Unable to run Phylosift on PSC Bridges

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szz...@gmail.com

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May 23, 2018, 11:39:11 AM5/23/18
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Dear support,

I have been troubleshooting with staff from PSC Bridges for a few weeks, but we still have not been able to run Phylosift successfully on PSC Bridges, so I'm posting here and hope to get some help. 

When I run the command below:

phylosift all --paired HMP_1.fastq HMP_2.fastq

I get the following error message after about an hour:

Can't call method "unlock" on an undefined value at /opt/packages/phylosift/phylosift_v1.0.1/bin/../lib/Phylosift/Phylosift.pm line 187.

--------------------------------------
Under the $PHYLOSIFT_HOME folder on the cluster, there are the following folders and files. Is there anything missing?

bin  build.log  legacy  lib  osx  phylosift  phylosiftrc  phylosiftrc~  README  results  tutorial_data  writing
--------------------------------------


Thanks,

Nick

Guillaume Jospin

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May 23, 2018, 2:09:56 PM5/23/18
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Hi Nick,
I folder looks fine to me.
The unlock error is related to the locking of the data base to prevent a modification mid run. 
Does the user have write permission to the database folder?  that might not be ideal when it comes to shared resources ... 
In any case, if you are confident in your database integrity you can ignore the message. 

You can check the progress of a run by looking at the PS_temp folder. That should tell me how far a run went.
The run_info.txt should have time stamps for the various steps.



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szz...@gmail.com

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May 23, 2018, 3:19:22 PM5/23/18
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Hi Guillaume,

Thanks for getting back to me promptly!

The run_info.txt suggests that the run was fine (see below for the full text).

As a user of the PSC Bridges, I don't have write permission to the database folder. 

Is there a way for me to check the database integrity? 

Cheers,

Nick


----------------------------
run_info.txt
Program run as:

phylosift all --paired HMP_1.fastq HMP_2.fastq
Marker database version:
http://edhar.genomecenter.ucdavis.edu/~koadman/phylosift_markers/markers.tgz
1413946442
Chunk 1 sequences processed 994a43118e7d640b92e426c9feafb248
Chunk 1 Search completed 2018-05-17 12:43:12 2018-05-17 12:43:50 38
Chunk 1 Align completed 2018-05-17 12:43:50 2018-05-17 12:46:04 134
Chunk 1 Place completed 2018-05-17 12:46:04 2018-05-17 13:16:57 1853
Chunk 1 Summarize completed 2018-05-17 13:16:57 2018-05-17 13:21:37 280



On Wednesday, May 23, 2018 at 11:09:56 AM UTC-7, Guillaume Jospin wrote:
Hi Nick,
I folder looks fine to me.
The unlock error is related to the locking of the data base to prevent a modification mid run. 
Does the user have write permission to the database folder?  that might not be ideal when it comes to shared resources ... 
In any case, if you are confident in your database integrity you can ignore the message. 

You can check the progress of a run by looking at the PS_temp folder. That should tell me how far a run went.
The run_info.txt should have time stamps for the various steps.


On Wed, May 23, 2018 at 8:39 AM, <szz...@gmail.com> wrote:
Dear support,

I have been troubleshooting with staff from PSC Bridges for a few weeks, but we still have not been able to run Phylosift successfully on PSC Bridges, so I'm posting here and hope to get some help. 

When I run the command below:

phylosift all --paired HMP_1.fastq HMP_2.fastq

I get the following error message after about an hour:

Can't call method "unlock" on an undefined value at /opt/packages/phylosift/phylosift_v1.0.1/bin/../lib/Phylosift/Phylosift.pm line 187.

--------------------------------------
Under the $PHYLOSIFT_HOME folder on the cluster, there are the following folders and files. Is there anything missing?

bin  build.log  legacy  lib  osx  phylosift  phylosiftrc  phylosiftrc~  README  results  tutorial_data  writing
--------------------------------------


Thanks,

Nick

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Guillaume Jospin

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May 23, 2018, 4:27:22 PM5/23/18
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well we used to have an automatic way of checking for a newer version of the DB and installing that. 
Now it has to be done manually so unless someone messes with the DB on purpose you should be fine. The code hasn't be updated to reflect this change unfortunately.


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