Comments (5)
simoncchu
commented on July 30, 2024
hmm, didn't meet this error before. What's the python version?
If you run python from your virtual environment, and directly run import pysam from terminal. Does the error show up?
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BenjaminSSimpson
commented on July 30, 2024
I am using python3.7. If I run python directly from the virtual environment and run "import pysam" it returns no error, suggesting it has imported. Typing "pysam" gives "module pysam" then the full path to the installed folder.
Really odd one. I have also tried adding "module load anaconda" and"source activate your_env" to the running scripts, but still having the issue. May I ask, what version of python and pysam you originally write the tool? I might downgrade my environment and see if this runs okay? Any other suggestions are welcome!
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simoncchu
commented on July 30, 2024
python3.7 should work. Maybe try with python3.8? It's also stable on 3.8.
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BenjaminSSimpson
commented on July 30, 2024
I have updated to 3.8 but the same error I am afraid.
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simoncchu
commented on July 30, 2024
Have you solved this problem? It doesn't like a technic issue. I'll close the ticket for now.
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Related Issues (20)
- x_TEA_main.py: error: no such option: --bamsnap HOT 2
- Very long length of L1 insertion HOT 1
- Long_reads: File detailing which reads show transductions of deletions HOT 1
- temp files burst out HOT 2
- Possible to merge TE sites and do genotyping in each sample? HOT 1
- Alu output didn't go through filter step? HOT 2
- xTea_long getting stuck, no errors, during wtpoa-cns, running HG38 HOT 2
- default slurm script with wrong email HOT 1
- -f: steps to run. (5907 means run all the steps); HOT 1
- long read support with chm13 HOT 3
- Using the code in github still doesn't solve the problem HOT 2
- Questions about the output file HOT 3
- visual inspection using IGV
- Merge clip and disc step error HOT 12
- Sporadic inconsistent errors with xtea_long HOT 5
- WES issues HOT 1
- interpretation of GENE_INFO in output file HOT 1
- Long read cannot find temp files HOT 1
- xTea Long_read SyntaxWarning HOT 6
- line 1133, IOError: [Errno 2] No such file or directory: 'null' HOT 1
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