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MOSAIK PE and SE #16

Open GoogleCodeExporter opened 9 years ago

GoogleCodeExporter commented 9 years ago 
Hi,

I ran MOSAIK, and everything went ok other than the MosaikText step. The error 
stream  is empty though in: 

/usr/pl_cache/pipeline/2011August08_17h26m48s975ms/streams

/usr/pl_cache/pipeline/2011August08_17h26m37s881ms/streams/

...and also the output folder is empty as expected. I checked in the cache and 
there is a trunk .sam.gz file:

fgene3 [/usr/pl_cache/pipeline/2011August08_17h26m48s975ms] gunzip 
MosaikText_1.samoutput-1.sam.gz 

gunzip: MosaikText_1.samoutput-1.sam.gz: unexpected end of file.

I ran the same command by command line and I had back this error in the 
conversion of the file:

fgene3 [/usr/pl_cache/pipeline/2011August08_17h26m48s975ms] 
/projects1/idinov/projects/Pipeline_genomics_informatics_2011/scripts/Mosaik/Mos
aikText -in /usr/p                                                              

       put-1_bis.sam
------------------------------------------------------------------------------
MosaikText 1.1.0021                                                 2010-11-10
Michael Stromberg & Wan-Ping Lee  Marth Lab, Boston College Biology Department
------------------------------------------------------------------------------

- converting the alignment archive to the following formats: SAM

Converting alignment archive:
 0% [                                                                                                               ]                                  |ERROR: The base quality is larger than 60.

I found this discussion about this error: 
http://code.google.com/p/mosaik-aligner/issues/detail?id=79

SO I tried to visualize the .dat file 
(/projects1/idinov/projects/Pipeline_genomics_informatics_2011/scripts/Mosaik/Mo
saikText -in MosaikBuild_2.Outputfileforreads-1.dat -screen) as suggested, and 
I had back:

fgene3 [/usr/pl_cache/pipeline/2011August08_17h26m48s975ms] 
/projects1/idinov/projects/Pipeline_genomics_informatics_2011/scripts/Mosaik/Mos
aikText -in MosaikBuild_2.Outputfileforreads-1.dat -screen
------------------------------------------------------------------------------
MosaikText 1.1.0021                                                 2010-11-10
Michael Stromberg & Wan-Ping Lee  Marth Lab, Boston College Biology Department
------------------------------------------------------------------------------

ERROR: It seems that the input file (MosaikBuild_2.Outputfileforreads-1.dat) is 
not in the MOSAIK alignment format.

I remember you told me you ha dto modify some scripts to make it run because 
MOSAIK was not compatible with the PIPELINE environment. I have never 
encountered this kind of error, so I was wondering what may be the reason.

Federica

Original issue reported on code.google.com by federica...@gmail.com on 10 Aug 2011 at 6:24

Attachments:

GoogleCodeExporter commented 9 years ago 
Hi Federica,

I originally modified the source code to get around some errors but discovered 
a much simpler fix in the pipeline interface, so the programs you are using are 
unedited. 

From the discussion you linked, it seems this error does not really indicate a 
problem and should be circumvented by either suppressing the base quality error 
code or modifying it to output an error only if the number is something much 
higher in /mosaik-aligner/src/CommonSource/DataStructures/Mosaikstring.cpp. Are 
you able to do this? If not, I can edit it, recompile, and  send it to you. 

Sam

Original comment by shobe...@gmail.com on 10 Aug 2011 at 6:51

GoogleCodeExporter commented 9 years ago 
Hi Sam, 

first of all thanks for your help! No, actually I don't feel confident enough 
to modify the .cpp. If you can do it would be great...thanks

Federica

Original comment by federica...@gmail.com on 10 Aug 2011 at 7:07

GoogleCodeExporter commented 9 years ago 
No problem. I'm not sure how you have the Mosaik folder organized so here is 
the edited Mosaikstring.cpp. Just overwrite the current one you are using with 
this. Then run 'make clean' and 'make; make utils' to rebuild the source. Let 
me know if you have questions.

Sam

Original comment by shobe...@gmail.com on 10 Aug 2011 at 7:29

Attachments:

GoogleCodeExporter commented 9 years ago 
Perfect Sam! I am already running them.

thanks

Original comment by federica...@gmail.com on 10 Aug 2011 at 7:48

GoogleCodeExporter commented 9 years ago 
Hi Sam, the SE run has finished this morning..but I have the same error even 
with the modified .cpp. I didn't have any problems or errors in compiling it. I 
attach here the two .pipe (SE and PE). The PE is still running.

fed

Original comment by federica...@gmail.com on 11 Aug 2011 at 5:32

Attachments:

GoogleCodeExporter commented 9 years ago 
Does the error say the base quality is larger than 60 or 104? I edited the code 
so that it will only display an error if >104 but won't exit. 

I cannot test this workflow using gatk-hg18_ensembl.fa as the reference because 
we don't have enough RAM on our system so I apologize if these problems take 
longer to resolve.

Original comment by shobe...@gmail.com on 11 Aug 2011 at 7:09

GoogleCodeExporter commented 9 years ago 
It says larger than 60...super weird...

fgene3 [/raid/users/ftorri] 
/projects1/idinov/projects/Pipeline_genomics_informatics_2011/scripts/Mosaik/Mos
aikText -in 
/usr/pl_cache/pipeline/2011August10_12h46m22s746ms/MosaikAligner_1.Output-1.dat 
-sam 
/usr/pl_cache/pipeline/2011August10_12h46m22s746ms/MosaikText_1.samoutput-1.sam
------------------------------------------------------------------------------
MosaikText 1.1.0021                                                 2010-11-10
Michael Stromberg & Wan-Ping Lee  Marth Lab, Boston College Biology Department
------------------------------------------------------------------------------

- converting the alignment archive to the following formats: SAM

Converting alignment archive:
 0% [                                     ]                                  |ERROR: The base quality is larger than 60.

Original comment by federica...@gmail.com on 11 Aug 2011 at 7:14

GoogleCodeExporter commented 9 years ago 
Are you keeping the source files anywhere on fgene1 or did you get rid of them 
after compiling?

Original comment by shobe...@gmail.com on 11 Aug 2011 at 7:23

GoogleCodeExporter commented 9 years ago 
Try putting the attached binary in 
/projects1/idinov/projects/Pipeline_genomics_informatics_2011/scripts/Mosaik
and overwriting the previous version. If you get the same error, I'll go back 
and look at the code some more.

Sam

Original comment by shobe...@gmail.com on 11 Aug 2011 at 11:47

Attachments:

GoogleCodeExporter commented 9 years ago 
The SE and PE are running right now. Will let you know.

tks!

Original comment by federica...@gmail.com on 12 Aug 2011 at 6:53

GoogleCodeExporter commented 9 years ago 
Hi Sam,

unfortunately the MOSAIK run is still giving problems. Now the error is red 
(see attached pic) and always in the text step.

Thanks!

fed

Original comment by federica...@gmail.com on 15 Aug 2011 at 4:44

Attachments:

GoogleCodeExporter commented 9 years ago 
[deleted comment]
GoogleCodeExporter commented 9 years ago 
It seems you don't have permission to run MosaikTest. If you change the 
execution permissions, it should work. 
You can use chmod +x 
/projects1/test_pipeline/NEW_ORGANIZATION/scripts/MosaikText

Sam

Original comment by shobe...@gmail.com on 17 Aug 2011 at 10:02

GoogleCodeExporter commented 9 years ago 
Yes, I had changed it and running on fgene2.

Fed

Original comment by federica...@gmail.com on 17 Aug 2011 at 11:42

GoogleCodeExporter commented 9 years ago 
You should receive a data sink copying error. To fix this, you'll have to 
change the output file type of MosaikText from .sam to .sam.gz (which means the 
file path you specify in the data sink will also have to end in .sam.gz) I 
attached a workflow with this change, or you can change it directly on the 
workflow you are using. Let me know how the run went or if you have questions 
about this.

Sam

Original comment by shobe...@gmail.com on 18 Aug 2011 at 8:14

GoogleCodeExporter commented 9 years ago 
Here is the workflow I said I attached.

Original comment by shobe...@gmail.com on 18 Aug 2011 at 8:41

Attachments:

GoogleCodeExporter commented 9 years ago 
Thanks, I am running both SE and PE.

Fed

Original comment by federica...@gmail.com on 19 Aug 2011 at 12:41

GoogleCodeExporter commented 9 years ago 
Ok, weird: now I have an error in the alignment...The run was on fgene 1 and I 
used your pipe as template. I am attaching the SE and PE workflows here, and 
the pic of the error. The error stream is empty. I have the same error for both 
SE and PE runs.

Thanks!

fed

Original comment by federica...@gmail.com on 19 Aug 2011 at 4:56

Attachments:

GoogleCodeExporter commented 9 years ago 
In the output stream, the error is "ERROR: Run out the allocated position 
memory." Ironically, it seems that the addition of the low memory (-lm) 
parameter is what caused this. I disabled it and am testing both se and pe 
workflows. I will let you know how it goes; feel free to test it as well. 

Sam

Original comment by shobe...@gmail.com on 22 Aug 2011 at 8:38

GoogleCodeExporter commented 9 years ago 
Hi, thank you so much! It is really ironic actually this issue about the 
lm..yes I will try the run. I am actually in vacation in Italy and I ahve some 
connection issues btw I will try. If the run goes well please feel free to copy 
the working pipes into projects2/ServerLibrary/Aligners...it would be so 
helpful for me, so I am sure that all the pipes in the library have been tested 
and working. SO many thanks!
Fed

Original comment by federica...@gmail.com on 26 Aug 2011 at 8:04

GoogleCodeExporter commented 9 years ago 
Hi all,

thank you for your help! I am fully back woth a good connection now. I am 
running the two MOSAIK modules having disabled the lm paramter. I'll let you 
know.

Federica

Original comment by federica...@gmail.com on 6 Sep 2011 at 6:20

GoogleCodeExporter commented 9 years ago 
Hi,
how was your MOSAIK (both SE and PE) run? Mine is running since 2 days...

Fed

Original comment by federica...@gmail.com on 8 Sep 2011 at 11:28

GoogleCodeExporter commented 9 years ago 
When I ran it last week, it seemed to be doing something but extremely slowly. 
In the error stream, I saw it was calculating at something like .05 reads/s 
instead of 1/s or higher. I thought maybe it was a problem with the fgene 
server so I cancelled it. Does your error stream show something similar to this?

Sam

Original comment by shobe...@gmail.com on 9 Sep 2011 at 12:08

GoogleCodeExporter commented 9 years ago 
It is stuck on the alignment module, and I don't have any error stream...the 
file is empty.

Federica

Original comment by federica...@gmail.com on 9 Sep 2011 at 1:41

GoogleCodeExporter commented 9 years ago 
I meant the output stream, sorry. It should look something like this: 
/projects/pipelineCache/pipeline/2011August17_14h34m21s599ms/streams/MosaikAlign
er_1_1.out

I dug up my old run of this workflow and the output seems good, so at least it 
was working at one point. Here's the output file - it looks good to me: 
/projects/pipelineCache/pipeline/2011August17_14h34m21s599ms/MosaikText_1.samout
put-1.sam.

We haven't changed anything really other than the hash size. Perhaps try 
setting the hash size back to the default 15 (I think it is currently set to 
10?). Either way, something seems wrong with the server. I cannot even get the 
data files to validate anymore, despite them being correct. Perhaps you could 
ask Bernard to investigate what's happening at the server end, if possible.

Sam

Original comment by shobe...@gmail.com on 9 Sep 2011 at 5:20

GoogleCodeExporter commented 9 years ago 
It's hard to see what the output stream looks like in that file because it uses 
a dynamic progress bar, but it is aligning the reads at about 0.7 reads/s. My 
guess is that the Aligner module is going much slower in our latest runs which 
is why it is taking so long.

Original comment by shobe...@gmail.com on 9 Sep 2011 at 5:24

GoogleCodeExporter commented 9 years ago 
Ah, ok..yes in the output stream is:

:39 \
 8% [=>                                   ]    0.0526 reads/s  ETA 181:59:20 |
 8% [=>                                   ]    0.0526 reads/s  ETA 181:59:20 /
 8% [=>                                   ]    0.0526 reads/s  ETA 181:59:20 -
 8% [=>                                   ]    0.0526 reads/s  ETA 181:59:20 \
 8

I write now to Bernard putting you in cc.

fed

Original comment by federica...@gmail.com on 9 Sep 2011 at 5:24

GoogleCodeExporter commented 9 years ago 
..I checked, the hash siz eis the same as before (see pic) and is teh default 
one....

fed

Original comment by federica...@gmail.com on 9 Sep 2011 at 5:28

Attachments:

GoogleCodeExporter commented 9 years ago 
Thanks for emailing Bernard. There is not much we can do about this problem 
unless Bernard wants to actually look at whats happening with this job. 

Also, the hash size will be set in one of little circular parameters of the 
Jump and Aligner modules. If you hover your mouse over each circle, one of them 
will say Hash  size=10 and you can double click it to change the number. If the 
parameter is not there, it will default to 15. What you are looking at is the 
parameter settings which don't tell you want the value is currently set at, it 
just describes the function.

Sam

Original comment by shobe...@gmail.com on 9 Sep 2011 at 6:41

GoogleCodeExporter commented 9 years ago 
yes, you are right. Thanks for the indication about the parameters, I am 
re-running it with hash size of 15, as is the only thing I can do right now by 
myself. I will write him again if teh problem still comes up with this more 
traditional run (I am rpetty sure yes...but lets see).

Thank you so much,

fed

Original comment by federica...@gmail.com on 9 Sep 2011 at 6:47

GoogleCodeExporter commented 9 years ago 
When you get a chance, could you run the attached module and let me know what 
it says in the output stream? Also, are you running the mosaik workflow on 
fgene1 or fgene3? We are trying to debug some permissions issues and this will 
be helpful. 

Thanks,

Sam

Original comment by shobe...@gmail.com on 9 Sep 2011 at 9:12

Attachments:

GoogleCodeExporter commented 9 years ago 
Hi Sam,

I am running MOSAIK on fgene3. 

For whoami.pipe:

fgene1 the output stream is: 
/projects/pipelineCache/pipeline/2011September09_14h24m33s446ms/streams/whoami_1
_1.out

pipeline

fgene2: pipeline
fgene3: pipeline as well

fed

Original comment by federica...@gmail.com on 9 Sep 2011 at 9:26

GoogleCodeExporter commented 9 years ago 
Great! The two pipe worked on fgene3! I am putting them in the server library!!

Tks

fed

Original comment by federica...@gmail.com on 12 Sep 2011 at 4:32

GoogleCodeExporter commented 9 years ago 
Hi,

I was running MOSAIK PE on the simulation data (I was running the the last 
version of the pipeline)everything went well before the alignment...I ahd an 
error for that, no error stream but in the output stream I noticed that the 
state has always been 0%.

An teh same 0% is for the upstream module (even if they seemed green). My guess 
is that the simulation data are fastq (not solexa format) so it is necessary to 
enable the -q argument. If I do it in the parameters of the Mosaik BUILD of the 
forward read
 I have this weird error (see the pic).

I also tried to disable the techonology parameter (as those simulated data are 
general fastq, NOT solexa.txt) but still I have errors. I am asking to Bernard 
to re-start the server as I am experiencing super weird errors..but I would 
like to check with you if using the simulated data also you have 0% in all the 
modules.

tks,

Fed
-----------------------------------------------------------------------------
MosaikAligner 1.1.0021                                              
2010-11-10
Michael Stromberg & Wan-Ping Lee  Marth Lab, Boston College Biology Department
------------------------------------------------------------------------------

- Using the following alignment algorithm: all positions
- Using the following alignment mode: aligning reads to all possible locations
- Using a maximum mismatch threshold of 2
- Using a hash size of 10
- Setting hash position threshold to 100
- Using a jump database for hashing. Storing keys & positions in memory.

Aligning chromosome 1 (of 25):
- loading jump key database into memory... finished.
- loading jump positions database into memory... flushed...finished.
- loading reference sequence... finished.
Aligning read library (10000039):

 0% [                                     ]                                  |
 0% [                                     ]                                  /
 0% [                                     ]                                  -
 0% [                                     ]                                  \
 0% [                                     ]                                  |
 0% [                                     ]                                  /
 0% [                                     ]    0.9980 reads/s ETA 116.0 days -
 0% [                                     ]    0.9980 reads/s ETA 116.0 days \
 0% [                                     ]    0.9980 reads/s ETA 116.0 days |
 0% [                                     ]    0.9980 reads/s ETA 116.0 days /
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 0% [                                     ]    0.8289 reads/s ETA 139.6 days \
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 0% [                                     ]    0.7288 reads/s ETA 158.8 days |
 0% [                                     ]    0.7288 reads/s ETA 158.8 days /
 0% [                                     ]    0.7288 reads/s ETA 158.8 days -
 0% [                                     ]    0.7288 reads/s ETA 158.8 days \
 0% [                                     ]    0.7261 reads/s ETA 159.4 days |
 0% [                                     ]    0.7261 reads/s ETA 159.4 days /

Original comment by federica...@gmail.com on 29 Sep 2011 at 8:36

Attachments:

GoogleCodeExporter commented 9 years ago 
Our servers don't have enough memory to run this workflow. I don't think you 
need to change any of the parameters. The -q flag does not apply to the 
reference file (only works for the top Mosaik: Build module for read files) so 
adding that will cause errors. The workflow seemed to be working fine, because 
even though it said 0% it was still analyzing the reads at "0.9980 reads/s ETA 
116.0 days" so it looks like it will just take a ridiculous amount of time. 
There isn't much you can do about this. You can send me the pipe file if there 
are still errors you cannot resolve.

Original comment by shobe...@gmail.com on 29 Sep 2011 at 8:56

GoogleCodeExporter commented 9 years ago 
No actually even after the restarting I have the same behavior. The pipe is 
attached. I am attaching also the PE because I am having an error in the text 
that doesn't make any sense (to me maybe :) )

Fed

Original comment by federica...@gmail.com on 29 Sep 2011 at 8:56

Attachments:

GoogleCodeExporter commented 9 years ago 
I'm not able to connect to fgene1 right now but I'll test these workflows as 
soon as I can.

Original comment by shobe...@gmail.com on 29 Sep 2011 at 9:13

GoogleCodeExporter commented 9 years ago 
Sorry for the delay on this issue. I ran both of these workflows on fgene1 and 
did not receive any weird errors. Both workflows got to the aligner module 
which takes 150+ days to complete. If there is still a problem here, other than 
the fact that it takes a very long time, could you explain it to me again?

thanks,
Sam

Original comment by shobe...@gmail.com on 6 Oct 2011 at 11:40