Closed crazyhottommy closed 7 years ago
I fooled pRSEM by using the same ChIP-seq target fastq twice (same name), the above error disappeared, but some new error occurred. what's the name convention for the fastq? H3K27ac-rep1.fastq, H3K27ac-rep2.fastq? seems pRSEM is parsing the fastq names.
update: pRSEM errored at the phantompeakqual step.
# reads with alignments suppressed due to -m: 7411281 (14.13%)
Reported 42273553 alignments to 1 output stream(s)
# reads processed: 52467512
# reads with at least one reported alignment: 42273553 (80.57%)
# reads that failed to align: 2782678 (5.30%)
# reads with alignments suppressed due to -m: 7411281 (14.13%)
Reported 42273553 alignments to 1 output stream(s)
# reads processed: 121283189
# reads with at least one reported alignment: 79412215 (65.48%)
# reads that failed to align: 16999116 (14.02%)
# reads with alignments suppressed due to -m: 24871858 (20.51%)
Reported 79412215 alignments to 1 output stream(s)
Loading required package: caTools
Loading required package: caTools
Loading required package: caTools
Error: protect(): protection stack overflow
Execution halted
Error: protect(): protection stack overflow
Execution halted
Failed with return code 1
Error: protect(): protection stack overflow
Execution halted
Error: protect(): protection stack overflow
Execution halted
Failed with return code 1
Error: protect(): protection stack overflow
Execution halted
Error: protect(): protection stack overflow
Execution halted
Failed with return code 1
File not found: Hs_940_pRSEM.temp/M940_Crep1.tagAlign_VS_control.tagAlign.regionPeak.gz
any help here for Error: protect(): protection stack overflow? I googled and found http://stackoverflow.com/questions/28728774/how-to-set-max-ppsize-in-r how to solve it in pRSEM?
THanks!
Hi @crazyhottommy
Thanks for your interest in using pRSEM. Could you please send me a mocked version of the ChIP-seq FASTQ files your are using so that I can replicate the error on my end? Thanks.
Best, Peng
Hi, please find the download links, thanks! IP: https://drive.google.com/open?id=0B6NrxMpU91qELTUwNjFKVkJ4SlU Input: https://drive.google.com/open?id=0B6NrxMpU91qEbEx6MGx4aGgyVG8
I do not have replicate for IP, you can just pass it twice to pRSEM, but you may need to make a different name.
Thanks! Tommy
@pliu55 please let me know if you got a chance to test. Thank you for your help.
Tommy
@crazyhottommy
I could not replicate the error at my end. Below is the command I used:
rsem-calculate-expression \
--estimate-rspd \
--seed 12345 \
--num-threads 16 \
--paired-end \
--forward-prob 0 \
--keep-intermediate-files \
--calc-pme \
--gibbs-number-of-samples 100 \
--no-bam-output \
--star \
--star-path $starpath \
--star-gzipped-read-file \
--run-pRSEM \
--partition-model pk \
--chipseq-target-read-files M940_Crep1.fq.gz,M940_Crep2.fq.gz \
--chipseq-control-read-files M-940-R1-07-G-NC.sorted.fq.gz \
--bowtie-path $bowtiepath \
mmliver_1.fq.gz mmliver_2.fq.gz $refdir/$runid $runid
where
$startpath
and $bowtiepath
are directories containing STAR and Bowtie binariesM940_Crep1.fq.gz
is from the file your provided. I un-tar and gzip it.M940_Crep2.fq.gz
is identical to M940_Crep1.fq.gz
mmliver_1.fq.gz
and mmliver_2.fq.gz
are fake RNA-seq input from pRSEM demo$refdir/$runid
is obtained from pRSEM demo as well, where you can define $runid
yourselfCould you please try the above command at your end to see if you still receive the error? And please let me know if more details are needed. Thanks.
I switched to LSF system and this error disappeared. but I had a new error, opening a new issue.
Thanks! Tommy
Hi, I was testing pRSEM, and got error below. do you know why is that?
I only provided one ChIP-seq target fastq, so the IDR is complaining?
Thanks! Tommy