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ylab-hi / ScanExitron

A computational workflow for exitron splicing identification
MIT License
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Error happened!: Command 'regtools junctions extract -i 5 -I 10000000 tests/test.bam -o test.bed' returned non-zero exit status 1. #1

Closed ptnaimelmm closed 3 years ago

ptnaimelmm commented 3 years ago

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. test error 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

dolittle007 commented 3 years ago

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.

ptnaimelmm commented 3 years ago

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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dolittle007 commented 3 years ago

The error message clearly showed that you were using RegTools 0.5.2. "got the same error" means you were using the same version of RegTools, even you installed a different version. You can type in the command line: regtools to check the output. Like the following information.

Program: regtools Version: 0.4.0 Usage: regtools [options] Command: junctions Tools that operate on feature junctions. (eg. exon-exon junctions from RNA-seq.) cis-ase Tools related to allele specific expression in cis. cis-splice-effects Tools related to splicing effects of variants. variants Tools that operate on variants.

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.

dolittle007 commented 3 years ago

I've made a small modification to ScanExitron, it can work with RegTools v0.5.0 now. Thank you.

ptnaimelmm commented 3 years ago

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.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/ylab-hi/ScanExitron/issues/1#issuecomment-824355307, or unsubscribe https://github.com/notifications/unsubscribe-auth/AHIUFGAYTIETSZC2KF6VILLTJ44NPANCNFSM43INLI4Q .

dolittle007 commented 3 years ago

I have updated the README. I've tested it. It works fine on RegTools v0.4.2.

ptnaimelmm commented 3 years ago

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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dolittle007 commented 3 years ago

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).

ptnaimelmm commented 3 years ago

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).

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/ylab-hi/ScanExitron/issues/1#issuecomment-825173984, or unsubscribe https://github.com/notifications/unsubscribe-auth/AHIUFGFQCRMYZARHQ7AHR5LTKCDMPANCNFSM43INLI4Q .

ptnaimelmm commented 3 years ago

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).

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/ylab-hi/ScanExitron/issues/1#issuecomment-825173984, or unsubscribe https://github.com/notifications/unsubscribe-auth/AHIUFGFQCRMYZARHQ7AHR5LTKCDMPANCNFSM43INLI4Q .

dolittle007 commented 3 years ago

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

ptnaimelmm commented 3 years ago

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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fuhao1216 commented 3 years ago

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. test error 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?

dolittle007 commented 3 years ago

@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.

dolittle007 commented 3 years ago

@ptnaimelmm GTF2BED will add additional "zero_length_insertion" tag to BED file. ScanExitron can handle it correctly, after a small modification.

ptnaimelmm commented 3 years ago

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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ptnaimelmm commented 3 years ago

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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dolittle007 commented 3 years ago

@ptnaimelmm, Researchers can do a lot of downstream analysis using the identified exitrons based on their projects. The output files are tab-delimited text files, you can achieve your goal using R or Python or any programing language.

dolittle007 commented 3 years ago

The problems have been solved.