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liulab-dfci / RIMA_pipeline

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Job Execution failed during RSEQC stage #22

Open ZHawul opened 9 months ago

ZHawul commented 9 months ago

I have installed the package as detailed in the Tutorial of RNA-seq tumor immunity analysis using Google Cloud Platform on my institute’s HPC. The pipeline completes the star aligning, salmon and down sampling on the house keeping genes. But fails when running the tin_score, read_distrib_qc and junction_saturation jobs from RSEQC. I have included the .snakemake.log files which detail the errors. I have tried with different fastq files and the pipeline fails at the same stage. Any assistance would be greatly appreciated. 2023-12-04T152042.960586.snakemake.log RIMA_Error_Log.txt

ZHawul commented 9 months ago

After some deeper reading of the error messages. I think I have identified the issue. Below are my troubleshooting to get the rseqc part of the pipeline working. Error 1 (as seen in the RIMA_Error_Log.txt) - 'ImportError: No module named _sysconfigdata_x86_64_conda_linux_gnu' Step one: make the _sysconfigdata_x86_64_conda_linux_gnu.py file cd /QRISdata/Q6233/RIMA/miniconda3/envs/rseqc_env/lib/python2.7 cp _sysconfigdata_x86_64_conda_cos6_linux_gnu.py _sysconfigdata_x86_64_conda_linux_gnu.py cp _sysconfigdata_x86_64_conda_cos6_linux_gnu.pyc _sysconfigdata_x86_64_conda_linux_gnu.pyc Step two: Edit the newly created file edit _sysconfigdata_x86_64_conda_linux_gnu.py to change all references of 'x86_64-conda_cos6-linux-gnu' to 'x86_64-conda-linux-gnu'

Once these changes were made the following error occurred, 'ImportError: libhts.so.2: cannot open shared object file: No such file or directory'

I tried creating the libhts.so.2 file by duplicating the libhts.so.3 file. However, this resulted in an additional error 'ImportError: /QRISdata/Q6233/RIMA/miniconda3/envs/rseqc_env/lib/python2.7/site-packages/pysam/libchtslib.so: undefined symbol: hts_utell'

In the end I just tried uninstalling pysam with the intention of reinstalling it again. Using 'conda uninstall -n rseqc_env pysam' But the whole environment was just downgraded from 2.6.4-py27hf8a1672_2 --> 2.6.2-0 using the uninstall command and so far, this seems to have fixed the problem.