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)

[imendes93]

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]

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]

@cgpu - what were the action items for this problem?

1. Rebuild container 2) Add GLIB to container 3) Soemthing else?

[marina-yurieva]

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