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Failed to execute command: partig #9

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xiekunwhy opened this issue Jan 4, 2025 · 4 comments
Open

Failed to execute command: partig #9

xiekunwhy opened this issue Jan 4, 2025 · 4 comments

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@xiekunwhy
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Hi,

Always can not run partig even partig executable binary was copied into cphasing conda env and/or copied into CPhasing/bin, so there must be some thing wrong in alleles.py where trying to execute partig.

The CPhasing/bin
image

The partig also in conda env bin directory
image

The command line

#!/bin/bash
source /public2/home/sl_qybio/sl_qybio/miniforge3/bin/activate cphasing
export PATH=/public2/home/sl_qybio/sl_qybio/software/biosoft/CPhasing/bin:$PATH
export PYTHONPATH=/public2/home/sl_qybio/sl_qybio/software/biosoft/CPhasing:$PYTHONPATH
export LD_LIBRARY_PATH=/public2/home/sl_qybio/sl_qybio/miniforge3/envs/cphasing/lib:$LD_LIBRARY_PATH
cphasing pipeline -f gra.2hap.fa --steps 1,2,3,4,5 -hic1 gra.hic_1.fq.gz -hic2 gra.hic_2.fq.gz -t 64 -n 19:2 --pattern GATC

The error

[10:11:15] INFO     C-Phasing version: 0.2.0.r282                pipeline.py:118
           INFO     Pipeline is started on 2025-01-04.           pipeline.py:120
           INFO     Working on existing directory:               pipeline.py:140
                    `cphasing_output`                                           
           INFO     Total size of contig-level assembly: 6g      pipeline.py:585
           INFO                                                  pipeline.py:587
                    #----------------------------------#                        
                    #      Running step 1. alleles     #                        
                    #----------------------------------#                        
           INFO     Calculating the similarity of sequences ...   alleles.py:265
Traceback (most recent call last):
  File "/public2/home/sl_qybio/sl_qybio/software/biosoft/CPhasing/bin/cphasing", line 7, in <module>
    sys.exit(cli())
             ^^^^^
  File "/public2/home/sl_qybio/sl_qybio/miniforge3/envs/cphasing/lib/python3.12/site-packages/click/core.py", line 1161, in __call__
    return self.main(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/public2/home/sl_qybio/sl_qybio/miniforge3/envs/cphasing/lib/python3.12/site-packages/rich_click/rich_command.py", line 126, in main
    rv = self.invoke(ctx)
         ^^^^^^^^^^^^^^^^
  File "/public2/home/sl_qybio/sl_qybio/miniforge3/envs/cphasing/lib/python3.12/site-packages/click/core.py", line 1697, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
                           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/public2/home/sl_qybio/sl_qybio/miniforge3/envs/cphasing/lib/python3.12/site-packages/click/core.py", line 1443, in invoke
    return ctx.invoke(self.callback, **ctx.params)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/public2/home/sl_qybio/sl_qybio/miniforge3/envs/cphasing/lib/python3.12/site-packages/click/core.py", line 788, in invoke
    return __callback(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/public2/home/sl_qybio/sl_qybio/software/biosoft/CPhasing/cphasing/cli.py", line 1023, in pipeline
    run(fasta, 
    ^^^^^^^^^^
  File "/public2/home/sl_qybio/sl_qybio/software/biosoft/CPhasing/cphasing/pipeline/pipeline.py", line 613, in run
    alleles.main(args=args,
  File "/public2/home/sl_qybio/sl_qybio/miniforge3/envs/cphasing/lib/python3.12/site-packages/rich_click/rich_command.py", line 126, in main
    rv = self.invoke(ctx)
         ^^^^^^^^^^^^^^^^
  File "/public2/home/sl_qybio/sl_qybio/miniforge3/envs/cphasing/lib/python3.12/site-packages/click/core.py", line 1443, in invoke
    return ctx.invoke(self.callback, **ctx.params)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/public2/home/sl_qybio/sl_qybio/miniforge3/envs/cphasing/lib/python3.12/site-packages/click/core.py", line 788, in invoke
    return __callback(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/public2/home/sl_qybio/sl_qybio/software/biosoft/CPhasing/cphasing/cli.py", line 2344, in alleles
    pa.run()
  File "/public2/home/sl_qybio/sl_qybio/software/biosoft/CPhasing/cphasing/alleles.py", line 298, in run
    self.partig()
  File "/public2/home/sl_qybio/sl_qybio/software/biosoft/CPhasing/cphasing/alleles.py", line 285, in partig
    raise Exception('Failed to execute command:' 
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Exception: Failed to execute command:   partig -k19 -w19 -m0.5 -c60 -n5 -d0.1 -t64 ../gra.2hap.fa.

Best,
Kun
@xiekunwhy
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The error still take place even I chang partig to absolute path
image

cat cphasing.sh_2401556.err
[10:54:22] INFO     C-Phasing version: 0.2.0.r282                pipeline.py:118
           INFO     Pipeline is started on 2025-01-04.           pipeline.py:120
           INFO     Working on existing directory:               pipeline.py:140
                    `cphasing_output`                                           
           INFO     Total size of contig-level assembly: 6g      pipeline.py:585
           INFO                                                  pipeline.py:587
                    #----------------------------------#                        
                    #      Running step 1. alleles     #                        
                    #----------------------------------#                        
[10:54:23] INFO     Calculating the similarity of sequences ...   alleles.py:265
Traceback (most recent call last):
  File "/public2/home/sl_qybio/sl_qybio/software/biosoft/CPhasing/bin/cphasing", line 7, in <module>
    sys.exit(cli())
             ^^^^^
  File "/public2/home/sl_qybio/sl_qybio/miniforge3/envs/cphasing/lib/python3.12/site-packages/click/core.py", line 1161, in __call__
    return self.main(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/public2/home/sl_qybio/sl_qybio/miniforge3/envs/cphasing/lib/python3.12/site-packages/rich_click/rich_command.py", line 126, in main
    rv = self.invoke(ctx)
         ^^^^^^^^^^^^^^^^
  File "/public2/home/sl_qybio/sl_qybio/miniforge3/envs/cphasing/lib/python3.12/site-packages/click/core.py", line 1697, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
                           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/public2/home/sl_qybio/sl_qybio/miniforge3/envs/cphasing/lib/python3.12/site-packages/click/core.py", line 1443, in invoke
    return ctx.invoke(self.callback, **ctx.params)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/public2/home/sl_qybio/sl_qybio/miniforge3/envs/cphasing/lib/python3.12/site-packages/click/core.py", line 788, in invoke
    return __callback(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/public2/home/sl_qybio/sl_qybio/software/biosoft/CPhasing/cphasing/cli.py", line 1023, in pipeline
    run(fasta, 
    ^^^^^^^^^^
  File "/public2/home/sl_qybio/sl_qybio/software/biosoft/CPhasing/cphasing/pipeline/pipeline.py", line 613, in run
    alleles.main(args=args,
  File "/public2/home/sl_qybio/sl_qybio/miniforge3/envs/cphasing/lib/python3.12/site-packages/rich_click/rich_command.py", line 126, in main
    rv = self.invoke(ctx)
         ^^^^^^^^^^^^^^^^
  File "/public2/home/sl_qybio/sl_qybio/miniforge3/envs/cphasing/lib/python3.12/site-packages/click/core.py", line 1443, in invoke
    return ctx.invoke(self.callback, **ctx.params)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/public2/home/sl_qybio/sl_qybio/miniforge3/envs/cphasing/lib/python3.12/site-packages/click/core.py", line 788, in invoke
    return __callback(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/public2/home/sl_qybio/sl_qybio/software/biosoft/CPhasing/cphasing/cli.py", line 2344, in alleles
    pa.run()
  File "/public2/home/sl_qybio/sl_qybio/software/biosoft/CPhasing/cphasing/alleles.py", line 298, in run
    self.partig()
  File "/public2/home/sl_qybio/sl_qybio/software/biosoft/CPhasing/cphasing/alleles.py", line 285, in partig
    raise Exception('Failed to execute command:' 
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Exception: Failed to execute command:   /public2/home/sl_qybio/sl_qybio/software/biosoft/CPhasing/bin/partig -k19 -w19 -m0.5 -c60 -n5 -d0.1 -t64 ../gra.2hap.fa.

@xiekunwhy
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partig core dumped
image

@wangyibin
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Owner

Hi,
This a limitation of C-Phasing, alleles can not process contig that length larger than 135Mb. A temporary solution is to break the long contigs, and then merge them after scaffolding. We are trying to remove this limitation in the next minor release.

Best,
Yibin

@xiekunwhy
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Thank you for your reply, hope new release coming soon.
This limitation also limit user to use exists mapping results.

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@xiekunwhy @wangyibin