LeeLee

> The problem has been solved and can be run according to this version of the software > > ``` > tophat2：tophat-2.0.12.Linux_x86_64---------------------http://ccb.jhu.edu/software/tophat/downloads/ > samtools：0.1.18.0------------------------- > bowtie：1.0.0.0--------------------------https://sourceforge.net/projects/bowtie-bio/files/bowtie/1.0.0/bowtie-1.0.0-linux-x86_64.zip/download > ``` Hi, zxclovezby...

Oh, it suddenly occurred to me that I could run the files in test_data, and I got the desired result. It seems that the software did not find circularRNA in...

> FragPipe/TMT-Integrator does not have the isotope impurity correction. We used to have it but removed because it was creating some new problems. When you have empty channels, annotate them...

The treated_array.txt file does not seem to be uploaded well, I will upload it again [treated_array.txt](https://github.com/YuLab-SMU/MicrobiotaProcess/files/11269290/treated_array.txt)

Yes, this greatly improves the speed of mp_rrarefy, but it seems to be still slow for mp_cal_rarecurve

[slurm-6804377.out.zip](https://github.com/Nesvilab/FragPipe/files/14900867/slurm-6804377.out.zip)

Not sure if this helps, but I also encountered an error when using peptideprophet ``` Exception in thread "main" java.lang.NoSuchMethodError: 'java.lang.ClassLoader ch.qos.logback.core.util.Loader.systemClassloaderIfNull(java.lang.ClassLoader)' at ch.qos.logback.classic.util.ContextInitializer.autoConfig(ContextInitializer.java:73) at ch.qos.logback.classic.util.ContextInitializer.autoConfig(ContextInitializer.java:66) at ch.qos.logback.classic.spi.LogbackServiceProvider.initializeLoggerContext(LogbackServiceProvider.java:52) at ch.qos.logback.classic.spi.LogbackServiceProvider.initialize(LogbackServiceProvider.java:41)...

Hi Yuk, here are the parameters I used: ``` m6anet dataprep --eventalign /scratch/lb4489/project/dRNA/WT1_temp/ALL_eventalign.txt \ --out_dir WT_1_m6anet \ --n_processes 120 m6anet inference --input_dir WT_1_m6anet --out_dir WT_1_m6anet_result --pretrained_model HEK293T_RNA004 --n_processes 120 --num_iterations...

Hi [HalfPhoton](https://github.com/HalfPhoton), This result is from dorado version 0.9.6 with the model “sup,inosine_m6A,m5C,pseU”, but I get similar results in the latest released “sup,m5C_2OmeC,inosine_m6A_2OmeA,pseU_2OmeU,2OmeG” model.

> I would expect that the RNA models in the latest release would handle this situation a bit better if those are false positive calls. For example, the m5C model...