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deweylab / RSEM

RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
http://deweylab.biostat.wisc.edu/rsem/
GNU General Public License v3.0
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rsem-simulate-reads in RSEM 1.3.3 #145

Open mhjiang97 opened 3 years ago

mhjiang97 commented 3 years ago

I followed the documentation and used a model file generated by rsem-calculate-expression from a pair-end fastq data. but rsem-simulate-reads function can't output pair-end fq files but always a .fa file. I switched the model file, and used a random path. rsem-simulate-reads still worked and generated .fa file all the time.

There maybe a bug that the rsem-simulate-reads function disregards the model file in RSEM version 1.3.3.

what I did:

rsem-calculate-expression --paired-end \
--alignments \
--no-bam-output \
-p 50 \
/path/to/mybam \
/path/to/reference \
/output/prefix \

rsem-simulate-reads /path/to/reference \
/output/prefix/prefix.stat/prefix.model \
isoforms.results 0.1 50000000 \
simulation_out_put
mhjiang97 commented 3 years ago

I'm sure its a bug in version 1.3.3: rsem-simulate-reads function discards the model file always, and generates .fa files every time. I installed rsem 1.3.3 through conda.

bli25 commented 3 years ago

Hi Minghao,

Can you send me a minimal set of files to trigger this bug? I'll take a look.

Thanks, Bo

Bo Li, Ph.D. Assistant Professor of Medicine, Harvard Medical School Director, Bioinformatics and Computational Biology Program, Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital Associate Member, Broad Institute of MIT & Harvard 149 13th Street, Room 8214, Charlestown, MA 02129

On Sat, Sep 12, 2020 at 2:12 AM Minghao Jiang notifications@github.com wrote:

I'm sure its a bug in version 1.3.3: rsem-simulate-reads function discards the model file always, and generates .fa files every time. I installed rsem 1.3.3 through conda.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/deweylab/RSEM/issues/145#issuecomment-691422147, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACPHRF3LEPSXPXDQW55XLELSFMGMDANCNFSM4RFAA62Q .

mhjiang97 commented 3 years ago

Hi Bo Li,

My operating system: CentOS Linux release 7.7.1908 (Core) Python version: 2.7.18 RSEM version: 1.3.3

I tried to install RSEM on my own Mac, and the simulation process with the model file ran as expected. But on the server, RSEM 1.3.3 installed through conda seems to skip model files and generate .fa files every time.

What’s more, I git clone RSEM 1.3.3, and ran rsem-simulate-reads without compiling RSEM. It generated 2 .fq files as expected.

Thank you very much, Minghao Jiang

At 2020-09-13 03:44:53, "Bo Li" notifications@github.com wrote:

Hi Minghao,

Can you send me a minimal set of files to trigger this bug? I'll take a look.

Thanks, Bo

Bo Li, Ph.D. Assistant Professor of Medicine, Harvard Medical School Director, Bioinformatics and Computational Biology Program, Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital Associate Member, Broad Institute of MIT & Harvard 149 13th Street, Room 8214, Charlestown, MA 02129

On Sat, Sep 12, 2020 at 2:12 AM Minghao Jiang notifications@github.com wrote:

I'm sure its a bug in version 1.3.3: rsem-simulate-reads function discards the model file always, and generates .fa files every time. I installed rsem 1.3.3 through conda.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/deweylab/RSEM/issues/145#issuecomment-691422147, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACPHRF3LEPSXPXDQW55XLELSFMGMDANCNFSM4RFAA62Q .

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe.

bli25 commented 3 years ago

Hi Minghao,

It seems to be a bioconda issue. Maybe you should ask the Bioconda people instead?

Best, Bo

Bo Li, Ph.D. Assistant Professor of Medicine, Harvard Medical School Director, Bioinformatics and Computational Biology Program, Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital Associate Member, Broad Institute of MIT & Harvard 149 13th Street, Room 8214, Charlestown, MA 02129

On Mon, Sep 14, 2020 at 2:52 AM Minghao Jiang notifications@github.com wrote:

Hi Bo Li,

My operating system: CentOS Linux release 7.7.1908 (Core) Python version: 2.7.18 RSEM version: 1.3.3

I tried to install RSEM on my own Mac, and the simulation process with the model file ran as expected. But on the server, RSEM 1.3.3 installed through conda seems to skip model files and generate .fa files every time.

What’s more, I git clone RSEM 1.3.3, and ran rsem-simulate-reads without compiling RSEM. It generated 2 .fq files as expected.

Thank you very much, Minghao Jiang

At 2020-09-13 03:44:53, "Bo Li" notifications@github.com wrote:

Hi Minghao,

Can you send me a minimal set of files to trigger this bug? I'll take a look.

Thanks, Bo

Bo Li, Ph.D. Assistant Professor of Medicine, Harvard Medical School Director, Bioinformatics and Computational Biology Program, Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital Associate Member, Broad Institute of MIT & Harvard 149 13th Street, Room 8214, Charlestown, MA 02129

On Sat, Sep 12, 2020 at 2:12 AM Minghao Jiang notifications@github.com wrote:

I'm sure its a bug in version 1.3.3: rsem-simulate-reads function discards the model file always, and generates .fa files every time. I installed rsem 1.3.3 through conda.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/deweylab/RSEM/issues/145#issuecomment-691422147, or unsubscribe < https://github.com/notifications/unsubscribe-auth/ACPHRF3LEPSXPXDQW55XLELSFMGMDANCNFSM4RFAA62Q

.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/deweylab/RSEM/issues/145#issuecomment-691854991, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACPHRF6YSZ25I6QFOGCB4I3SFW4TXANCNFSM4RFAA62Q .

MikeWLloyd commented 2 years ago

I am having this exact same issue. The latest bioconda image dumps the model file, and returns only *.fa. Any chance of resolution on the issue?

mhjiang97 commented 2 years ago

I am having this exact same issue. The latest bioconda image dumps the model file, and returns only *.fa. Any chance of resolution on the issue?

I gave up the bioconda RSEM. My advice: just clone the RSEM (1.3.3), and install it manually.