Closed acesnik closed 4 years ago
In terms of setup, I did two-pass alignment with STAR, sorted the BAM files, converted them to SAM files to have those around, and changed the names of the files to follow your naming conventions.
Hi Anthony,
Could you provide me the commands you used, and also, the results of running "ls -l -t" from the directory where you ran JUM?
Thanks,
Qingqing
On Tue, Aug 13, 2019 at 1:12 PM Anthony notifications@github.com wrote:
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,
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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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!
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/home/tools/JUM_2.0.2/JUM_A.sh --Folder /home/tools/JUM_2.0.2 --JuncThreshold 5 --Condition1SampleName G1_1.,G1_2.,G1_3. --Condition1_fileNum_threshold 2 --Condition2SampleName S_1.,S_2.,S_3. --Condition2_fileNum_threshold 2 --Thread 2
I'm attaching the listed files here: lslt.txt
Thanks!
I used samtools view -h /home/output/JUM_Analysis/G1_1.Aligned.out_sorted.bam > /home/output/JUM_Analysis/G1_1.Aligned.out.sam
and such to get the SAM files for the tool. I output sorted BAMs by default from STAR, so I had to convert them.
From the command it looks like you did not specify a couple specific parameters:
Your original command /home/tools/JUM_2.0.2/JUM_A.sh --Folder /home/tools/JUM_2.0.2 --JuncThreshold 5 --Condition1SampleName G1_1.,G1_2.,G1_3. --Condition1_fileNum_threshold 2 --Condition2SampleName S_1.,S_2.,S_3. --Thread 2
should be: /home/tools/JUM_2.0.2/JUM_A.sh --Folder /home/tools/JUM_2.0.2 --JuncThreshold 5 --Condition1_fileNum_threshold X --Condition2_fileNum_threshold X --IRthreshold X --Readlength X --Thread 2 --Condition1SampleName G1_1.,G1_2.,G1_3. --Condition1_fileNum_threshold 2 --Condition2SampleName S_1.,S_2.,S_3.
X will a user chosen number.
On Wed, Aug 21, 2019 at 6:37 PM Anthony notifications@github.com wrote:
/home/tools/JUM_2.0.2/JUM_A.sh --Folder /home/tools/JUM_2.0.2 --JuncThreshold 5 --Condition1SampleName G1_1.,G1_2.,G1_3. --Condition1_fileNum_threshold 2 --Condition2SampleName S_1.,S_2.,S_3. --Thread 2
I'm attaching the listed files here: lslt.txt https://github.com/qqwang-berkeley/JUM/files/3527606/lslt.txt
Thanks!
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Okay, that fixed this issue. I think the main thing that was missing from my command was IRthreshold.
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:
and this:
and then it fails with:
Any help would be appreciated. Thanks!