rsem-simulate-reads in RSEM 1.3.3

[mhjiang97]

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]

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]

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 ***@***.***> 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 <#145 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACPHRF3LEPSXPXDQW55XLELSFMGMDANCNFSM4RFAA62Q> .

[mhjiang97]

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 ***@***.***> 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 <#145 (comment)>, 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]

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" ***@***.***> 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 ***@***.***> 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 > <#145 (comment)>, 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 <#145 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACPHRF6YSZ25I6QFOGCB4I3SFW4TXANCNFSM4RFAA62Q> .

[MikeWLloyd]

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]

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.