qqwang-berkeley / jum

A tool for annotation-free differential analysis of tissue-specific pre-mRNA alternative splicing patterns

The Junction Usage Model (JUM)

• JUM is a tool that offers a completely annotation-free approach to analyze alternative pre-mRNA splicing patterns that are specific to a tissue or sample of interest from RNA-seq datasets.

  • Stable performance package for V3.0.0: https://github.com/qqwang-berkeley/JUM/releases/tag/v3.0.0
  • Complete manual for V3.0.0 and V2.0.2: https://github.com/qqwang-berkeley/JUM/wiki/A-Hitchhiker's-guide-to-JUM-(version-2.0.2--and-3.0.0)
  • Legacy release for V2.0.2: https://github.com/qqwang-berkeley/JUM/releases/tag/JUM_v2.0.2
  • For differential AS analysis among multiple experimental conditions see: https://github.com/qqwang-berkeley/JUM/wiki/6.-Running-JUM-for-differential-AS-analysis-among-multiple-experimental-conditions-(multiple-tissues,-patients,-time-series-experiments-etc.)

• JUM reports alternative splicing events in six categories: cassette exon, mutually exclusive exons, alternative 5' splice site, alternative 3' splice site, intron retention, Composite patterns

• JUM does not depend on any prior knowledge of a transcriptome annotation nor known libraries of AS events.

• The JUM method is published: https://www.ncbi.nlm.nih.gov/pubmed/30104386 The simulated RNA-seq datasets and ground truth (true AS genes and non-AS genes) described in the paper are deposited in GEO with accession number GSE118193.

• Feel free to post any questions or comments on the Google group for JUM users: https://groups.google.com/forum/#!forum/jum-users

• Legacy manual for V2.0 and V2.0.1: https://github.com/qqwang-berkeley/JUM/wiki/A-Hitchhiker's-guide-to-JUM-(version-2.0-and-version-2.0.1)
• Legacy manual for V1.3.12: https://github.com/qqwang-berkeley/JUM/wiki/A-Hitchhiker's-guide-to-JUM-(version-1.3.12)

jum's Issues

JUM_2-3.sh missing in JUM_3.0.0

Can't open perl script "/prepare_count_file_after_STAR_2_pass_mapping.pl": No such file or directory

Hi, I got this issue, could you know how to figure out this? thank you.
I use the new version of JUM-JUM_v2.0.2.
working fold is under fastq, JUM is also under fastq.

root@debian:/mnt/hgfs/rawdata/fastq/N2F# bash ../JUM/JUM_2-2.sh ../JUM 6 3 N2F
Can't open perl script "/prepare_count_file_after_STAR_2_pass_mapping.pl": No such file or directory

Why the input needs different format of sam and bam?

According to the manual of JUM 2.0.2:
Under your working folder (/user/home/AS_analysis), you should have the following input files ready for JUM analysis ("*" indicates ctrl1, ctrl2, ctrl3, treat1, treat2 and treat3):
*Aligned.out.sam files
*SJ.out.tab files
*Aligned.out_sorted.bam files

Why does it require different format: sam for *Aligned.out.sam and bam for Aligned.out_sorted.bam? All of my STAR output were in bam format and the program turned out unable to find the *.Aligned.out.sam. I am wondering whether I should convert them to sam format.

Perl Error due to a sample not having AS on one contig

Hi!

I encounter the following Error Running JUM_A:
ERROR: Database file output_long_intron_sorted.gff contains chromosome X_3, but the query file does not.
Please rerun with the -g option for a genome file.
See documentation for details.

the following command shows results for all except one sample.
grep X_3 control_vs_Treat/*Aligned.out.sorted.bed

I believe the error come from the process_sortedbam() function
During the intersection steps!

May be a way to resolve this issue is to extract from all sample the @sq tag and merge them to build a bed genome.txt file.
and then give this genome to the bedtools intersect inside process_sortedbam.

Could you help me? my perl is very bad....

Error of Rscript at write.table step

Hi,
I tried several ways to get the result of Rscript step but it doesn't write the table for me.
This is the error I get:

Error in write.table(dxr1, "AS_differential.txt", sep = "\t", quote = F) : 
  unimplemented type 'list' in 'EncodeElement'
Execution halted

I think it might be due to having a list but my tries for flattening the list (which I don't know which column might be) didn't work. I tried this flattening code: df <- apply(df,2,as.character) and then tried to write.csv but no luck, either.

Before that error there is a warning as well:

converting counts to integer mode
Warning message:
In DESeqDataSet(rse, design, ignoreRank = TRUE) :
  some variables in design formula are characters, converting to factors

I should also mention that I get one text file (AS_differential.txt) but it just has one row!

Can someone help to solve this issue please? Thanks a lot. :)

JUM (v2.0.2 and up) stops and get killed at a certain step

Hi,
The JUM_A.bash stops and get killed at this step:

    process_sortedbam () {
    sortfile=$1;
    bamfiletobed=${sortfile%_sorted.bam}.bed;
    bamsortedbed=${sortfile%_sorted.bam}.sorted.bed;
    intersect_bam_long_intron=${sortfile%_sorted.bam}"_"intersect_long_intron.txt;
    intersect_bam_short_intron1=${sortfile%_sorted.bam}"_"intersect_short_intron1.txt;
    intersect_bam_short_intron2=${sortfile%_sorted.bam}"_"intersect_short_intron2.txt;
    bedtools bamtobed -i $sortfile > $bamfiletobed;
    sort -k1,1 -k2,2n $bamfiletobed > $bamsortedbed;
    intersectBed -a $bamsortedbed -b output_long_intron_sorted.gff -sorted -wa -u -f 1 > $intersect_bam_long_intron 
    intersectBed -a $bamsortedbed -b output_short_intron1_sorted.gff -sorted -wa -u -f 1 > $intersect_bam_short_intron1 
    intersectBed -a $bamsortedbed -b output_short_intron2_sorted.gff -sorted -wa -u -F 1 > $intersect_bam_short_intron2 
}

Exact error:
Killed sort -k1,1 -k2,2n $bamfiletobed > $bamsortedbed

I'm guessing it might be a CPU error as it gets killed but more than that, not sure. I'm working with a 16 threads system and once used all and other times just 14 of them, but it gets killed anyway.
Code I'm using:
bash /path/JUM_2.0.2_multi/JUM_A.sh --Folder /path/JUM_2.0.2_multi --JuncThreshold 5 --Condition1_fileNum_threshold 2 --Condition2_fileNum_threshold 2 --IRthreshold 5 --Readlength 101 --Thread 16 --Condition1SampleName cntrl1,cntrl2,cntrl3 --Condition2SampleName treat1,treat2,treat3

Does anyone know what might be wrong and how can I fix it please?
Thanks.

Huge amount of space required!!!

Hi!
I would like to ask about the temporal intermediate files generated during JUM_B.sh step. Among the generated files are those named
*temp_long_intron_retention_junction_coordinate_with_read_num_pvalue_1.txt.
Is it normal that these text files reach the astronomic sizes of 27-30 GB for bam files with average size of 5 GB?
I'm trying to analyze a 3 vs 3 experiment and so far the folder with all the required data for this script is about 366 GB in size, so I suppose analyzing an experiment of 10 vs 10 is simply unfeasible, no to say large experiments.
Please comment on this.
Thanks in advance.
Ivó

PSI values per condition

How would I go about calculating the PSI values per condition (i.e. PSI for control and PSI for treatment) for each event type? Currently, I only see the delta PSI values reported from both the simplified and detailed output files. Any help would be greatly appreciated! Thanks!

second pass STAR

Issue with JUM_3.sh script

I’ve encountered an issue with the JUM_3.sh script.

Runs OK until reaching the “long_intron_retention” processing steps. At this point it generates enormous temp files (e.g. IndexA_temp_long_intron_retention_junction_coordinate_with_read_num_pvalue_0.05) that are 20-200 GB.

At this point it also reports millions of identical errors:
Use of uninitialized value in print at count_intron_read_long_intron_retention_step2.pl line 44, <IN2> line 1

These millions of errors are preceded by this single error:
ERROR: illegal character ‘+’ found in integer conversion of string “+”. Exiting…
Argument “+” isn’t numeric in subtraction (-) at count_intron_read_long_intron_retention_step2.pl line 40, <IN2> line 1.

Any ideas? All the other classes of Alternative splicing (e.g. 5’SS, etc.) seem to have been computed just fine. Thanks!

JUM a lot of error... but finish runnnig an output empty file.

I am trying to run JUM on a custom genome.
I don't really understand what I did wrong, any help appreciated.
Because the genome is really fragmented, I only kept the read that align over contig >100kb

JUM_log.txt

The log is quite long.
I attached it

after double checking I believe my refFlat format is incorrect. Does that would explain the absence of results from JUM_C?
But I don't understand why I got so much error message before this step....

Regarding Error "NONE" after running JUM_C.sh

Hello everyone,

After running JUM_C.sh, the output files from FINAL_JUM_OUTPUT_pvalue_0.05, have all the identified events as "NONE". Not even single event is annotated to transcript_id. Please help me to figure out what exactly is the error, because atleast some of the events should be annotated to a gene or transcript id.

I have attached below first 10 lines of genePred file used for --REF argument.
MSU_v7_genepred_first_10_lines.txt

Could you please help me to troubleshoot this?
Thank you so much

JUM_A: ERROR: ... not sorted lexicographically

Hello,
Thank you so much for developing this tool.
I'm running JUM_A and finding the error bellow.
Could you please help me troubleshoot?
Please let me know if you need any more information from me.

Best wishes
Neuza

Sample names are:
ctrl_1_R01_
ctrl_2_R01_
treat_1_R01_
treat_2_R01_
2 input samples to consider under the current condition
2 input samples to consider under the current condition
Preparing for intron retention AS events analyses...
Processing junction overhangs for Sample treat_1_R01_... Success.
Processing junction overhangs for Sample ctrl_2_R01_... Success.
Processing junction overhangs for Sample ctrl_1_R01_... Success.
Processing junction overhangs for Sample treat_2_R01_... Success.
ERROR: Sort order was unspecified, and file output_long_intron_sorted.gff is not sorted lexicographically.
Please rerun with the -g option for a genome file.
See documentation for details.
ERROR: Sort order was unspecified, and file output_long_intron_sorted.gff is not sorted lexicographically.
Please rerun with the -g option for a genome file.
See documentation for details.
ERROR: Sort order was unspecified, and file output_long_intron_sorted.gff is not sorted lexicographically.
Please rerun with the -g option for a genome file.
See documentation for details.
ERROR: Sort order was unspecified, and file output_long_intron_sorted.gff is not sorted lexicographically.
Please rerun with the -g option for a genome file.
See documentation for details.
awk: fatal: cannot open file *intersect_short_intron1.txt' for reading (No such file or directory) awk: fatal: cannot open file *intersect_short_intron2.txt' for reading (No such file or directory)
can't open input1 file: No such file or directory at /labs/mtfuller/Eric/JUM_2.0.2/preparing_intron_retention_count_table_short_intron.pl line 18.

How to match sub-junctions to PSI value in composite events?

Hi,

For composite events which contain a very high number of sub-junctions, we often get multiple PSI values. How do we know which sub-junctions each of the PSI values refer to?

In other words, how do we determine the local exon connectivity associated with each PSI value? There is no explicit information in the output tables about this.

I've looked at the AS_structure_ID in the detailed tables, but they all seem to describe junctions contributing to A3SS or A5SS. But there doesn't ever seem to be splice junctions that are characteristic of cassette exon or MXE, even though there clearly is a cassette event (as determined from IGV and other AS detection programs). Not sure if this is a bug? Could you please advise whether JUM is able to consider all of A3SS, A5SS, cassette exon, MXE and IR (where observed) in the composite events category?

Thanks

AS junction co-ordinates are sometimes wrong.

Hi,

I've been using the time-series pipeline of JUM and noticed that the junction co-ordinates are consistently lower compared to when viewed in IGV as well as the reference annotation. This problem seems to begin all the way from the JUM_temp_A step, with the UNION_junc_coor co-ordinates already different to those in the SJ.out.tab file from STAR.

Upon further exploration, I noticed that the co-ordinates are usually 1 less than expected. Under certain circumstances (mostly in cassette exon calls), some co-ordinates may be correct and some may be short between sub-junctions with in the same AS junction.

I hope that this issue can be looked into.
Best wishes

Empty results of JUM_C.sh; lots of perl errors again

Hi again,

I ran into another road block. I'm getting the scripts to run, but there are perl errors in both the outputs from JUM_B and JUM_C. I'll attach the logs here.

jum_b.log

The jum_c.log was too big to attach. This is the gist of it:

Smartmatch is experimental at /home/tools/JUM_2.0.2/identify_gene_name_for_JUM_output_1.pl line 55.
Smartmatch is experimental at /home/tools/JUM_2.0.2/identify_gene_name_for_JUM_output_1.pl line 55.
Smartmatch is experimental at /home/tools/JUM_2.0.2/identify_gene_name_for_JUM_output_1.pl line 55.
Smartmatch is experimental at /home/tools/JUM_2.0.2/identify_gene_name_for_JUM_output_1.pl line 55.
Smartmatch is experimental at /home/tools/JUM_2.0.2/identify_gene_name_for_JUM_output_1.pl line 55.
Smartmatch is experimental at /home/tools/JUM_2.0.2/identify_gene_name_for_JUM_output_1.pl line 55.
Smartmatch is experimental at /home/tools/JUM_2.0.2/identify_gene_name_for_JUM_output_1.pl line 55.
Use of uninitialized value $junctionID[10] in pattern match (m//) at /home/tools/JUM_2.0.2/identify_gene_name_for_JUM_output_1.pl line 50, <IN2> line 1.
Use of uninitialized value $junctionID[10] in pattern match (m//) at /home/tools/JUM_2.0.2/identify_gene_name_for_JUM_output_1.pl line 50, <IN2> line 1.
Use of uninitialized value in string eq at /home/tools/JUM_2.0.2/identify_gene_name_for_JUM_output_1.pl line 53, <IN2> line 1.
Use of uninitialized value $junctionID[10] in pattern match (m//) at /home/tools/JUM_2.0.2/identify_gene_name_for_JUM_output_1.pl line 50, <IN2> line 1.
Use of uninitialized value in string eq at /home/tools/JUM_2.0.2/identify_gene_name_for_JUM_output_1.pl line 53, <IN2> line 1.
Use of uninitialized value in string eq at /home/tools/JUM_2.0.2/identify_gene_name_for_JUM_output_1.pl line 53, <IN2> line 1.
Use of uninitialized value $junctionID[10] in pattern match (m//) at /home/tools/JUM_2.0.2/identify_gene_name_for_JUM_output_1.pl line 50, <IN2> line 1.
Use of uninitialized value $junctionID[10] in pattern match (m//) at /home/tools/JUM_2.0.2/identify_gene_name_for_JUM_output_1.pl line 50, <IN2> line 1.
Use of uninitialized value in string eq at /home/tools/JUM_2.0.2/identify_gene_name_for_JUM_output_1.pl line 53, <IN2> line 1.
Use of uninitialized value in string eq at /home/tools/JUM_2.0.2/identify_gene_name_for_JUM_output_1.pl line 53, <IN2> line 1.

^ that times 200M lines

Use of uninitialized value in print at /home/tools/JUM_2.0.2/identify_gene_name_for_JUM_output_1.pl line 66, <IN2> line 1.
Use of uninitialized value in print at /home/tools/JUM_2.0.2/identify_gene_name_for_JUM_output_1.pl line 66, <IN2> line 1.
Use of uninitialized value in print at /home/tools/JUM_2.0.2/identify_gene_name_for_JUM_output_1.pl line 66, <IN2> line 1.
Use of uninitialized value in print at /home/tools/JUM_2.0.2/identify_gene_name_for_JUM_output_2.pl line 60.
Use of uninitialized value $array[0] in hash element at /home/tools/JUM_2.0.2/identify_gene_name_for_JUM_output_3.pl line 27, <IN1> line 1.
Use of uninitialized value $temp[0] in hash element at /home/tools/JUM_2.0.2/identify_gene_name_for_JUM_output_3.pl line 45, <IN2> line 1.
Use of uninitialized value in print at /home/tools/JUM_2.0.2/identify_gene_name_for_JUM_output_3.pl line 45, <IN2> line 1.
Use of uninitialized value in print at /home/tools/JUM_2.0.2/identify_gene_name_for_JUM_output_2.pl line 60.
Use of uninitialized value $array[0] in hash element at /home/tools/JUM_2.0.2/identify_gene_name_for_JUM_output_3.pl line 27, <IN1> line 1.
Use of uninitialized value $temp[0] in hash element at /home/tools/JUM_2.0.2/identify_gene_name_for_JUM_output_3.pl line 45, <IN2> line 1.
Use of uninitialized value in print at /home/tools/JUM_2.0.2/identify_gene_name_for_JUM_output_3.pl line 45, <IN2> line 1.
Use of uninitialized value in print at /home/tools/JUM_2.0.2/identify_gene_name_for_JUM_output_2.pl line 60.
Use of uninitialized value in print at /home/tools/JUM_2.0.2/identify_gene_name_for_JUM_output_2.pl line 60.
Use of uninitialized value in print at /home/tools/JUM_2.0.2/identify_gene_name_for_JUM_output_2.pl line 60.
Use of uninitialized value $array[0] in hash element at /home/tools/JUM_2.0.2/identify_gene_name_for_JUM_output_3.pl line 27, <IN1> line 1.
Use of uninitialized value $temp[0] in hash element at /home/tools/JUM_2.0.2/identify_gene_name_for_JUM_output_3.pl line 45, <IN2> line 1.
Use of uninitialized value in print at /home/tools/JUM_2.0.2/identify_gene_name_for_JUM_output_3.pl line 45, <IN2> line 1.
Use of uninitialized value $array[0] in hash element at /home/tools/JUM_2.0.2/identify_gene_name_for_JUM_output_3.pl line 27, <IN1> line 1.
Use of uninitialized value $temp[0] in hash element at /home/tools/JUM_2.0.2/identify_gene_name_for_JUM_output_3.pl line 45, <IN2> line 1.
Use of uninitialized value in print at /home/tools/JUM_2.0.2/identify_gene_name_for_JUM_output_3.pl line 45, <IN2> line 1.
Use of uninitialized value $array[0] in hash element at /home/tools/JUM_2.0.2/identify_gene_name_for_JUM_output_3.pl line 27, <IN1> line 1.
Use of uninitialized value $temp[0] in hash element at /home/tools/JUM_2.0.2/identify_gene_name_for_JUM_output_3.pl line 45, <IN2> line 1.
Use of uninitialized value in print at /home/tools/JUM_2.0.2/identify_gene_name_for_JUM_output_3.pl line 45, <IN2> line 1.
Use of uninitialized value $array[11] in concatenation (.) or string at /home/tools/JUM_2.0.2/final_process_cassette_exon_output1.pl line 58, <IN1> line 1.
Use of uninitialized value in concatenation (.) or string at /home/tools/JUM_2.0.2/final_process_cassette_exon_output1.pl line 58, <IN1> line 1.
Use of uninitialized value in concatenation (.) or string at /home/tools/JUM_2.0.2/final_process_cassette_exon_output1.pl line 58, <IN1> line 1.
Use of uninitialized value in concatenation (.) or string at /home/tools/JUM_2.0.2/final_process_cassette_exon_output1.pl line 58, <IN1> line 1.
Use of uninitialized value in concatenation (.) or string at /home/tools/JUM_2.0.2/final_process_cassette_exon_output1.pl line 58, <IN1> line 1.
Use of uninitialized value in subroutine entry at /home/tools/JUM_2.0.2/final_process_cassette_exon_output1.pl line 59, <IN1> line 1.
Use of uninitialized value in subroutine entry at /home/tools/JUM_2.0.2/final_process_cassette_exon_output1.pl line 59, <IN1> line 1.
Use of uninitialized value in subroutine entry at /home/tools/JUM_2.0.2/final_process_cassette_exon_output1.pl line 59, <IN1> line 1.
Use of uninitialized value $_ in substitution (s///) at /home/tools/JUM_2.0.2/final_process_cassette_exon_output1.pl line 60, <IN1> line 1.
Use of uninitialized value $_ in substitution (s///) at /home/tools/JUM_2.0.2/final_process_cassette_exon_output1.pl line 60, <IN1> line 1.
Use of uninitialized value $_ in substitution (s///) at /home/tools/JUM_2.0.2/final_process_cassette_exon_output1.pl line 60, <IN1> line 1.
Use of uninitialized value in subroutine entry at /home/tools/JUM_2.0.2/final_process_cassette_exon_output1.pl line 61, <IN1> line 1.
Use of uninitialized value in subroutine entry at /home/tools/JUM_2.0.2/final_process_cassette_exon_output1.pl line 61, <IN1> line 1.
Use of uninitialized value in subroutine entry at /home/tools/JUM_2.0.2/final_process_cassette_exon_output1.pl line 61, <IN1> line 1.
Use of uninitialized value in print at /home/tools/JUM_2.0.2/final_process_cassette_exon_output1.pl line 62, <IN1> line 1.
Use of uninitialized value in print at /home/tools/JUM_2.0.2/final_process_cassette_exon_output1.pl line 62, <IN1> line 1.
Use of uninitialized value in print at /home/tools/JUM_2.0.2/final_process_cassette_exon_output1.pl line 62, <IN1> line 1.
Use of uninitialized value in print at /home/tools/JUM_2.0.2/final_process_cassette_exon_output1.pl line 62, <IN1> line 1.
Use of uninitialized value in print at /home/tools/JUM_2.0.2/final_process_cassette_exon_output1.pl line 62, <IN1> line 1.
Use of uninitialized value in print at /home/tools/JUM_2.0.2/final_process_cassette_exon_output1.pl line 62, <IN1> line 1.
Use of uninitialized value $pmin in print at /home/tools/JUM_2.0.2/final_process_cassette_exon_output1.pl line 62, <IN1> line 1.
Use of uninitialized value $qmin in print at /home/tools/JUM_2.0.2/final_process_cassette_exon_output1.pl line 62, <IN1> line 1.
Use of uninitialized value in print at /home/tools/JUM_2.0.2/final_process_cassette_exon_output1.pl line 62, <IN1> line 1.
Use of uninitialized value in print at /home/tools/JUM_2.0.2/final_process_cassette_exon_output1.pl line 63, <IN1> line 1.
Use of uninitialized value $temp[1] in hash element at /home/tools/JUM_2.0.2/final_process_cassette_exon_output2.pl line 30, <IN2> line 1.
Use of uninitialized value within @temp in join or string at /home/tools/JUM_2.0.2/final_process_cassette_exon_output2.pl line 32, <IN2> line 1.
Use of uninitialized value in subroutine entry at /home/tools/JUM_2.0.2/final_process_IR_output_long.pl line 58, <IN1> line 1.
Use of uninitialized value in subroutine entry at /home/tools/JUM_2.0.2/final_process_IR_output_long.pl line 58, <IN1> line 1.
Use of uninitialized value in subroutine entry at /home/tools/JUM_2.0.2/final_process_IR_output_long.pl line 58, <IN1> line 1.
Use of uninitialized value $_ in substitution (s///) at /home/tools/JUM_2.0.2/final_process_IR_output_long.pl line 59, <IN1> line 1.
Use of uninitialized value $_ in substitution (s///) at /home/tools/JUM_2.0.2/final_process_IR_output_long.pl line 59, <IN1> line 1.
Use of uninitialized value $_ in substitution (s///) at /home/tools/JUM_2.0.2/final_process_IR_output_long.pl line 59, <IN1> line 1.
Use of uninitialized value in subroutine entry at /home/tools/JUM_2.0.2/final_process_IR_output_long.pl line 60, <IN1> line 1.
Use of uninitialized value in subroutine entry at /home/tools/JUM_2.0.2/final_process_IR_output_long.pl line 60, <IN1> line 1.
Use of uninitialized value in subroutine entry at /home/tools/JUM_2.0.2/final_process_IR_output_long.pl line 60, <IN1> line 1.
Use of uninitialized value in print at /home/tools/JUM_2.0.2/final_process_IR_output_long.pl line 61, <IN1> line 1.
Use of uninitialized value $coor in print at /home/tools/JUM_2.0.2/final_process_IR_output_long.pl line 61, <IN1> line 1.
Use of uninitialized value in print at /home/tools/JUM_2.0.2/final_process_IR_output_long.pl line 61, <IN1> line 1.
Use of uninitialized value in print at /home/tools/JUM_2.0.2/final_process_IR_output_long.pl line 61, <IN1> line 1.
Use of uninitialized value $start in print at /home/tools/JUM_2.0.2/final_process_IR_output_long.pl line 61, <IN1> line 1.
Use of uninitialized value $end in print at /home/tools/JUM_2.0.2/final_process_IR_output_long.pl line 61, <IN1> line 1.
Use of uninitialized value $pmin in print at /home/tools/JUM_2.0.2/final_process_IR_output_long.pl line 61, <IN1> line 1.
Use of uninitialized value $qmin in print at /home/tools/JUM_2.0.2/final_process_IR_output_long.pl line 61, <IN1> line 1.
Use of uninitialized value in print at /home/tools/JUM_2.0.2/final_process_IR_output_long.pl line 61, <IN1> line 1.
Use of uninitialized value in print at /home/tools/JUM_2.0.2/final_process_IR_output_long.pl line 62, <IN1> line 1.
Use of uninitialized value $coor in print at /home/tools/JUM_2.0.2/final_process_IR_output_long.pl line 62, <IN1> line 1.
Use of uninitialized value $array[0] in hash element at /home/tools/JUM_2.0.2/final_process_cassette_exon_output2.pl line 23, <IN1> line 1.
Use of uninitialized value $temp[1] in hash element at /home/tools/JUM_2.0.2/final_process_cassette_exon_output2.pl line 30, <IN2> line 1.
Use of uninitialized value within @temp in join or string at /home/tools/JUM_2.0.2/final_process_cassette_exon_output2.pl line 32, <IN2> line 1.
Use of uninitialized value $temp[1] in join or string at /home/tools/JUM_2.0.2/final_process_cassette_exon_output2.pl line 32, <IN2> line 1.
Use of uninitialized value in subroutine entry at /home/tools/JUM_2.0.2/final_process_IR_output_short.pl line 46, <IN1> line 1.
Use of uninitialized value $_ in substitution (s///) at /home/tools/JUM_2.0.2/final_process_IR_output_short.pl line 47, <IN1> line 1.
Use of uninitialized value in subroutine entry at /home/tools/JUM_2.0.2/final_process_IR_output_short.pl line 48, <IN1> line 1.
Use of uninitialized value in print at /home/tools/JUM_2.0.2/final_process_IR_output_short.pl line 49, <IN1> line 1.
Use of uninitialized value $coor in print at /home/tools/JUM_2.0.2/final_process_IR_output_short.pl line 49, <IN1> line 1.
Use of uninitialized value in print at /home/tools/JUM_2.0.2/final_process_IR_output_short.pl line 49, <IN1> line 1.
Use of uninitialized value in print at /home/tools/JUM_2.0.2/final_process_IR_output_short.pl line 49, <IN1> line 1.
Use of uninitialized value $start in print at /home/tools/JUM_2.0.2/final_process_IR_output_short.pl line 49, <IN1> line 1.
Use of uninitialized value $end in print at /home/tools/JUM_2.0.2/final_process_IR_output_short.pl line 49, <IN1> line 1.
Use of uninitialized value $pmin in print at /home/tools/JUM_2.0.2/final_process_IR_output_short.pl line 49, <IN1> line 1.
Use of uninitialized value $qmin in print at /home/tools/JUM_2.0.2/final_process_IR_output_short.pl line 49, <IN1> line 1.
Use of uninitialized value in print at /home/tools/JUM_2.0.2/final_process_IR_output_short.pl line 49, <IN1> line 1.
Use of uninitialized value in print at /home/tools/JUM_2.0.2/final_process_IR_output_short.pl line 50, <IN1> line 1.
Use of uninitialized value $coor in print at /home/tools/JUM_2.0.2/final_process_IR_output_short.pl line 50, <IN1> line 1.
Use of uninitialized value $array[0] in hash element at /home/tools/JUM_2.0.2/final_process_cassette_exon_output2.pl line 23, <IN1> line 1.
Use of uninitialized value $temp[1] in hash element at /home/tools/JUM_2.0.2/final_process_cassette_exon_output2.pl line 30, <IN2> line 1.
Use of uninitialized value within @temp in join or string at /home/tools/JUM_2.0.2/final_process_cassette_exon_output2.pl line 32, <IN2> line 1.
Use of uninitialized value $temp[1] in join or string at /home/tools/JUM_2.0.2/final_process_cassette_exon_output2.pl line 32, <IN2> line 1.
Use of uninitialized value in string eq at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 74, <IN1> line 1.
Use of uninitialized value $as in string eq at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 74, <IN1> line 1.
Use of uninitialized value $lineid in hash element at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 75, <IN1> line 1.
Use of uninitialized value $lineid in addition (+) at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 76, <IN1> line 1.
Use of uninitialized value $i in numeric le (<=) at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 191, <IN1> line 1.
Use of uninitialized value $i in numeric le (<=) at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 199, <IN1> line 1.
Use of uninitialized value $i in numeric le (<=) at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 202, <IN1> line 1.
Use of uninitialized value $i in numeric le (<=) at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 199, <IN1> line 1.
Use of uninitialized value $i in numeric le (<=) at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 202, <IN1> line 1.
Use of uninitialized value $i in numeric le (<=) at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 199, <IN1> line 1.
Use of uninitialized value $i in numeric le (<=) at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 202, <IN1> line 1.
Use of uninitialized value $i in numeric le (<=) at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 199, <IN1> line 1.
Use of uninitialized value $i in numeric le (<=) at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 202, <IN1> line 1.
Use of uninitialized value $i in numeric le (<=) at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 199, <IN1> line 1.
Use of uninitialized value $i in numeric le (<=) at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 202, <IN1> line 1.
Use of uninitialized value $i in numeric le (<=) at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 199, <IN1> line 1.
Use of uninitialized value $i in numeric le (<=) at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 202, <IN1> line 1.
Use of uninitialized value $unique_id[0] in sort at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 215, <IN1> line 1.
Use of uninitialized value in subroutine entry at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 218, <IN1> line 1.
Use of uninitialized value $_ in substitution (s///) at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 219, <IN1> line 1.
Use of uninitialized value in subroutine entry at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 220, <IN1> line 1.
Use of uninitialized value $as in print at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 221, <IN1> line 1.
Use of uninitialized value $chr in print at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 222, <IN1> line 1.
Use of uninitialized value $strand in print at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 222, <IN1> line 1.
Use of uninitialized value $sorted_id[0] in print at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 222, <IN1> line 1.
Use of uninitialized value $sorted_id[-1] in print at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 226, <IN1> line 1.
Use of uninitialized value $gene in print at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 228, <IN1> line 1.
Use of uninitialized value $chr in print at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 228, <IN1> line 1.
Use of uninitialized value $strand in print at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 228, <IN1> line 1.
Use of uninitialized value $sorted_id[0] in print at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 228, <IN1> line 1.
Use of uninitialized value $sorted_id[-1] in print at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 232, <IN1> line 1.
Use of uninitialized value $chr in print at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 233, <IN1> line 1.
Use of uninitialized value $strand in print at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 233, <IN1> line 1.
Use of uninitialized value $sorted_id[0] in print at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 233, <IN1> line 1.
Use of uninitialized value within @sorted_id in addition (+) at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 237, <IN1> line 1.
Use of uninitialized value in print at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 237, <IN1> line 1.
Use of uninitialized value $sorted_id[-1] in print at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 238, <IN1> line 1.
Use of uninitialized value $pmin in print at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 239, <IN1> line 1.
Use of uninitialized value $qmin in print at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 239, <IN1> line 1.
Use of uninitialized value $i in subtraction (-) at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 241, <IN1> line 1.
Use of uninitialized value in addition (+) at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 259, <IN1> line 1.
Use of uninitialized value in addition (+) at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 259, <IN1> line 1.
Use of uninitialized value in addition (+) at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 259, <IN1> line 1.
Use of uninitialized value in addition (+) at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 262, <IN1> line 1.
Use of uninitialized value in addition (+) at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 262, <IN1> line 1.
Use of uninitialized value in addition (+) at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 262, <IN1> line 1.
Use of uninitialized value $temp[1] in hash element at /home/tools/JUM_2.0.2/final_process_cassette_exon_output2.pl line 30, <IN2> line 1.
Use of uninitialized value within @temp in join or string at /home/tools/JUM_2.0.2/final_process_cassette_exon_output2.pl line 32, <IN2> line 1.
Use of uninitialized value in string eq at /home/tools/JUM_2.0.2/final_process_A5SS_output.pl line 64, <IN1> line 1.
Use of uninitialized value $as in string eq at /home/tools/JUM_2.0.2/final_process_A5SS_output.pl line 64, <IN1> line 1.
Use of uninitialized value $strand in string eq at /home/tools/JUM_2.0.2/final_process_A5SS_output.pl line 65, <IN1> line 1.
Use of uninitialized value $strand in string eq at /home/tools/JUM_2.0.2/final_process_A5SS_output.pl line 65, <IN1> line 1.
Use of uninitialized value $unique_id[0] in sort at /home/tools/JUM_2.0.2/final_process_A5SS_output.pl line 125, <IN1> line 1.
Use of uninitialized value in subroutine entry at /home/tools/JUM_2.0.2/final_process_A5SS_output.pl line 126, <IN1> line 1.
Use of uninitialized value $_ in substitution (s///) at /home/tools/JUM_2.0.2/final_process_A5SS_output.pl line 127, <IN1> line 1.
Use of uninitialized value in subroutine entry at /home/tools/JUM_2.0.2/final_process_A5SS_output.pl line 128, <IN1> line 1.
Use of uninitialized value $as in print at /home/tools/JUM_2.0.2/final_process_A5SS_output.pl line 129, <IN1> line 1.
Use of uninitialized value $chr in print at /home/tools/JUM_2.0.2/final_process_A5SS_output.pl line 130, <IN1> line 1.
Use of uninitialized value $strand in print at /home/tools/JUM_2.0.2/final_process_A5SS_output.pl line 130, <IN1> line 1.
Use of uninitialized value $sorted_id[0] in join or string at /home/tools/JUM_2.0.2/final_process_A5SS_output.pl line 130, <IN1> line 1.
Use of uninitialized value $gene in print at /home/tools/JUM_2.0.2/final_process_A5SS_output.pl line 131, <IN1> line 1.
Use of uninitialized value $chr in print at /home/tools/JUM_2.0.2/final_process_A5SS_output.pl line 131, <IN1> line 1.
Use of uninitialized value $strand in print at /home/tools/JUM_2.0.2/final_process_A5SS_output.pl line 131, <IN1> line 1.
Use of uninitialized value $sorted_id[0] in join or string at /home/tools/JUM_2.0.2/final_process_A5SS_output.pl line 131, <IN1> line 1.
Use of uninitialized value $chr in print at /home/tools/JUM_2.0.2/final_process_A5SS_output.pl line 131, <IN1> line 1.
Use of uninitialized value $strand in print at /home/tools/JUM_2.0.2/final_process_A5SS_output.pl line 131, <IN1> line 1.
Use of uninitialized value $common3prime in print at /home/tools/JUM_2.0.2/final_process_A5SS_output.pl line 131, <IN1> line 1.
Use of uninitialized value $a5ss[0] in join or string at /home/tools/JUM_2.0.2/final_process_A5SS_output.pl line 131, <IN1> line 1.
Use of uninitialized value $pmin in print at /home/tools/JUM_2.0.2/final_process_A5SS_output.pl line 132, <IN1> line 1.
Use of uninitialized value $qmin in print at /home/tools/JUM_2.0.2/final_process_A5SS_output.pl line 132, <IN1> line 1.
Use of uninitialized value $dpsi[0] in join or string at /home/tools/JUM_2.0.2/final_process_A5SS_output.pl line 133, <IN1> line 1.
Use of uninitialized value $temp[1] in hash element at /home/tools/JUM_2.0.2/final_process_cassette_exon_output2.pl line 30, <IN2> line 1.
Use of uninitialized value within @temp in join or string at /home/tools/JUM_2.0.2/final_process_cassette_exon_output2.pl line 32, <IN2> line 1.
Use of uninitialized value in string eq at /home/tools/JUM_2.0.2/final_process_A3SS_output.pl line 64, <IN1> line 1.
Use of uninitialized value $as in string eq at /home/tools/JUM_2.0.2/final_process_A3SS_output.pl line 64, <IN1> line 1.
Use of uninitialized value $strand in string eq at /home/tools/JUM_2.0.2/final_process_A3SS_output.pl line 65, <IN1> line 1.
Use of uninitialized value $strand in string eq at /home/tools/JUM_2.0.2/final_process_A3SS_output.pl line 65, <IN1> line 1.
Use of uninitialized value $unique_id[0] in sort at /home/tools/JUM_2.0.2/final_process_A3SS_output.pl line 124, <IN1> line 1.
Use of uninitialized value in subroutine entry at /home/tools/JUM_2.0.2/final_process_A3SS_output.pl line 125, <IN1> line 1.
Use of uninitialized value $_ in substitution (s///) at /home/tools/JUM_2.0.2/final_process_A3SS_output.pl line 126, <IN1> line 1.
Use of uninitialized value in subroutine entry at /home/tools/JUM_2.0.2/final_process_A3SS_output.pl line 127, <IN1> line 1.
Use of uninitialized value $as in print at /home/tools/JUM_2.0.2/final_process_A3SS_output.pl line 128, <IN1> line 1.
Use of uninitialized value $chr in print at /home/tools/JUM_2.0.2/final_process_A3SS_output.pl line 129, <IN1> line 1.
Use of uninitialized value $strand in print at /home/tools/JUM_2.0.2/final_process_A3SS_output.pl line 129, <IN1> line 1.
Use of uninitialized value $sorted_id[0] in join or string at /home/tools/JUM_2.0.2/final_process_A3SS_output.pl line 129, <IN1> line 1.
Use of uninitialized value $gene in print at /home/tools/JUM_2.0.2/final_process_A3SS_output.pl line 130, <IN1> line 1.
Use of uninitialized value $chr in print at /home/tools/JUM_2.0.2/final_process_A3SS_output.pl line 130, <IN1> line 1.
Use of uninitialized value $strand in print at /home/tools/JUM_2.0.2/final_process_A3SS_output.pl line 130, <IN1> line 1.
Use of uninitialized value $sorted_id[0] in join or string at /home/tools/JUM_2.0.2/final_process_A3SS_output.pl line 130, <IN1> line 1.
Use of uninitialized value $chr in print at /home/tools/JUM_2.0.2/final_process_A3SS_output.pl line 130, <IN1> line 1.
Use of uninitialized value $strand in print at /home/tools/JUM_2.0.2/final_process_A3SS_output.pl line 130, <IN1> line 1.
Use of uninitialized value $common5prime in print at /home/tools/JUM_2.0.2/final_process_A3SS_output.pl line 130, <IN1> line 1.
Use of uninitialized value $a3ss[0] in join or string at /home/tools/JUM_2.0.2/final_process_A3SS_output.pl line 130, <IN1> line 1.
Use of uninitialized value $pmin in print at /home/tools/JUM_2.0.2/final_process_A3SS_output.pl line 131, <IN1> line 1.
Use of uninitialized value $qmin in print at /home/tools/JUM_2.0.2/final_process_A3SS_output.pl line 131, <IN1> line 1.
Use of uninitialized value $dpsi[0] in join or string at /home/tools/JUM_2.0.2/final_process_A3SS_output.pl line 132, <IN1> line 1.
Use of uninitialized value $temp[1] in hash element at /home/tools/JUM_2.0.2/final_process_cassette_exon_output2.pl line 30, <IN2> line 1.
Use of uninitialized value within @temp in join or string at /home/tools/JUM_2.0.2/final_process_cassette_exon_output2.pl line 32, <IN2> line 1.
Use of uninitialized value in string eq at /home/tools/JUM_2.0.2/final_process_composite_output.pl line 54, <IN1> line 1.
Use of uninitialized value $as in string eq at /home/tools/JUM_2.0.2/final_process_composite_output.pl line 54, <IN1> line 1.
Use of uninitialized value $unique_id[0] in sort at /home/tools/JUM_2.0.2/final_process_composite_output.pl line 99, <IN1> line 1.
Use of uninitialized value in subroutine entry at /home/tools/JUM_2.0.2/final_process_composite_output.pl line 100, <IN1> line 1.
Use of uninitialized value $_ in substitution (s///) at /home/tools/JUM_2.0.2/final_process_composite_output.pl line 101, <IN1> line 1.
Use of uninitialized value in subroutine entry at /home/tools/JUM_2.0.2/final_process_composite_output.pl line 102, <IN1> line 1.
Use of uninitialized value $as in print at /home/tools/JUM_2.0.2/final_process_composite_output.pl line 103, <IN1> line 1.
Use of uninitialized value $chr in print at /home/tools/JUM_2.0.2/final_process_composite_output.pl line 104, <IN1> line 1.
Use of uninitialized value $strand in print at /home/tools/JUM_2.0.2/final_process_composite_output.pl line 104, <IN1> line 1.
Use of uninitialized value $sorted_id[0] in join or string at /home/tools/JUM_2.0.2/final_process_composite_output.pl line 104, <IN1> line 1.
Use of uninitialized value $gene in print at /home/tools/JUM_2.0.2/final_process_composite_output.pl line 105, <IN1> line 1.
Use of uninitialized value $chr in print at /home/tools/JUM_2.0.2/final_process_composite_output.pl line 105, <IN1> line 1.
Use of uninitialized value $strand in print at /home/tools/JUM_2.0.2/final_process_composite_output.pl line 105, <IN1> line 1.
Use of uninitialized value $sorted_id[0] in join or string at /home/tools/JUM_2.0.2/final_process_composite_output.pl line 105, <IN1> line 1.
Use of uninitialized value $chr in print at /home/tools/JUM_2.0.2/final_process_composite_output.pl line 105, <IN1> line 1.
Use of uninitialized value $strand in print at /home/tools/JUM_2.0.2/final_process_composite_output.pl line 105, <IN1> line 1.
Use of uninitialized value $sorted_id[0] in join or string at /home/tools/JUM_2.0.2/final_process_composite_output.pl line 105, <IN1> line 1.
Use of uninitialized value $pmin in print at /home/tools/JUM_2.0.2/final_process_composite_output.pl line 106, <IN1> line 1.
Use of uninitialized value $qmin in print at /home/tools/JUM_2.0.2/final_process_composite_output.pl line 106, <IN1> line 1.
Use of uninitialized value $dpsi[0] in join or string at /home/tools/JUM_2.0.2/final_process_composite_output.pl line 107, <IN1> line 1.
Use of uninitialized value $temp[1] in hash element at /home/tools/JUM_2.0.2/final_process_cassette_exon_output2.pl line 30, <IN2> line 1.
Use of uninitialized value within @temp in join or string at /home/tools/JUM_2.0.2/final_process_cassette_exon_output2.pl line 32, <IN2> line 1.

Here are the commands I used:

JUM_B.sh command
cd output/JUM_Analysis/JUM_diff && (../../../tools/JUM_2.0.2/JUM_B.sh --Folder $(readlink -f ../../../tools/JUM_2.0.2/) --Test pvalue --Cutoff 1 --TotalFileNum 6 --Condition1SampleName G1_1.,G1_2.,G1_3. --Condition2SampleName S_1.,S_2.,S_3. --Condition1_fileNum_threshold 2 --Condition2_fileNum_threshold 2) 2> ../../jum_b.log && cd ../../..

JUM_C command
cd output/JUM_Analysis/JUM_diff/FINAL_JUM_OUTPUT_pvalue_1 && (../../../../tools/JUM_2.0.2/JUM_C.sh --Folder $(readlink -f ../../../../tools/JUM_2.0.2/) --Test pvalue --Cutoff 1 --TotalCondition1FileNum 3 --TotalCondition2FileNum 3 --REF ../../../../ensembl/Homo_sapiens.GRCh38.96.gff3.refflat.fi x.txt) 2> ../../../jum_c.log && cd ../../../..

Some of the output files have weird stuff like __ARRAY(0x7fffebd2d1e0)___ written in them:

AS_differential_JUM_output_cassette_exon_events_pvalue_1_final_detailed.txt

Missing the AS_differential_JUM_output_intron_retention_adjusted_pvalue_0.05.txt file

Hello,

So I think I have a bug to report. I ran the R script (successfully I think) and generated a lot of scripts from this. However, when I run the third shell script, I get an error for a missing file (AS_differential_JUM_output_intron_retention_adjusted_pvalue_0.05.txt). I can find many files with a similar name but not this one. Is there a bug with making a file with this name or did I run something incorrectly. Please see the commands and files below.

bash /lab/app/JUM/JUM_170323/JUM_1.3.1/JUM_3.sh /lab/app/JUM/JUM_170323/JUM_1.3.1 adjusted_pvalue 0.05 6 3 Use of uninitialized value in print at /lab/app/JUM/JUM_170323/JUM_1.3.1/count_intron_read_long_intron_retention_step2.pl line 47, <IN2> line 261. Use of uninitialized value in print at /lab/app/JUM/JUM_170323/JUM_1.3.1/count_intron_read_long_intron_retention_step2.pl line 47, <IN2> line 505. Use of uninitialized value $_ in pattern match (m//) at /lab/app/JUM/JUM_170323/JUM_1.3.1/determining_rightful_total_cassette_exon_event.pl line 52. Use of uninitialized value $_ in pattern match (m//) at /lab/app/JUM/JUM_170323/JUM_1.3.1/determining_rightful_total_cassette_exon_event.pl line 52. Use of uninitialized value in print at /lab/app/JUM/JUM_170323/JUM_1.3.1/count_intron_read_long_intron_retention_step2.pl line 47, <IN2> line 261. Use of uninitialized value in print at /lab/app/JUM/JUM_170323/JUM_1.3.1/count_intron_read_long_intron_retention_step2.pl line 47, <IN2> line 505. Use of uninitialized value $_ in pattern match (m//) at /lab/app/JUM/JUM_170323/JUM_1.3.1/determining_rightful_total_cassette_exon_event.pl line 52. Use of uninitialized value $_ in pattern match (m//) at /lab/app/JUM/JUM_170323/JUM_1.3.1/determining_rightful_total_cassette_exon_event.pl line 52. Use of uninitialized value in print at /lab/app/JUM/JUM_170323/JUM_1.3.1/count_intron_read_long_intron_retention_step2.pl line 47, <IN2> line 261. Use of uninitialized value in print at /lab/app/JUM/JUM_170323/JUM_1.3.1/count_intron_read_long_intron_retention_step2.pl line 47, <IN2> line 505. Use of uninitialized value $_ in pattern match (m//) at /lab/app/JUM/JUM_170323/JUM_1.3.1/determining_rightful_total_cassette_exon_event.pl line 52. Use of uninitialized value $_ in pattern match (m//) at /lab/app/JUM/JUM_170323/JUM_1.3.1/determining_rightful_total_cassette_exon_event.pl line 52. Use of uninitialized value in print at /lab/app/JUM/JUM_170323/JUM_1.3.1/count_intron_read_long_intron_retention_step2.pl line 47, <IN2> line 261. Use of uninitialized value in print at /lab/app/JUM/JUM_170323/JUM_1.3.1/count_intron_read_long_intron_retention_step2.pl line 47, <IN2> line 505. Use of uninitialized value $_ in pattern match (m//) at /lab/app/JUM/JUM_170323/JUM_1.3.1/determining_rightful_total_cassette_exon_event.pl line 52. Use of uninitialized value $_ in pattern match (m//) at /lab/app/JUM/JUM_170323/JUM_1.3.1/determining_rightful_total_cassette_exon_event.pl line 52. Use of uninitialized value in print at /lab/app/JUM/JUM_170323/JUM_1.3.1/count_intron_read_long_intron_retention_step2.pl line 47, <IN2> line 261. Use of uninitialized value in print at /lab/app/JUM/JUM_170323/JUM_1.3.1/count_intron_read_long_intron_retention_step2.pl line 47, <IN2> line 505. Use of uninitialized value $_ in pattern match (m//) at /lab/app/JUM/JUM_170323/JUM_1.3.1/determining_rightful_total_cassette_exon_event.pl line 52. Use of uninitialized value $_ in pattern match (m//) at /lab/app/JUM/JUM_170323/JUM_1.3.1/determining_rightful_total_cassette_exon_event.pl line 52. Use of uninitialized value in print at /lab/app/JUM/JUM_170323/JUM_1.3.1/count_intron_read_long_intron_retention_step2.pl line 47, <IN2> line 261. Use of uninitialized value in print at /lab/app/JUM/JUM_170323/JUM_1.3.1/count_intron_read_long_intron_retention_step2.pl line 47, <IN2> line 505. Use of uninitialized value $_ in pattern match (m//) at /lab/app/JUM/JUM_170323/JUM_1.3.1/determining_rightful_total_cassette_exon_event.pl line 52. Use of uninitialized value $_ in pattern match (m//) at /lab/app/JUM/JUM_170323/JUM_1.3.1/determining_rightful_total_cassette_exon_event.pl line 52. mv: cannot stat AS_differential_JUM_output_intron_retention_adjusted_pvalue_0.05.txt': No such file or directory`

The last line seems to be the most informative about what went wrong. I looked to see if I had this file but I do not, instead I have some with a similar name but without the JUMoutput

ls -lh *AS_differential*intron* -rw-r--r-- 1 jamesl lab 2.2K Apr 11 17:26 AS_differential_adjusted_pvalue_0.05_long_intron_retention_passing_filter_combined_list.txt -rw-r--r-- 1 jamesl lab 13K Apr 11 17:18 AS_differential_adjusted_pvalue_0.05_non_intron_retention_AS_structure_list.txt -rw-r--r-- 1 jamesl lab 2.2K Apr 11 17:26 AS_differential_adjusted_pvalue_0.05_valid_long_intron_retention_list.txt -rw-r--r-- 1 jamesl lab 148 Apr 11 17:18 AS_differential_adjusted_pvalue_0.05_valid_short_intron_retention_list.txt -rw-r--r-- 1 jamesl lab 11K Apr 11 17:26 AS_differential_total_long_intron_retention_passing_filter_combined_list.txt -rw-r--r-- 1 jamesl lab 11K Apr 11 17:26 AS_differential_total_valid_long_intron_retention_list.txt -rw-r--r-- 1 jamesl lab 7.4K Apr 11 17:18 AS_differential_total_valid_short_intron_retention_list.txt

Error when running JUM step A

Hi,

I keep encountering an error while running JUM step A. I am using JUM 3.0.0.
The error is:
"ERROR: Sort order was unspecified, and file treat1Aligned.out.sorted.bed is not sorted lexicographically.
Please rerun with the -g option for a genome file.
See documentation for details."

The error appears after line 238. I did STAR mapping for my control and treatment RNA seq data sets before running JUM step A.

Please let me know if there is any other information you need from me or if you have any idea how I might be able to fix this error.

Thank you so much!

NA qvalues

Hello,

I ran JUM 2.0, the final output files generated had very few differentially spliced genes (qvalue 0.05). And also the qvalue was listed as NA for a lot of genes, though the pvalue was not NA, I'm not sure if the qvalues were calculated correctly, I'm attaching one of the output files. Please let me know if you need any other files for troubleshooting.

Thanks!
AS_differential_JUM_output_cassette_exon_events_pvalue_1_final_simplified.txt

total AS events output just contain intron_retention

total AS events output just contain intron_retention(1062). All other AS events is 0. such as A3SS A5SS MXE and cassette_exon

Potential missing "

Hi All,
Just a quick issue I have been having with running this software. A premature termination seems to occur due to a missing " at the very end of the JUM_A_multi_1.sh script.
Best wishes and thank you for an excellent script!
Alex

_trash_out file should be empty!

JUM output this error
Error:control_2_trash_out file should be empty!
for all sample control + treatment

Should I worry about it?

Regarding delta-PSI value, control-treatment vs treatment-control

I have a query regarding the resultant delta-Psi value.

After running the JUM_C.sh, deltaPSI value is provided for control-treatment.

Can we calculate the deltaPSI value for treatment-Control ?

Thank you

License + open-sourcing development

Hello,
What is the license for the code? Choose a license is a great resource for choosing a license. For academic software, I suggest the MIT license.

Also, can you make the repository the raw source code, rather than individual tarballs? The "release" feature of Github can be used for posting tarballs of specific versions.
Warmest,
Olga

Strange warnings from Shell script 2

Hey,

So I got a lot of strange warnings from running the second shell script. I am not sure what part is generating the warnings and how big a problem they are. But I do know that at the end of shell script 3 I get a LOT of errors and the final output files are nearly all empty. I am not sure if that problem is related to this or not but thought I would check what is is about (some of the whitespace has been removed from the warnings to make it easier to read).

bash /lab/app/JUM/JUM_170323/JUM_1.3.1/JUM_2.sh /lab/app/JUM/JUM_170323/JUM_1.3.1 5 2 150
Preparing for non-intron retention AS events analyses...
6 input samples for JUM analyses
Preparing for intron retention AS events analyses...
Processing junction overhangs for Sample S100... Success.
Processing junction overhangs for Sample S104... Success.
Processing junction overhangs for Sample S108... Success.
Processing junction overhangs for Sample S102... Success.

---

WARNING: -wb is ignored with -abam**********WARNING: -wb is ignored with -abam
**********WARNING: -wb is ignored with -abam

---

WARNING: -wb is ignored with -abam

---

---

*****WARNING: -wb is ignored with -abam
WARNING: -wb is ignored with -abamWARNING: -wb is ignored with -abam

---

---

WARNING: -wb is ignored with -abam
**********WARNING: -wb is ignored with -abam
*****WARNING: -wb is ignored with -abam

---

**********WARNING: -wb is ignored with -abam

---

WARNING: -wb is ignored with -abam

---

ready to performing differential AS analyses...
find: warning: you have specified the -maxdepth option after a non-option argument -type, but options are not positional (-maxdepth affects tests specified before it as well as those specified after it). Please specify options before other arguments.

Best,
James

If it helps, the error message from shell script 3 is below:
(It might be an issue with the process_raw_AS_differential_output.pl script but I do not know enough perl to comment on any further)

bash /lab/app/JUM/JUM_170323/JUM_1.3.1/JUM_3.sh /lab/app/JUM/JUM_170323/JUM_1.3.1 adjusted_pvalue 0.05 6 3
can't open input1 file: No such file or directory at /lab/app/JUM/JUM_170323/JUM_1.3.1/process_raw_AS_differential_output.pl line 20.
awk: cmd. line:1: fatal: cannot open file AS_differential.txt' for reading (No such file or directory) AS_differential.txt: No such file or directory AS_differential.txt: No such file or directory AS_differential.txt: No such file or directory Error: The requested bed file (temp_long_intron_retention_junction_coordinate_adjusted_pvalue_0.05.txt) could not be opened. Exiting! Error: The requested bed file (temp_long_intron_retention_junction_coordinate_total.txt) could not be opened. Exiting! Error: The requested bed file (temp_long_intron_retention_junction_coordinate_adjusted_pvalue_0.05.txt) could not be opened. Exiting! Error: The requested bed file (temp_long_intron_retention_junction_coordinate_total.txt) could not be opened. Exiting! Error: The requested bed file (temp_long_intron_retention_junction_coordinate_adjusted_pvalue_0.05.txt) could not be opened. Exiting! Error: The requested bed file (temp_long_intron_retention_junction_coordinate_total.txt) could not be opened. Exiting! Error: The requested bed file (temp_long_intron_retention_junction_coordinate_adjusted_pvalue_0.05.txt) could not be opened. Exiting! Error: The requested bed file (temp_long_intron_retention_junction_coordinate_total.txt) could not be opened. Exiting! Error: The requested bed file (temp_long_intron_retention_junction_coordinate_adjusted_pvalue_0.05.txt) could not be opened. Exiting! Error: The requested bed file (temp_long_intron_retention_junction_coordinate_total.txt) could not be opened. Exiting! Error: The requested bed file (temp_long_intron_retention_junction_coordinate_adjusted_pvalue_0.05.txt) could not be opened. Exiting! Error: The requested bed file (temp_long_intron_retention_junction_coordinate_total.txt) could not be opened. Exiting! Can't locate Array/Utils.pm in @INC (@INC contains: /etc/perl /usr/local/lib/perl/5.14.2 /usr/local/share/perl/5.14.2 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.14 /usr/share/perl/5.14 /usr/local/lib/site_perl .) at /lab/app/JUM/JUM_170323/JUM_1.3.1/screening_cassette_exon_events.pl line 4. BEGIN failed--compilation aborted at /lab/app/JUM/JUM_170323/JUM_1.3.1/screening_cassette_exon_events.pl line 4. Error: The requested bed file (cassette_exon_coordinate.bed) could not be opened. Exiting! can't open input2 file: No such file or directory at /lab/app/JUM/JUM_170323/JUM_1.3.1/count_intron_read_long_intron_retention_step2.pl line 17. can't open input1 file: No such file or directory at /lab/app/JUM/JUM_170323/JUM_1.3.1/determining_rightful_total_cassette_exon_event.pl line 17. awk: cmd. line:1: fatal: cannot open file S100_temp_total_cassette_with_indicator.txt' for reading (No such file or directory)
Error: The requested bed file (cassette_exon_coordinate.bed) could not be opened. Exiting!
can't open input2 file: No such file or directory at /lab/app/JUM/JUM_170323/JUM_1.3.1/count_intron_read_long_intron_retention_step2.pl line 17.
can't open input1 file: No such file or directory at /lab/app/JUM/JUM_170323/JUM_1.3.1/determining_rightful_total_cassette_exon_event.pl line 17.
awk: cmd. line:1: fatal: cannot open file S104_temp_total_cassette_with_indicator.txt' for reading (No such file or directory) Error: The requested bed file (cassette_exon_coordinate.bed) could not be opened. Exiting! can't open input2 file: No such file or directory at /lab/app/JUM/JUM_170323/JUM_1.3.1/count_intron_read_long_intron_retention_step2.pl line 17. can't open input1 file: No such file or directory at /lab/app/JUM/JUM_170323/JUM_1.3.1/determining_rightful_total_cassette_exon_event.pl line 17. awk: cmd. line:1: fatal: cannot open file S108_temp_total_cassette_with_indicator.txt' for reading (No such file or directory)
Error: The requested bed file (cassette_exon_coordinate.bed) could not be opened. Exiting!
can't open input2 file: No such file or directory at /lab/app/JUM/JUM_170323/JUM_1.3.1/count_intron_read_long_intron_retention_step2.pl line 17.
can't open input1 file: No such file or directory at /lab/app/JUM/JUM_170323/JUM_1.3.1/determining_rightful_total_cassette_exon_event.pl line 17.
awk: cmd. line:1: fatal: cannot open file S102_temp_total_cassette_with_indicator.txt' for reading (No such file or directory) Error: The requested bed file (cassette_exon_coordinate.bed) could not be opened. Exiting! can't open input2 file: No such file or directory at /lab/app/JUM/JUM_170323/JUM_1.3.1/count_intron_read_long_intron_retention_step2.pl line 17. can't open input1 file: No such file or directory at /lab/app/JUM/JUM_170323/JUM_1.3.1/determining_rightful_total_cassette_exon_event.pl line 17. awk: cmd. line:1: fatal: cannot open file SC2_S106_temp_total_cassette_with_indicator.txt' for reading (No such file or directory)
Error: The requested bed file (cassette_exon_coordinate.bed) could not be opened. Exiting!
can't open input2 file: No such file or directory at /lab/app/JUM/JUM_170323/JUM_1.3.1/count_intron_read_long_intron_retention_step2.pl line 17.
can't open input1 file: No such file or directory at /lab/app/JUM/JUM_170323/JUM_1.3.1/determining_rightful_total_cassette_exon_event.pl line 17.
awk: cmd. line:1: fatal: cannot open file S110_temp_total_cassette_with_indicator.txt' for reading (No such file or directory) awk: cmd. line:1: fatal: cannot open file cassette_exon_coordinate.bed' for reading (No such file or directory)
Can't locate Array/Utils.pm in @inc (@inc contains: /etc/perl /usr/local/lib/perl/5.14.2 /usr/local/share/perl/5.14.2 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.14 /usr/share/perl/5.14 /usr/local/lib/site_perl .) at /lab/app/JUM/JUM_170323/JUM_1.3.1/screening_MXE_events.pl line 4.
BEGIN failed--compilation aborted at /lab/app/JUM/JUM_170323/JUM_1.3.1/screening_MXE_events.pl line 4.
Error: The requested bed file (MXE_coordinate.bed) could not be opened. Exiting!
can't open input2 file: No such file or directory at /lab/app/JUM/JUM_170323/JUM_1.3.1/count_intron_read_long_intron_retention_step2.pl line 17.
can't open input1 file: No such file or directory at /lab/app/JUM/JUM_170323/JUM_1.3.1/determining_rightful_total_cassette_exon_event.pl line 17.
awk: cmd. line:1: fatal: cannot open file S100_temp_total_MXE_with_indicator.txt' for reading (No such file or directory) Error: The requested bed file (MXE_coordinate.bed) could not be opened. Exiting! can't open input2 file: No such file or directory at /lab/app/JUM/JUM_170323/JUM_1.3.1/count_intron_read_long_intron_retention_step2.pl line 17. can't open input1 file: No such file or directory at /lab/app/JUM/JUM_170323/JUM_1.3.1/determining_rightful_total_cassette_exon_event.pl line 17. awk: cmd. line:1: fatal: cannot open file S104_temp_total_MXE_with_indicator.txt' for reading (No such file or directory)
Error: The requested bed file (MXE_coordinate.bed) could not be opened. Exiting!
can't open input2 file: No such file or directory at /lab/app/JUM/JUM_170323/JUM_1.3.1/count_intron_read_long_intron_retention_step2.pl line 17.
can't open input1 file: No such file or directory at /lab/app/JUM/JUM_170323/JUM_1.3.1/determining_rightful_total_cassette_exon_event.pl line 17.
awk: cmd. line:1: fatal: cannot open file S108_temp_total_MXE_with_indicator.txt' for reading (No such file or directory) Error: The requested bed file (MXE_coordinate.bed) could not be opened. Exiting! can't open input2 file: No such file or directory at /lab/app/JUM/JUM_170323/JUM_1.3.1/count_intron_read_long_intron_retention_step2.pl line 17. can't open input1 file: No such file or directory at /lab/app/JUM/JUM_170323/JUM_1.3.1/determining_rightful_total_cassette_exon_event.pl line 17. awk: cmd. line:1: fatal: cannot open file S102_temp_total_MXE_with_indicator.txt' for reading (No such file or directory)
Error: The requested bed file (MXE_coordinate.bed) could not be opened. Exiting!
can't open input2 file: No such file or directory at /lab/app/JUM/JUM_170323/JUM_1.3.1/count_intron_read_long_intron_retention_step2.pl line 17.
can't open input1 file: No such file or directory at /lab/app/JUM/JUM_170323/JUM_1.3.1/determining_rightful_total_cassette_exon_event.pl line 17.
awk: cmd. line:1: fatal: cannot open file S106_temp_total_MXE_with_indicator.txt' for reading (No such file or directory) Error: The requested bed file (MXE_coordinate.bed) could not be opened. Exiting! can't open input2 file: No such file or directory at /lab/app/JUM/JUM_170323/JUM_1.3.1/count_intron_read_long_intron_retention_step2.pl line 17. can't open input1 file: No such file or directory at /lab/app/JUM/JUM_170323/JUM_1.3.1/determining_rightful_total_cassette_exon_event.pl line 17. awk: cmd. line:1: fatal: cannot open file S110_temp_total_MXE_with_indicator.txt' for reading (No such file or directory)
Can't locate Array/Utils.pm in @inc (@inc contains: /etc/perl /usr/local/lib/perl/5.14.2 /usr/local/share/perl/5.14.2 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.14 /usr/share/perl/5.14 /usr/local/lib/site_perl .) at /lab/app/JUM/JUM_170323/JUM_1.3.1/screening_A5SS_A3SS_events.pl line 4.
BEGIN failed--compilation aborted at /lab/app/JUM/JUM_170323/JUM_1.3.1/screening_A5SS_A3SS_events.pl line 4.
awk: cmd. line:1: fatal: cannot open file Valid_total_A5SS_event.txt' for reading (No such file or directory) can't open input2 file: No such file or directory at /lab/app/JUM/JUM_170323/JUM_1.3.1/profiling_splicing_patterns_from_AS_events_4.pl line 18. awk: cmd. line:1: fatal: cannot open file Valid_total_A3SS_event.txt' for reading (No such file or directory)
can't open input2 file: No such file or directory at /lab/app/JUM/JUM_170323/JUM_1.3.1/profiling_splicing_patterns_from_AS_events_4.pl line 18.
can't open input2 file: No such file or directory at /lab/app/JUM/JUM_170323/JUM_1.3.1/profiling_splicing_patterns_from_AS_events_5.pl line 18.
can't open input2 file: No such file or directory at /lab/app/JUM/JUM_170323/JUM_1.3.1/profiling_splicing_patterns_from_AS_events_5.pl line 18.
can't open input2 file: No such file or directory at /lab/app/JUM/JUM_170323/JUM_1.3.1/profiling_splicing_patterns_from_AS_events_5.pl line 18.
can't open input2 file: No such file or directory at /lab/app/JUM/JUM_170323/JUM_1.3.1/profiling_splicing_patterns_from_AS_events_6.pl line 20.
mkdir: cannot create directory FINAL_JUM_OUTPUT': File exists mv: cannot stat AS_differential_JUM_output_intron_retention_adjusted_pvalue_0.05.txt': No such file or directory
mv: cannot stat `*coordinate.bed': No such file or directory

The length of the RNA-seq reads is inconsistent

Hi,
i need to give a Readlength when running JUM_A.sh,but the length in my data is inconsistent.
what shou i do with that

Correcting for batch effects while running JUM

Running JUM v2.02, the example design file given in the manual contains only the experimental condition:

      condition
ctrl1 control
ctrl2 control
ctrl3 control
treat1 treatment
treat2 treatment
treat3 treatment

Is it possible to include batch effects (e.g. sequencing batch) in the experimental design for JUM? Would this be as simple as adding another column to the design matrix or more complex?

Thank you for the help!

Purl programs not found in bin folder

When running JUM_2-1.sh with the directory structure as provided upon installation the program throws a 'file not found' error. Transferring the purl files to the JUM main folder corrects the issue.

Can JUM be run on a single bam file ( only one treatment bam or only one control bam)

Hi,

Can JUM be run on a single bam file ( only one treatment bam or only one control bam)? What if I just want to get the gene corresponding splicing event and psi value? Thank you.

Adding threads to JUM_2-3.sh job submission

Hi,

Thank you so much for this great tool and the very intuitive instructions on how to use it. I'm on the JUM_2-3.sh running step and it's taking over 8 hours to run. I was wondering if there is any way to add threads to the JUM_2-3.sh step?

Thank you,
Bina

filtering outputs from cutoff p-value=1

I have run JUM twice on the same dataset, once with an adjusted p-value cutoff = 1 and once with an adjusted p-value cutoff = 0.05. I got the simplified and detailed results from both runs.

However, I find that I cannot reproduce the results from the padj=0.05 run simply by thresholding the padj=1 run.

For example, when I look at the AS_differential_JUM_output_intron_retention_adjusted_pvalue_1_final_simplified.txt output and threshold it by qvalue < .05, this returns 18 significant events that have q-value < .05. However, when I look at the AS_differential_JUM_output_intron_retention_adjusted_pvalue_0.05_final_simplified.txt output, it contains only 3 events, not 18.

Is this expected behavior?

Run time for JUM_B.sh

Hello!

I'm very interested in seeing what kind of data comes out of this novel analysis. I've encountered an issue with running the JUM_B.sh step where it appears to be taking an exceptional amount of time (>12 hrs). Is this normal or is the code I'm running (below) incomplete? The hardware I'm running it on is designated for running bioinformatic analysis, so that shouldn't be the issue.

#Template
bash /user/home/JUM_2.0.2/JUM_B.sh --Folder /user/home/JUM_2.0.2/JUM_diff --Test pvalue --Cutoff 0.05 --TotalFileNum 6 --Condition1_fileNum_threshold 2 --Condition2_fileNum_threshold 2 --Condition1SampleName ctrl1,ctrl2,ctrl3 --Condition2SampleName treat1,treat2,treat3

Much obliged,
Andrew

regarding input files

Hi Qingqing,
When I run STAR with the options you have specified here "https://github.com/qqwang-berkeley/JUM/wiki/0.b.-Input-files" , it does not create the Log.final.out. Can I ignore that, since it is just a log file?
Also, regarding 2nd pass mapping the option you have specified is as follows
STAR --runThreadN 3
--genomeDir genome_index_STAR_r1
--outFileNamePrefix ctrl_1
--readFilesIn ctrl_1_R01.fastq ctrl_1_R02.fastq
--outSJfilterReads Unique \
--outSAMstrandField intronMotif
--outFilterMultimapNmax 1
-sjdbFileChrStartEnd 1st_SJ/ctrl_1SJ.out.tab 1st_SJ/ctrl_2SJ.out.tab 1st_SJ/ctrl_3SJ.out.tab
1st_SJ/treat_1SJ.out.tab 1st_SJ/treat_2SJ.out.tab 1st_SJ/treat_3SJ.out.tab

My question is regarding the order of input files to be specified with --readFilesIn switch. I presume I specify it in the order the *SJ.out.tab are given. Or do I specify the fastq files for only ctrl_1, since the outFileNamePrefix is ctrl_1. I would appreciate if you could clarify this for me.
Thanks ../Murli

error occurred when running JUM_B.sh

Hi, I got errors when running JUM_B.sh

what I ran:

cd ~/projects/AS/analysis/paper_gb/
sim_1//JUM/JUM_diff/ && bash ~/bin/JUM-JUMv2.0.2_short_user_argument_BSD//JUM_B.sh --Folder ~/bin/JUM-JUMv2.0.2_short
_user_argument_BSD/ --Test adjusted_pvalue --Cutoff 0.05 --TotalFileNum 8 --Condition1_fileNum_threshold 3 --Conditio
n2_fileNum_threshold 3 --Condition1SampleName s1 --Condition2SampleName s2

the error:

ERROR: Sort order was unspecified, and file sample7Aligned.out_coverage_sorted.bed is not sorted lexicographically.
       Please rerun with the -g option for a genome file.
       See documentation for details.
ERROR: Sort order was unspecified, and file sample8Aligned.out_coverage_sorted.bed is not sorted lexicographically.
       Please rerun with the -g option for a genome file.
       See documentation for details.
ERROR: Sort order was unspecified, and file sample5Aligned.out_coverage_sorted.bed is not sorted lexicographically.
       Please rerun with the -g option for a genome file.
       See documentation for details.
ERROR: Sort order was unspecified, and file sample6Aligned.out_coverage_sorted.bed is not sorted lexicographically.
       Please rerun with the -g option for a genome file.
       See documentation for details.
ERROR: Sort order was unspecified, and file sample3Aligned.out_coverage_sorted.bed is not sorted lexicographically.
       Please rerun with the -g option for a genome file.
       See documentation for details.
ERROR: Sort order was unspecified, and file sample1Aligned.out_coverage_sorted.bed is not sorted lexicographically.
       Please rerun with the -g option for a genome file.
       See documentation for details.
ERROR: Sort order was unspecified, and file sample2Aligned.out_coverage_sorted.bed is not sorted lexicographically.
       Please rerun with the -g option for a genome file.
       See documentation for details.
ERROR: Sort order was unspecified, and file sample4Aligned.out_coverage_sorted.bed is not sorted lexicographically.
       Please rerun with the -g option for a genome file.
       See documentation for details.
ERROR: Sort order was unspecified, and file sample7Aligned.out_coverage_sorted.bed is not sorted lexicographically.
       Please rerun with the -g option for a genome file.
       See documentation for details.
ERROR: Sort order was unspecified, and file sample8Aligned.out_coverage_sorted.bed is not sorted lexicographically.
       Please rerun with the -g option for a genome file.
       See documentation for details.
ERROR: Sort order was unspecified, and file sample5Aligned.out_coverage_sorted.bed is not sorted lexicographically.
       Please rerun with the -g option for a genome file.
       See documentation for details.
ERROR: Sort order was unspecified, and file sample6Aligned.out_coverage_sorted.bed is not sorted lexicographically.
       Please rerun with the -g option for a genome file.
       See documentation for details.
ERROR: Sort order was unspecified, and file sample3Aligned.out_coverage_sorted.bed is not sorted lexicographically.
       Please rerun with the -g option for a genome file.
       See documentation for details.
ERROR: Sort order was unspecified, and file sample1Aligned.out_coverage_sorted.bed is not sorted lexicographically.
       Please rerun with the -g option for a genome file.
       See documentation for details.
ERROR: Sort order was unspecified, and file sample2Aligned.out_coverage_sorted.bed is not sorted lexicographically.
       Please rerun with the -g option for a genome file.
       See documentation for details.
ERROR: Sort order was unspecified, and file sample4Aligned.out_coverage_sorted.bed is not sorted lexicographically.
       Please rerun with the -g option for a genome file.
       See documentation for details.
...

The previous steps ran successfully. How can I fix this problem? Thank you very much.

Uninitialized value errors when running JUM_C.sh

Hello,

I am encountering a lot of uninitialized value errors when running JUM_C.sh and am not sure what is wrong. These include:

• in print at /DATA5/JUM/JUM_2.0.2/identify_gene_name_for_JUM_output_3.pl line 45, line 1278 on
• Lots of things in /media/nkaplin1/DATA5/JUM/JUM_2.0.2/final_process_MXE_output.pl lines 191-262, line 1
• $junctionID[10] in pattern match (m//) at /DATA5/JUM/JUM_2.0.2/identify_gene_name_for_JUM_output_1.pl line 50, line 428/435
• in string eq at /DATA5/JUM/JUM_2.0.2/identify_gene_name_for_JUM_output_1.pl line 53, line 428/435
• in print at /DATA5/JUM/JUM_2.0.2/identify_gene_name_for_JUM_output_2.pl line 60
• in print at /DATA5/JUM/JUM_2.0.2/identify_gene_name_for_JUM_output_3.pl line 45, line 2 on

I am trying to use JUM to identify IR events. More than half of the identified IR events have gene="NONE" or even nothing (empty string?) in the final IR output. This behavior is not exactly expected because IR events should occur within genes, and some of these locations do map onto genes when inspected. I am guessing that these issues might be related to each other?

I tried to follow all the directions in the manual for v2.0.2 and ran the scripts as in the examples provided. I did not encounter any errors until this step, and I believe my refFlat file matches the format specifications. Would you be able to help me troubleshoot this please?

Thank you very much in advance!

Recommendations for sequencing depth

Hi, do you have recommendations for the number of aligned reads to genes? Is it possible to make JUM work with < 20M aligned reads mapping to mRNA/sample?

Also, do you recommend Poly-A or ribodepletion libraries for analysis with JUM?

Error when running JUM_A.sh

Hi，
The error is reported as follows
can't open input2 file: No such file or directory at /***/JUM_3.0.0/preparing_intron_retention_count_table_long_intron.pl line 20.
I can make sure this file exists. And what can I do to fix this issue? And this step is so time consuming that it is frustrating to run it for two days with an error.

adding covariates

Hi, this package looks like fun. I have 3 datasets where the same biological condition is compared to a set of controls. I was hoping to analyse the 3 datasets jointly adding a covariate for dataset. Is it possible to pass this to DEXSeq via the support file? So with DEXSeq I'd fit:

formulaFullModel = ~ sample + exon + dataset:exon + condition:exon
formulaReducedModel = ~ sample + exon + dataset:exon

What do you suggest?

perl errors while running JUM_B

Hi,

When executing the JUM_B.sh script, I kept getting the following errors

(base) dzijlmans@cn45:/scratch/dzijlmans/DZ046/JUM_single/Ctrl_vs_dTAG_4h/JUM_diff$ bash /scratch/dzijlmans/DZ046/JUM_single/JUM_2.0.2/JUM_B.sh --Folder /scratch/dzijlmans/DZ046/JUM_single/JUM_2.0.2 --Test pvalue --Cutoff 0.05 --TotalFileNum 8 --Condition1_fileNum_threshold 3 --Condition2_fileNum_threshold 3 --Condition1SampleName Ctrl_rep1,Ctrl_rep2,Ctrl_rep3,Ctrl_rep4 --Condition2SampleName dTAG_4h_rep1,dTAG_4h_rep2,dTAG_4h_rep3,dTAG_4h_rep4
Can't locate Statistics/Descriptive.pm in @INC (you may need to install the Statistics::Descriptive module) (@INC contains: /vol/mbconda/dzijlmans/lib/perl5/5.32/site_perl /vol/mbconda/dzijlmans/lib/perl5/site_perl /vol/mbconda/dzijlmans/lib/perl5/5.32/vendor_perl /vol/mbconda/dzijlmans/lib/perl5/vendor_perl /vol/mbconda/dzijlmans/lib/perl5/5.32/core_perl /vol/mbconda/dzijlmans/lib/perl5/core_perl .) at /scratch/dzijlmans/DZ046/JUM_single/JUM_2.0.2/determining_rightful_long_intron_retention_event_updated.pl line 4.
BEGIN failed--compilation aborted at /scratch/dzijlmans/DZ046/JUM_single/JUM_2.0.2/determining_rightful_long_intron_retention_event_updated.pl line 4.
awk: fatal: cannot open file `dTAG_4h_rep2_long_intron_retention_screening_pvalue_0.05.txt' for reading (No such file or directory)
Can't locate Statistics/Descriptive.pm in @INC (you may need to install the Statistics::Descriptive module) (@INC contains: /vol/mbconda/dzijlmans/lib/perl5/5.32/site_perl /vol/mbconda/dzijlmans/lib/perl5/site_perl /vol/mbconda/dzijlmans/lib/perl5/5.32/vendor_perl /vol/mbconda/dzijlmans/lib/perl5/vendor_perl /vol/mbconda/dzijlmans/lib/perl5/5.32/core_perl /vol/mbconda/dzijlmans/lib/perl5/core_perl .) at /scratch/dzijlmans/DZ046/JUM_single/JUM_2.0.2/determining_rightful_long_intron_retention_event_updated.pl line 4.
BEGIN failed--compilation aborted at /scratch/dzijlmans/DZ046/JUM_single/JUM_2.0.2/determining_rightful_long_intron_retention_event_updated.pl line 4.
awk: fatal: cannot open file `Ctrl_rep3_long_intron_retention_screening_pvalue_0.05.txt' for reading (No such file or directory)
Can't locate Statistics/Descriptive.pm in @INC (you may need to install the Statistics::Descriptive module) (@INC contains: /vol/mbconda/dzijlmans/lib/perl5/5.32/site_perl /vol/mbconda/dzijlmans/lib/perl5/site_perl /vol/mbconda/dzijlmans/lib/perl5/5.32/vendor_perl /vol/mbconda/dzijlmans/lib/perl5/vendor_perl /vol/mbconda/dzijlmans/lib/perl5/5.32/core_perl /vol/mbconda/dzijlmans/lib/perl5/core_perl .) at /scratch/dzijlmans/DZ046/JUM_single/JUM_2.0.2/determining_rightful_long_intron_retention_event_updated.pl line 4.
BEGIN failed--compilation aborted at /scratch/dzijlmans/DZ046/JUM_single/JUM_2.0.2/determining_rightful_long_intron_retention_event_updated.pl line 4.
awk: fatal: cannot open file `dTAG_4h_rep3_long_intron_retention_screening_pvalue_0.05.txt' for reading (No such file or directory)
Can't locate Statistics/Descriptive.pm in @INC (you may need to install the Statistics::Descriptive module) (@INC contains: /vol/mbconda/dzijlmans/lib/perl5/5.32/site_perl /vol/mbconda/dzijlmans/lib/perl5/site_perl /vol/mbconda/dzijlmans/lib/perl5/5.32/vendor_perl /vol/mbconda/dzijlmans/lib/perl5/vendor_perl /vol/mbconda/dzijlmans/lib/perl5/5.32/core_perl /vol/mbconda/dzijlmans/lib/perl5/core_perl .) at /scratch/dzijlmans/DZ046/JUM_single/JUM_2.0.2/determining_rightful_long_intron_retention_event_updated.pl line 4.
BEGIN failed--compilation aborted at /scratch/dzijlmans/DZ046/JUM_single/JUM_2.0.2/determining_rightful_long_intron_retention_event_updated.pl line 4.
awk: fatal: cannot open file `Ctrl_rep1_long_intron_retention_screening_pvalue_0.05.txt' for reading (No such file or directory)
Can't locate Statistics/Descriptive.pm in @INC (you may need to install the Statistics::Descriptive module) (@INC contains: /vol/mbconda/dzijlmans/lib/perl5/5.32/site_perl /vol/mbconda/dzijlmans/lib/perl5/site_perl /vol/mbconda/dzijlmans/lib/perl5/5.32/vendor_perl /vol/mbconda/dzijlmans/lib/perl5/vendor_perl /vol/mbconda/dzijlmans/lib/perl5/5.32/core_perl /vol/mbconda/dzijlmans/lib/perl5/core_perl .) at /scratch/dzijlmans/DZ046/JUM_single/JUM_2.0.2/determining_rightful_long_intron_retention_event_updated.pl line 4.
BEGIN failed--compilation aborted at /scratch/dzijlmans/DZ046/JUM_single/JUM_2.0.2/determining_rightful_long_intron_retention_event_updated.pl line 4.
awk: fatal: cannot open file `Ctrl_rep4_long_intron_retention_screening_pvalue_0.05.txt' for reading (No such file or directory)
Can't locate Statistics/Descriptive.pm in @INC (you may need to install the Statistics::Descriptive module) (@INC contains: /vol/mbconda/dzijlmans/lib/perl5/5.32/site_perl /vol/mbconda/dzijlmans/lib/perl5/site_perl /vol/mbconda/dzijlmans/lib/perl5/5.32/vendor_perl /vol/mbconda/dzijlmans/lib/perl5/vendor_perl /vol/mbconda/dzijlmans/lib/perl5/5.32/core_perl /vol/mbconda/dzijlmans/lib/perl5/core_perl .) at /scratch/dzijlmans/DZ046/JUM_single/JUM_2.0.2/determining_rightful_long_intron_retention_event_updated.pl line 4.
BEGIN failed--compilation aborted at /scratch/dzijlmans/DZ046/JUM_single/JUM_2.0.2/determining_rightful_long_intron_retention_event_updated.pl line 4.

and so on, similar to #7. While the script completed running, the output files were mostly empty, containing only headers and no AS sites.

It turned out the Statistics::Descriptive and Array::Utils modules were not installed and I had to install them manually using

mamba install perl-app-cpanminus cpanm Statistics::Descriptive cpanm Array::Utils

After installing these modules, the script ran with no further issues and generated output files containing AS events
Would it be possible for you to add the installation of these packages to the JUM_C script for future users?

Best,
Dick

JUM output Splicing events Visualization tools

Hi all,

greetings.

I was working on mRNA Splicing event analysis. I was using the JUM tool for mRNA splicing which gives 6 categories of splice patterns

for Visualizing these splice events I was looking for tools, came across IGV, LeafViz.

LeafViz is a Shiny app that is more interactive needs more scripting the inputs. moreover, LeafViz is part of Leafcutter it didn't accept other format files. I have started using LeafViz for JUM output files and I have troubleshooting errors that I encountered.

if anyone please let us know if it's possible to use JUM output files in Leafviz for the Visualization of splicing events or else please mention tools that are most useful for Visualization of Splice events.

Hope to hear good suggestions.

Thank you

Error running R_script_JUM.R

I am trying to run through the JUM pipeline comparing aligned sequencing data from 2 conditions each with 4 replicates.

I got as far as running R_script_JUM.R but then I encountered a problem. The error message was:

Error in .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges") :
solving row 3717: range cannot be determined from the supplied arguments (too many NAs)

Looking into it a bit further it seems the error is caused by some rows in the combined_AS_JUM.gff file not having both start and end genomic coordinates. Do you have any suggestions as I can't work out where the issue is coming from? Thanks.

can --Condition1_fileNum_threshold and --Condition2_fileNum_threshold be unequal?

Can --Condition1_fileNum_threshold and --Condition2_fileNum_threshold be unequal? I mean maybe we have 3 disease samples and 2 normal samples, or 20 disease samples and 40 normal samples (all the samples have no replicate).

Tons of stderr output; problem with preparing_intron_retention_count_table_short_intron.pl

Hi there! I'm excited to use your tool and am testing it out.

With some test files, I'm getting about 4,000,000 lines of stderr output like this:

Use of uninitialized value $readlength in numeric lt (<) at /home/JUM_2.0.2/profile_overhang_from_STAR_output_step_1.pl line 39, <IN1> line 1.
Use of uninitialized value $readlength in subtraction (-) at /home/JUM_2.0.2/profile_overhang_from_STAR_output_step_1.pl line 43, <IN1> line 1.
Use of uninitialized value $readlength in numeric lt (<) at /home/JUM_2.0.2/profile_overhang_from_STAR_output_step_1.pl line 45, <IN1> line 1.
Use of uninitialized value $readlength in subtraction (-) at /home/JUM_2.0.2/profile_overhang_from_STAR_output_step_1.pl line 49, <IN1> line 1.
Use of uninitialized value $readlength in numeric lt (<) at /home/JUM_2.0.2/profile_overhang_from_STAR_output_step_1.pl line 39, <IN1> line 2.
Use of uninitialized value $readlength in subtraction (-) at /home/JUM_2.0.2/profile_overhang_from_STAR_output_step_1.pl line 43, <IN1> line 2.
Use of uninitialized value $readlength in numeric lt (<) at /home/JUM_2.0.2/profile_overhang_from_STAR_output_step_1.pl line 45, <IN1> line 2.
Use of uninitialized value $readlength in subtraction (-) at /home/JUM_2.0.2/profile_overhang_from_STAR_output_step_1.pl line 49, <IN1> line 2.
Use of uninitialized value $readlength in numeric lt (<) at /home/JUM_2.0.2/profile_overhang_from_STAR_output_step_1.pl line 39, <IN1> line 3.
Use of uninitialized value $readlength in subtraction (-) at /home/JUM_2.0.2/profile_overhang_from_STAR_output_step_1.pl line 43, <IN1> line 3.
Use of uninitialized value $readlength in numeric lt (<) at /home/JUM_2.0.2/profile_overhang_from_STAR_output_step_1.pl line 45, <IN1> line 3.
Use of uninitialized value $readlength in subtraction (-) at /home/JUM_2.0.2/profile_overhang_from_STAR_output_step_1.pl line 49, <IN1> line 3.

and this:

Use of uninitialized value $threshold in numeric ge (>=) at /home/JUM_2.0.2/preparing_intron_retention_count_table_long_intron.pl line 73.
Use of uninitialized value $threshold in numeric ge (>=) at /home/JUM_2.0.2/preparing_intron_retention_count_table_long_intron.pl line 73.
Use of uninitialized value $threshold in numeric ge (>=) at /home/JUM_2.0.2/preparing_intron_retention_count_table_long_intron.pl line 73.
Use of uninitialized value $threshold in numeric ge (>=) at /home/JUM_2.0.2/preparing_intron_retention_count_table_long_intron.pl line 73.
Use of uninitialized value $threshold in numeric ge (>=) at /home/JUM_2.0.2/preparing_intron_retention_count_table_long_intron.pl line 73.
Use of uninitialized value $threshold in numeric ge (>=) at /home/JUM_2.0.2/preparing_intron_retention_count_table_long_intron.pl line 73.
Use of uninitialized value $threshold in numeric ge (>=) at 

and then it fails with:

can't open input1 file: No such file or directory at /home/JUM_2.0.2/preparing_intron_retention_count_table_short_intron.pl line 18.

Any help would be appreciated. Thanks!