irmode = 0, report no results

[mhjiang97]

Hi, I'm here again.

I tried to build docker image using the dockerfile you mentioned, but I failed. I modified the dockerfile by myself:

# COPY environment.yml /
# RUN conda env create -f /environment.yml && conda clean -a
RUN mkdir -p /project /nl /mnt /share
RUN conda config --add channels bioconda
RUN echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc
RUN conda create -n dolphinnext-PSI-Sigma-2.0
#RUN source activate dolphinnext-PSI-Sigma-2.0
RUN conda install samtools==1.3.1 -n dolphinnext-PSI-Sigma-2.0
ENV PATH /opt/conda/envs/dolphinnext-PSI-Sigma-2.0/bin:$PATH

After the image was built, I completely followed your quick start (the same mapping parameter, the same sorted gtf file). (after sorting, transcript terms are behind exon terms belonging to the same gene.) However, irmode seems the algorithm can't handle the whole genome (doing chr1 and exited unfavorably):

Getting intron reads....
Checking sample8.Aligned.sortedByCoord.out.bam...
Checking sample8.IR.out.tab...
Generating .IR.out for sample8
Processing sample8.Aligned.sortedByCoord.out.bam...
read format = paired-end
Doing... chr1
Checking sample3.Aligned.sortedByCoord.out.bam...
Checking sample3.IR.out.tab...
Generating .IR.out for sample3
Processing sample3.Aligned.sortedByCoord.out.bam...
read format = paired-end
mkdir: cannot create directory ‘_wososatmp’: File exists
Doing... chr1
Checking sample2.Aligned.sortedByCoord.out.bam...
Checking sample2.IR.out.tab...
Generating .IR.out for sample2
Processing sample2.Aligned.sortedByCoord.out.bam...
read format = paired-end
mkdir: cannot create directory ‘_wososatmp’: File exists
Doing... chr1
Checking sample7.Aligned.sortedByCoord.out.bam...
Checking sample7.IR.out.tab...
Generating .IR.out for sample7
Processing sample7.Aligned.sortedByCoord.out.bam...
read format = paired-end
mkdir: cannot create directory ‘_wososatmp’: File exists
Doing... chr1
Checking sample1.Aligned.sortedByCoord.out.bam...
Checking sample1.IR.out.tab...
Generating .IR.out for sample1
Processing sample1.Aligned.sortedByCoord.out.bam...
read format = paired-end
mkdir: cannot create directory ‘_wososatmp’: File exists
Doing... chr1
Checking sample4.Aligned.sortedByCoord.out.bam...
Checking sample4.IR.out.tab...
Generating .IR.out for sample4
Processing sample4.Aligned.sortedByCoord.out.bam...
read format = paired-end
mkdir: cannot create directory ‘_wososatmp’: File exists
Doing... chr1
Checking sample6.Aligned.sortedByCoord.out.bam...
Checking sample6.IR.out.tab...
Generating .IR.out for sample6
Processing sample6.Aligned.sortedByCoord.out.bam...
read format = paired-end
mkdir: cannot create directory ‘_wososatmp’: File exists
Doing... chr1
Checking sample5.Aligned.sortedByCoord.out.bam...
Checking sample5.IR.out.tab...
Generating .IR.out for sample5
Processing sample5.Aligned.sortedByCoord.out.bam...
read format = paired-end
mkdir: cannot create directory ‘_wososatmp’: File exists
Doing... chr1

I'm so confused. I can only run PSI-Sigma with irmode=2

[wososa]

Hi @mhjiang97,

Sorry about making you confused. It looks like that PSI-Sigma wasn't able to generate IR.out.tab files. This error is likely to be due to samtools or chromosome name. Could you please try this:

perl ~/PSI-Sigma-1.9k/PSIsigma-ir-v.1.2.pl PSIsigma1d9k.db sample1.Aligned.sortedByCoord.out.bam 1

The PSIsigma1d9k.db is the .db file that PSI-Sigma generated. You can find more details here: https://github.com/wososa/PSI-Sigma/blob/master/Parallele.md. You should see error messages when you run this.

Thanks, Woody

[mhjiang97]

Thank you very much for your kind reply. On my MacBook, I ran perl /usr/local/bin/PSI-Sigma-1.9k/PSIsigma-ir-v.1.2.pl s1_s2.db sample1.Aligned.sortedByCoord.out.bam 1 through docker, and the output and error is:

Processing sample1.Aligned.sortedByCoord.out.bam...
read format = paired-end
Doing... chr1
Killed

[wososa]

Hi @mhjiang97 , The Killed message suggests that your MacBook might have ran out of memory (RAM). Woody

[mhjiang97]

I can run PSI-Sigma successfully now! Thanks again!

[wososa]

hi @mhjiang97 ,

Great~! Let me know if you encounter more issues.

Woody