Error happened!: Command 'regtools junctions extract -i 5 -I 10000000 tests/test.bam -o test.bed' returned non-zero exit status 1. #1
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Please try to use RegTools v0.4.2 or a lower version. |
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Hi Carlos,
Thanks for your suggestion.
I tried to use regtools version 0.4.2 and even a lower one 0.1.0, but still
got the same error as attached. What do you think the problem is ? Would
you please share with me all the package version information? Do you have
any other suggestions? Thanks a lot.
Best regards,
Mingming
Mingming Liu, Ph.D.
Postdoctoral fellow, Dr. Jiou Wang's lab
Department of Biochemistry & Molecular Biology
Bloomberg School of Public Health
The Johns Hopkins University
…On Tue, Apr 20, 2021 at 12:11 PM Carlos D. Wang ***@***.***> wrote:
Please try to use RegTools v0.4.2 or a lower version.
It seems that RegTools v0.5 API has changed a lot, including the
parameters.
Thank you.
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The error message clearly showed that you were using RegTools 0.5.2.
You have to type "which regtools" to see which RegTools you were using. You may need to change the $PATH environment variable, as well. Thank you for your suggestions, I will update the README to emphasize that only RegTools (v0.4) works. |
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I've made a small modification to ScanExitron, it can work with RegTools v0.5.0 now. |
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Hi Carlos,
Thanks for your help. I ran this program with regtools 0.5.0, but still got
the same error as attached. Sorry for the trouble.
Best regards,
Mingming
Mingming Liu, Ph.D.
Postdoctoral fellow, Dr. Jiou Wang's lab
Department of Biochemistry & Molecular Biology
Bloomberg School of Public Health
The Johns Hopkins University
…On Wed, Apr 21, 2021 at 5:02 PM Carlos D. Wang ***@***.***> wrote:
I've made a small modification to ScanExitron, it can work with RegTools
v0.5.0 now.
Thank you.
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I have updated the README. |
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Hi Carlos,
Thanks for the update. I installed regtools-0.4.2 and ran ScanExitron
successfully with test data.
However, I got another error attached from ScanExitron.py when I ran my own
dataset. Which align software do you use to generate the input bam file?
Besides, it seems ScanExitron only accepts gencode.v19 and v21 gtf and its
CDS.bed. When I used gencode v33, it got several errors. Hope you can give
me some suggestions. Thanks.
Best regards,
Mingming
Mingming Liu, Ph.D.
Postdoctoral fellow, Dr. Jiou Wang's lab
Department of Biochemistry & Molecular Biology
Bloomberg School of Public Health
The Johns Hopkins University
…On Wed, Apr 21, 2021 at 7:20 PM Carlos D. Wang ***@***.***> wrote:
I have updated the README.
I've tested it. It works fine on RegTools v0.4.2.
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Hi, I've tested it using the latest Gencode v37 GTF and its corresponding CDS bed file. |
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Hi Carlos,
Sorry for the trouble. Could you show me all your conda package version
information? It seems something is wrong with bedtools. BTW, would you mind
running my bam file on your side if I send you one bam file? Thanks a lot.
Best regards,
Mingming
Mingming Liu, Ph.D.
Postdoctoral fellow, Dr. Jiou Wang's lab
Department of Biochemistry & Molecular Biology
Bloomberg School of Public Health
The Johns Hopkins University
…On Thu, Apr 22, 2021 at 4:47 PM Carlos D. Wang ***@***.***> wrote:
Hi, I've tested it using the latest Gencode v37 GTF and its corresponding
CDS bed file.
It works fine. The output is the same as the one in the tests folder,
except for the gene version (ENSG00000005379.17, ENSG00000005884.18).
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Hi Carlos,
I wish you had a nice weekend.
I exactly followed your updated information in README in github. I
successfully ran your test.bam in your package, but I failed at the last
part when I analyzed my own data. It said I got a valueError in
get_value_by_key m,n =k.split (delimiter). I tried to process my bam file
from both Hisat2 and STAR as that of your test.bam. Uniquely mapped reads
with MAPQ>50 were extracted from my BAM files with "samtools view -q 50 -b
chr17". I searched for a solution on the Internet, but I failed. I am a
rookie in programming, would you please give me any suggestions? Attached
are the error message and part of my bam file. Could you analyze my data
using Scanexitron when you are free? It is quite important to run
ScanExitron successfully, as we highly suspect exitrons exist in our
samples. Thanks very much in advance.
Best regards,
MIngming
SRR10316392q50chr17.rar
<https://drive.google.com/file/d/1u8R9On049w_sOdexYybal7gMq4pKL19G/view?usp=drive_web>
Mingming Liu, Ph.D.
Postdoctoral fellow, Dr. Jiou Wang's lab
Department of Biochemistry & Molecular Biology
Bloomberg School of Public Health
The Johns Hopkins University
…On Thu, Apr 22, 2021 at 4:47 PM Carlos D. Wang ***@***.***> wrote:
Hi, I've tested it using the latest Gencode v37 GTF and its corresponding
CDS bed file.
It works fine. The output is the same as the one in the tests folder,
except for the gene version (ENSG00000005379.17, ENSG00000005884.18).
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Thank you. |
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Hi Carlos,
Thanks for your help. I exactly used bedops (v2.4.38) to generate CDS.bed
files. If there was something wrong with the CDS.bed file, it is supposed I
should also get an error for test.bam in the package, but I ran it
successfully. I am not sure whether I understand it correctly or not.
Best regards,
Mingming
Mingming Liu, Ph.D.
Postdoctoral fellow, Dr. Jiou Wang's lab
Department of Biochemistry & Molecular Biology
Bloomberg School of Public Health
The Johns Hopkins University
…On Mon, Apr 26, 2021 at 5:17 PM Carlos D. Wang ***@***.***> wrote:
Thank you.
It is an issue introduced by gtf2bed.
I cannot access your attached files, but I analyzed SRR10316392 from NCBI
SRA.
SRR10316392.chr17.exitron.txt
<https://github.com/ylab-hi/ScanExitron/files/6380376/chr17.exitron.txt>
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same question ,have u solved it? |
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@fuhao1216, It seems that you used RegTools v0.5.2, If you install RegTools 0.4.2 as the README indicated the problem will disappear. |
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@ptnaimelmm GTF2BED will add additional "zero_length_insertion" tag to BED file. ScanExitron can handle it correctly, after a small modification. |
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Hi,
I installed regtools0.4.2 instead, then I can run it successfully.
Best regards,
Mingming Liu, Ph.D.
Postdoctoral fellow, Dr. Jiou Wang's lab
Department of Biochemistry & Molecular Biology
Bloomberg School of Public Health
The Johns Hopkins University
…On Fri, May 7, 2021 at 8:30 AM fuhao1216 ***@***.***> wrote:
Hi there,
An error occurred when I use ScanExitron to analyze test data in the
packages. Have you met this problem previously? Any suggestions? Thanks.
Error happened!: Command 'regtools junctions extract -i 5 -I 10000000
tests/test.bam -o test.bed' returned non-zero exit status 1.
[image: test error]
<https://user-images.githubusercontent.com/30491288/115424508-c4acee80-a1cc-11eb-8211-ed07454350a6.png>
File "ScanExitron.py", line 136, in junction_caller
cmd = 'regtools junctions annotate {0} {1} {2} -o {3}.janno'.format(bed,
fasta, gtf, out_name)
UnboundLocalError: local variable 'bed' referenced before assignment
same question ,have u solved it?
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Hi Carlos,
Thanks for your update. Have you ever tried to write a program to compare
exitron output files from two samples? Thanks.
Best regards,
Mingming
Mingming Liu, Ph.D.
Postdoctoral fellow, Dr. Jiou Wang's lab
Department of Biochemistry & Molecular Biology
Bloomberg School of Public Health
The Johns Hopkins University
…On Fri, May 7, 2021 at 11:05 AM Carlos D. Wang ***@***.***> wrote:
@ptnaimelmm <https://github.com/ptnaimelmm> GTF2BED will add additional
"zero_length_insertion" tag to BED file. ScanExitron can handle it
correctly, after a small modification.
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@ptnaimelmm, Researchers can do a lot of downstream analysis using the identified exitrons based on their projects. |
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The problems have been solved. |
Hi there,
An error occurred when I use ScanExitron to analyze test data in the packages. Have you met this problem previously? Any suggestions? Thanks.
Error happened!: Command 'regtools junctions extract -i 5 -I 10000000 tests/test.bam -o test.bed' returned non-zero exit status 1.
File "ScanExitron.py", line 136, in junction_caller
cmd = 'regtools junctions annotate {0} {1} {2} -o {3}.janno'.format(bed, fasta, gtf, out_name)
UnboundLocalError: local variable 'bed' referenced before assignment
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