Error PacBio SMRT Link

Question

[jacobnix]

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

[WouterDeCoster]

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[jacobnix]

Hello WouterDeCoster , sorry ,

I will keep it in mind

thank you !! :D

[sunilthorat]

I have installed PacBio SMRT Link Version 6.0. Installation was successful and worked well. However after rebooting, the following ERROR appeared:

$ ~/pacbio/admin/bin/services-start Checking system... Checking mount points...

Starting SMRT View Server Node... Existing PID file found during start. Removing/clearing stale PID file. Tomcat started. SMRT View Server Node started successfully..

Step #1 Attempting to apply-config Successfully Completed apply-config Successfully completed running smrtflow.tools.apply_config 0.3.0 (smrtflow 0.18.1+47825.0a8b7e0) in 6 sec. completed applying config Step #2 Checking system requirements (e.g., ulimits) /home/room/pacbio/install/smrtlink-release_6.0.0.47841/bundles/smrtlink-analysisservices-gui/install/smrtlink-analysisservices-gui-release_6.0.0.47836/private/pacbio/smrtlink-analysisservices-gui/bin/check-system-limits: line 7: netstat: command not found ERROR: The maximum number of open files is too low (currently 1024, at least 8192 recommended). You can fix this by running 'ulimit -n <LIMIT>'. services-start: Error! Services not started successfully.

WHEN I DO: $ulimit -n 8192, IT SAYS:

$ ~/pacbio/admin/bin/services-start Checking system... Checking mount points...

Starting SMRT View Server Node... Existing PID file found during start. Tomcat appears to still be running with PID 6905. Start aborted. If the following process is not a Tomcat process, remove the PID file and try again: UID PID PPID C STIME TTY
TIME CMD ibsdshl 6905 3204 5 10:47 pts/0 00:00:35 /home/room/pacbio/install/smrtlink-release_6.0.0.47 ERROR! SMRT View Server Node start unsuccessful.

services-start: Error! Services not started successfully.

I use to manullay perform clearing the effors as under:

$ulimit -n 8192 $kill 15 PID

OR

$kill 9 PID

Can anyone help me in removing the errors so that whenever I start after opening the browser at http://localhost:9090 and type the command below :

$~/pacbio/admin/bin/services-start

[William Rowell]

Please reach out to [e-mail] and they'll help you out with this.