.0.0/final_process_MXE_output.pl line 228, <IN1> line 1.
Use of uninitialized value in print at /net/beegfs/scratch/ikirdok/programs/JUM_3.0.0/final_process_MXE_output.pl line 228, <IN1> line 1.
Use of uninitialized value in print at /net/beegfs/scratch/ikirdok/programs/JUM_3.0.0/final_process_MXE_output.pl line 232, <IN1> line 1.
Use of uninitialized value $chr in print at /net/beegfs/scratch/ikirdok/programs/JUM_3.0.0/final_process_MXE_output.pl line 233, <IN1> line 1.
Use of uninitialized value $strand in print at /net/beegfs/scratch/ikirdok/programs/JUM_3.0.0/final_process_MXE_output.pl line 233, <IN1> line 1.
Use of uninitialized value in print at /net/beegfs/scratch/ikirdok/programs/JUM_3.0.0/final_process_MXE_output.pl line 233, <IN1> line 1.
Use of uninitialized value within @sorted_id in addition (+) at /net/beegfs/scratch/ikirdok/programs/JUM_3.0.0/final_process_MXE_output.pl line 237, <IN1> line 1.
Use of uninitialized value in print at /net/beegfs/scratch/ikirdok/programs/JUM_3.0.0/final_process_MXE_output.pl line 237, <IN1> line 1.
Use of uninitialized value in print at /net/beegfs/scratch/ikirdok/programs/JUM_3.0.0/final_process_MXE_output.pl line 238, <IN1> line 1.
Use of uninitialized value $pmin in print at /net/beegfs/scratch/ikirdok/programs/JUM_3.0.0/final_process_MXE_output.pl line 239, <IN1> line 1.
Use of uninitialized value $qmin in print at /net/beegfs/scratch/ikirdok/programs/JUM_3.0.0/final_process_MXE_output.pl line 239, <IN1> line 1.
Use of uninitialized value $i in subtraction (-) at /net/beegfs/scratch/ikirdok/programs/JUM_3.0.0/final_process_MXE_output.pl line 241, <IN1> line 1.
Use of uninitialized value in addition (+) at /net/beegfs/scratch/ikirdok/programs/JUM_3.0.0/final_process_MXE_output.pl line 259, <IN1> line 1.
Use of uninitialized value in addition (+) at /net/beegfs/scratch/ikirdok/programs/JUM_3.0.0/final_process_MXE_output.pl line 259, <IN1> line 1.
Use of uninitialized value in addition (+) at /net/beegfs/scratch/ikirdok/programs/JUM_3.0.0/final_process_MXE_output.pl line 262, <IN1> line 1.
Use of uninitialized value in addition (+) at /net/beegfs/scratch/ikirdok/programs/JUM_3.0.0/final_process_MXE_output.pl line 262, <IN1> line 1.
Use of uninitialized value $as in print at /net/beegfs/scratch/ikirdok/programs/JUM_3.0.0/final_process_composite_output.pl line 103, <IN1> line 1.
Use of uninitialized value $chr in print at /net/beegfs/scratch/ikirdok/programs/JUM_3.0.0/final_process_composite_output.pl line 104, <IN1> line 1.
Use of uninitialized value $strand in print at /net/beegfs/scratch/ikirdok/programs/JUM_3.0.0/final_process_composite_output.pl line 104, <IN1> line 1.
Use of uninitialized value $gene in print at /net/beegfs/scratch/ikirdok/programs/JUM_3.0.0/final_process_composite_output.pl line 105, <IN1> line 1.
Use of uninitialized value $chr in print at /net/beegfs/scratch/ikirdok/programs/JUM_3.0.0/final_process_composite_output.pl line 105, <IN1> line 1.
Use of uninitialized value $strand in print at /net/beegfs/scratch/ikirdok/programs/JUM_3.0.0/final_process_composite_output.pl line 105, <IN1> line 1.
Use of uninitialized value $chr in print at /net/beegfs/scratch/ikirdok/programs/JUM_3.0.0/final_process_composite_output.pl line 105, <IN1> line 1.
Use of uninitialized value $strand in print at /net/beegfs/scratch/ikirdok/programs/JUM_3.0.0/final_process_composite_output.pl line 105, <IN1> line 1.
Use of uninitialized value $pmin in print at /net/beegfs/scratch/ikirdok/programs/JUM_3.0.0/final_process_composite_output.pl line 106, <IN1> line 1.
Use of uninitialized value $qmin in print at /net/beegfs/scratch/ikirdok/programs/JUM_3.0.0/final_process_composite_output.pl line 106, <IN1> line 1.
From: Qingqing Wang ***@***.***>
Sent: Tuesday, November 19, 2024 5:40 PM
To: qqwang-berkeley/JUM ***@***.***>
Cc: Kirdök, I. (Idil) ***@***.***>; Comment ***@***.***>
Subject: Re: [qqwang-berkeley/JUM] JUM_C.sh (Issue #56)
This is not an error just a message to remind users about this command in
Perl may not be finalized. But it is working fine.
On Tue, Nov 19, 2024 at 11:06 AM ikirdok ***@***.***> wrote:
Hi, I have the same issue. I tried perl 5, version 32, subversion 1 and
perl 5, version 24, subversion 0. Both gave the smartwatch errors. Did you
find a solution? Thanks and good luck!
—
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Hi,
I was running JUM_C.sh as the following command:
When it is running, I am getting this message "Smartmatch is experimental at /home/jum-splicing/JUM_3.0.0/identify_gene_name_for_JUM_output_1.pl line 55." is it ok, or do I miss something and should I adjust something?
I am also attaching some lines of the refFlat.txt file that I used.
Many thanks!
refFlat.txt
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