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XWangLabTHU / cfDNApipe

cfDNApipe: A comprehensive quality control and analysis pipeline for cell-free DNA high-throughput sequencing data
https://xwanglabthu.github.io/cfDNApipe/
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Error occured in multi-core running #3

Closed StefaniaTuveri closed 2 years ago

StefaniaTuveri commented 3 years ago

I am trying to use cfDNApipe to analyse WGBS data. I have created the environment, I have successfully configured the references, but when I start the analysis I have this error:

Can't load '/perl5/lib/perl5/x86_64-linux-thread-multi/auto/Cwd/Cwd.so' for module Cwd: libimf.so: cannot open shared object file: No such file or directory at /miniconda3/envs/cfDNApipe/lib/5.2 6.2/XSLoader.pm line 96. at /perl5/lib/perl5/x86_64-linux-thread-multi/Cwd.pm line 82. Compilation failed in require at /miniconda3/envs/cfDNApipe/lib/5.26.2/FindBin.pm line 83 . BEGIN failed--compilation aborted at /miniconda3/envs/cfDNApipe/lib/5.26.2/FindBin.pm lin e 83. Compilation failed in require at /miniconda3/envs/cfDNApipe/bin/fastqc line 4. BEGIN failed--compilation aborted at /miniconda3/envs/cfDNApipe/bin/fastqc line 4.

Can you please help me figure it out?

Thank you.

Best regards, Stefania

Honchkrow commented 3 years ago

Hi, @StefaniaTuveri ,

Sorry for late reponse. Can you provide the source code and which line caused the problem? It seems that "libimf.so" is missing. I suggest to reinstall cfDNApipe and run the demo data for reproduce the problem.

Thanks for using cfDNApipe!

Wei

StefaniaTuveri commented 3 years ago

Thank you for your reply!

Here it is what I see:

(I tried also to reinstall the env, but the error remained the same)

An Error Occured During The Following Command Line Executing. ^^^ fastqc --outdir /staging/leuven/stg_00019/stefania_research/cfdnapipe_test/intermediate_result/step_02_fastqc --threads 60 /staging/leuven/stg_00019/stefania_research/cfdnapipe_test/GC112846_lane1.R1.fastq.gz /staging/leuven/stg_00019/stefania_research/cfdnapipe_test/GC112847_lane1.R1.fastq.gz /staging/leuven/stg_00019/stefania_research/cfdnapipe_test/GC112848_lane1.R1.fastq.gz /staging/leuven/stg_00019/stefania_research/cfdnapipe_test/GC112849_lane1.R1.fastq.gz /staging/leuven/stg_00019/stefania_research/cfdnapipe_test/GC112850_lane1.R1.fastq.gz /staging/leuven/stg_00019/stefania_research/cfdnapipe_test/final_result /staging/leuven/stg_00019/stefania_research/cfdnapipe_test/report_result /staging/leuven/stg_00019/stefania_research/cfdnapipe_test/GC112846_lane1.R2.fastq.gz /staging/leuven/stg_00019/stefania_research/cfdnapipe_test/GC112847_lane1.R2.fastq.gz /staging/leuven/stg_00019/stefania_research/cfdnapipe_test/GC112848_lane1.R2.fastq.gz /staging/leuven/stg_00019/stefania_research/cfdnapipe_test/GC112849_lane1.R2.fastq.gz /staging/leuven/stg_00019/stefania_research/cfdnapipe_test/GC112850_lane1.R2.fastq.gz /staging/leuven/stg_00019/stefania_research/cfdnapipe_test/intermediate_result^^^ Can't load '/user/leuven/329/vsc32941/perl5/lib/perl5/x86_64-linux-thread-multi/auto/Cwd/Cwd.so' for module Cwd: libimf.so: cannot open shared object file: No such file or directory at /vsc-hard-mounts/leuven-data/329/vsc32941/miniconda3/envs/cfDNApipe/lib/5.26.2/XSLoader.pm line 96. at /user/leuven/329/vsc32941/perl5/lib/perl5/x86_64-linux-thread-multi/Cwd.pm line 82. Compilation failed in require at /vsc-hard-mounts/leuven-data/329/vsc32941/miniconda3/envs/cfDNApipe/lib/5.26.2/FindBin.pm line 83. BEGIN failed--compilation aborted at /vsc-hard-mounts/leuven-data/329/vsc32941/miniconda3/envs/cfDNApipe/lib/5.26.2/FindBin.pm line 83. Compilation failed in require at /data/leuven/329/vsc32941/miniconda3/envs/cfDNApipe/bin/fastqc line 4. BEGIN failed--compilation aborted at /data/leuven/329/vsc32941/miniconda3/envs/cfDNApipe/bin/fastqc line 4. ^^^

     Please Stop The Program To Check The Error.

^^^ Traceback (most recent call last): File "", line 1, in File "/data/leuven/329/vsc32941/miniconda3/envs/cfDNApipe/lib/python3.6/site-packages/cfDNApipe/Pipeline.py", line 417, in cfDNAWGBS res_fastqc = fastqc(upstream=res_inputprocess, other_params=fastqcOP, verbose=verbose) File "/data/leuven/329/vsc32941/miniconda3/envs/cfDNApipe/lib/python3.6/site-packages/cfDNApipe/Fun_fastqc.py", line 104, in init self.multiRun(args=[cmd], func=None, nCore=1) File "/data/leuven/329/vsc32941/miniconda3/envs/cfDNApipe/lib/python3.6/site-packages/cfDNApipe/StepBase.py", line 672, in multiRun raise commonError("Error occured in multi-core running!") cfDNApipe.cfDNA_utils.commonError: Error occured in multi-core running!