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TheJacksonLaboratory / splicing-pipelines-nf

Repository for the Anczukow-Lab splicing pipeline
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ImportError: /lib/x86_64-linux-gnu/libm.so.6: version `GLIBC_2.29' not found (required by /home/yuriem/.local/lib/python3.9/site-packages/pyBigWig.cpython-39-x86_64-linux-gnu.so) #336

Open imendes93 opened 1 year ago

imendes93 commented 1 year ago

Possibly fix this issue

Command error:
 Traceback (most recent call last):
  File "/opt/conda/envs/splicing-pipelines-nf/bin/bamCoverage", line 5, in <module>
   from deeptools.bamCoverage import main
  File "/opt/conda/envs/splicing-pipelines-nf/lib/python3.9/site-packages/deeptools/bamCoverage.py", line 8, in <module>
   from deeptools import writeBedGraph # This should be made directly into a bigWig
  File "/opt/conda/envs/splicing-pipelines-nf/lib/python3.9/site-packages/deeptools/writeBedGraph.py", line 5, in <module>
   import pyBigWig
 ImportError: /lib/x86_64-linux-gnu/libm.so.6: version `GLIBC_2.29' not found (required by /home/yuriem/.local/lib/python3.9/site-packages/pyBigWig.cpython-39-x86_64-linux-gnu.so)
angarb commented 1 year ago

Christina and I tried: 1) Changing permissions on the singularity cache at "/projects/anczukow-lab/.singularity_cache/" 2) Adding --singularity_cache . \ to the main.pbs (This did not seem to overwrite the Sumner config!) 3) Changing the cacheDir in the Sumner config to "./.singularity_cache/"

This did not fix the error above.

angarb commented 1 year ago

@cgpu - what were the action items for this problem? 1) Rebuild container 2) Add GLIB to container 3) Soemthing else?

marina-yurieva commented 1 year ago

Christina and I had a debugging session - we were able to get inside the container and reproduce the error.

Singularity anczukowlab-splicing-pipelines-nf-3.0.img:/projects/anczukow-lab/yuriem/splicing_pipeline/splicing-pipelines-nf/work/6b/b497c8d890017cbc15b297d720b253> bamCoverage -b SRR4238359.Aligned.sortedByCoord.out.bam -o SRR4238359.bw Traceback (most recent call last): File "/opt/conda/envs/splicing-pipelines-nf/bin/bamCoverage", line 5, in from deeptools.bamCoverage import main File "/opt/conda/envs/splicing-pipelines-nf/lib/python3.9/site-packages/deeptools/bamCoverage.py", line 8, in from deeptools import writeBedGraph # This should be made directly into a bigWig File "/opt/conda/envs/splicing-pipelines-nf/lib/python3.9/site-packages/deeptools/writeBedGraph.py", line 5, in import pyBigWig ImportError: /lib/x86_64-linux-gnu/libm.so.6: version `GLIBC_2.29' not found (required by /home/yuriem/.local/lib/python3.9/site-packages/pyBigWig.cpython-39-x86_64-linux-gnu.so)

which bamCoverage
/opt/conda/envs/splicing-pipelines-nf/bin/bamCoverage
which deeptools
/opt/conda/envs/splicing-pipelines-nf/bin/deeptools