Sorry, I've just resolved this problem, but now, actually, another one is
persisting....the one I tried to explain in the beginning.
When I use the option "-DI:trt", the following error appears:
Deleting old directory UTT_as_MIRA_assembly ... done.
Creating directory UTT_as_MIRA_assembly ... done.
Creating directory UTT_as_MIRA_assembly/UTT_as_MIRA_d_results ... done.
Creating directory UTT_as_MIRA_assembly/UTT_as_MIRA_d_info ... done.
Creating directory UTT_as_MIRA_assembly/UTT_as_MIRA_d_chkpt ... done.
Could not create directory for temporary MIRA data
parameters/UTT_as_MIRA_d_tmp_6sFWhk: No such file or directory
Fatal error (may be due to problems of the input data or parameters):
********************************************************************************
* Could not create MIRA tmp directory
"parameters/UTT_as_MIRA_d_tmp_6sFWhk": *
* is some part of the path not existing or access protected?
*
********************************************************************************
Bastion suggested some points, but I don't know hot to solve it... Now I've
attached the files. :)
Thank you
Adriana M. Froes
Laboratório de Microbiologia, Instituto de Biologia, Depto de Biologia
Marinha
Universidade Federal do Rio de Janeiro
Av. Carlos Chagas Filho 373, Sala A3-202, Bloco A (Anexo) do CCS
21941-599, Ilha do Fundão, Rio de Janeiro, RJ
On Thu, May 7, 2015 at 2:17 PM, Adriana Fróes <dricamfroes@xxxxxxxxx> wrote:
The script and manifest file generated by the are attached on this email.
Now I removed the backslash but other error are appearing, as
========================= Parameter parsing error(s)
==========================
* Parameter section: '-ALIGN'
* Parameter 'min_relative_score' can only be set as sequencing type
specific
* parameter (SANGER_SETTINGS, 454_SETTINGS, etc.pp)
* and not for COMMON_SETTINGS.
* Parameter section: '-ASSEMBLY'
* Parameter 'minimum_read_length' can only be set as sequencing type
specific
* parameter (SANGER_SETTINGS, 454_SETTINGS, etc.pp)
* and not for COMMON_SETTINGS.
* Parameter section: '-OUTPUT'
* Parameter 'savesimplesingletsinproject' can only be set as sequencing
type specific
* parameter (SANGER_SETTINGS, 454_SETTINGS, etc.pp)
* and not for COMMON_SETTINGS.
* Parameter section: '-LR'
* Parameter 'wqf' can only be set as sequencing type specific
* parameter (SANGER_SETTINGS, 454_SETTINGS, etc.pp)
* and not for COMMON_SETTINGS.
* Parameter section: '-AS'
* Parameter 'epoq' can only be set as sequencing type specific
* parameter (SANGER_SETTINGS, 454_SETTINGS, etc.pp)
* and not for COMMON_SETTINGS.
===============================================================================
Fatal error (may be due to problems of the input data or parameters):
********************************************************************************
* Error while parsing parameters, sorry.
*
********************************************************************************
Adriana M. Froes
Laboratório de Microbiologia, Instituto de Biologia, Depto de Biologia
Marinha
Universidade Federal do Rio de Janeiro
Av. Carlos Chagas Filho 373, Sala A3-202, Bloco A (Anexo) do CCS
21941-599, Ilha do Fundão, Rio de Janeiro, RJ
On Wed, May 6, 2015 at 8:36 PM, Chris Hoefler <hoeflerb@xxxxxxxxx> wrote:
It is hard to tell from your screenshots (can you please just attach the
script and manifest file to the email?), but I see at least two different
potential problems:
1) You are mixing multiple "parameters =" syntax with escaping the
newline character on a long parameters line. Pick one or the other. In
other words,
THIS
parameters = -GE:not=8 (more params...) (NO backslash at the end of
the line)
parameters = (more params...)
etc...
OR
parameters = -GE:not=8 (more params...) \ <- note the backslash
(more params) \
(more params) (no backslash on the final line)
2) Your editor may be wrapping your long lines (from your screenshot see
the last commented out parameters line). I don't know if this is the case,
but check that, because it's bad.
On May 6, 2015, at 5:37 PM, Adriana Fróes <dricamfroes@xxxxxxxxx> wrote:
Sorry Bastien,
I thought it was a simple problem, actually.
Well, I used the script to generate the manifest files that Marcelo
shared here. I just modified the beginning, to another path, as show
below, and some settings to 454 technology.
#!/bin/bash
TMPDIR="/home/afroes/TRN/mira_UTT_TMP" #change it on the manifest file
RUNDIR="/home/afroes/TRN/MIRA/"
NORMDIR="/home/afroes/TRN/NORM_TRIM/"
# Open a temp dir at local machine
rm -rf $TMPDIR
if [ ! -d "$TMPDIR" ]; then
mkdir $TMPDIR
Parfi
if [ ! -d "$RUNDIR" ]; then
mkdir $RUNDIR
fi
#go to work directory
cd $RUNDIR
#CREATE THE MANIFEST FILE
echo "
#manifest file for testing mira 4
project = UTT_as_MIRA
job = genome,denovo,draft
#parameters = -SB:bft=caf -GE:not=14 -SK:mmhr=1:pr=70:hss=2
parameters = -GE:not=8:kpmf=5 -SK:mmhr=1:pr=70:hss=2 -CL:ascdc=no \
parameters = COMMON_SETTINGS -AS:sd=y:nop=2 -DI:trt=$TMPDIR \
parameters = 454_SETTINGS -ALIGN:min_relative_score=75 -ASSEMBLY
minimum_read_length=100 -OUTPUT:savesimplesingletsinproject=yes -LR:wqf=no
-AS:epoq=no \
#parameters = -OUT:savesimplesingletsinproject=yes -LR:wqf=no -AS:epoq=no
-CL:qc=no:bsqc=no
output_result_caf=no:output_result_maf=yes:output_result_fasta=ye$
# now the shotgun 454 data
readgroup = DataForShotgun454
data = /home/afroes/OMG/raw_data_original/Public_454_fasta_files/*.fasta
technology = 454
default_qual
autopairing
Actually, now it keeps saying this:
========================= Parameter parsing error(s)
==========================
* Parameter section: '-CL'
* unrecognised string or unexpected character: parameters
* Parameter section: '-DI'
* unrecognised string or unexpected character: parameters
* (may be due to previous errors)
===============================================================================
Fatal error (may be due to problems of the input data or parameters):
********************************************************************************
* Error while parsing parameters, sorry.
*
********************************************************************************
->Thrown: void MIRAParameters::parse(istream & is, vector<MIRAParameters>
& Pv)
->Caught: main
I don't know why the error changed...
Adriana M. Froes
Laboratório de Microbiologia, Instituto de Biologia, Depto de Biologia
Marinha
Universidade Federal do Rio de Janeiro
Av. Carlos Chagas Filho 373, Sala A3-202, Bloco A (Anexo) do CCS
21941-599, Ilha do Fundão, Rio de Janeiro, RJ
On Wed, May 6, 2015 at 6:18 PM, Bastien Chevreux <bach@xxxxxxxxxxxx>
wrote:
On 06 May 2015, at 23:50 , Adriana Fróes <dricamfroes@xxxxxxxxx> wrote:
The script is generating the manifest files, Great. But on the script,on the line 23, if I use as is in the script (parameters = COMMON_SETTINGS
-AS:sd=y:nop=2 -DI:trt=$TMPDIR) it gets an error when I try to run MIRA
because tmp directory is on a NFS mount. So, the program advise me to use
the option "-DI:trt". If I use this option, another error appears, as shown
below:
[…]parameters/UTT_as_MIRA_d_tmp_wln6ID: No such file or directory
Could not create directory for temporary MIRA data
********************************************************************************
* Could not create MIRA tmp directory"parameters/UTT_as_MIRA_d_tmp_wln6ID": *
* is some part of the path not existing or access protected?*
********************************************************************************
Do you know what can be done?
Well, MIRA tells you:
1. "Could not create directory for temporary MIRA data …”
2. Could not create MIRA tmp directory
"parameters/UTT_as_MIRA_d_tmp_wln6ID”
And it asks whether it may be possible that some part of the path you
specified is not existing or has been create with access protection flags.
As I suspect the latter is pretty improbable, the former must be the case.
That is: your manifest file probably contains a line
-DI:trt=parameters
and there is no “parameters” subdirectory in the directory you launched
MIRA from, so MIRA cannot create temporary files there and that the program
thinks is fishy and stops.
Which brings me to my next point: that directory name seems suspicious,
as if the $TMPDIR variable of your manifest generating script were empty.
Or some other problem.
Which brings me to yet another point: Adriana, when you have questions
like these and seek help, please append enough information to your mails so
that people can help you efficiently without relying too much on guessing.
In this case: attaching the script which generates the manifest files as
well as the manifest file which led to the error would be *extremely*
helpful. Just a screenshot of the error is … not terribly informative.
B.
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