Error PacBio SMRT Link
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Entering edit mode
4.9 years ago
jacobnix • 0

when I run the pacbio smrtlink everyhing works well but in the following phase the process failed , the stderr message is :

The entries you tried to add are out of order, precede already added entries, or otherwise use illegal values.
 Please correct this and try again.

if you have experience with pacbio , the error message do you know what means ? my data ?

[ERROR] 2017-05-27 01:30:49,610Z [pbsmrtpipe.tools.runner run_task 274] Failed task pbcoretools.tasks.gather_bigwig exit code 2 in 17.12 sec (See file '/opt/pacbio/smrtlink/userdata/jobs_root/000/000017/tasks/pbcoretools.tasks.gather_bigwig-1/stderr'.)
Extracted from stderr
The entries you tried to add are out of order, precede already added entries, or otherwise use illegal values.
 Please correct this and try again.

Traceback (most recent call last):
  File "/opt/pacbio/smrtlink/install/smrtlink-fromsrc_4.0.0.190159+190159-190159-189856-189856-189856/bundles/smrttools/install/smrttools-fromsrc_4.0.0.190159/private/pacbio/pythonpkgs/pbcommand/lib/python2.7/site-packages/pbcommand/cli/core.py", line 136, in _pacbio_main_runner
    return_code = exe_main_func(*args, **kwargs)
  File "/opt/pacbio/smrtlink/install/smrtlink-fromsrc_4.0.0.190159+190159-190159-189856-189856-189856/bundles/smrttools/install/smrttools-fromsrc_4.0.0.190159/private/pacbio/pythonpkgs/pbcoretools/lib/python2.7/site-packages/pbcoretools/tasks/gather_bigwig.py", line 50, in rtc_runner
    return run_main_gather_bigwig(rtc.task.input_files[0], rtc.task.output_files[0], rtc.task.chunk_key)
  File "/opt/pacbio/smrtlink/install/smrtlink-fromsrc_4.0.0.190159+190159-190159-189856-189856-189856/bundles/smrttools/install/smrttools-fromsrc_4.0.0.190159/private/pacbio/pythonpkgs/pbcoretools/lib/python2.7/site-packages/pbcoretools/chunking/gather.py", line 378, in __gather_runner
    _ = func(chunked_files, output_file, **kwargs)
  File "/opt/pacbio/smrtlink/install/smrtlink-fromsrc_4.0.0.190159+190159-190159-189856-189856-189856/bundles/smrttools/install/smrttools-fromsrc_4.0.0.190159/private/pacbio/pythonpkgs/pbcoretools/lib/python2.7/site-packages/pbcoretools/chunking/gather.py", line 293, in gather_bigwig
    bw.addEntries(seqids, starts, ends=ends, values=values)

RuntimeError: The entries you tried to add are out of order, precede already added entries, or otherwise use illegal values.
 Please correct this and try again.

Thanks in advance

pacbio smrtlink • 2.3k views
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Hello WouterDeCoster , sorry ,

I will keep it in mind

thank you !! :D

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