Also consider using a development version of mira.
On Tuesday, 19 April 2016, Robert Bruccoleri <bruc@xxxxxxxxxxxxxxxxxxxxx>
wrote:
Dear Julien,
The problem is the use of the NFS mount for the temporary directory.
If you can't use faster disk storage than NFS, then just add
parameters= COMMON_SETTINGS -NW:cnfs=warn
after the job line to your manifest, and Mira will continue past this
problem.
Cheers,
Bob
On 04/19/2016 01:14 PM, VARALDI JULIEN wrote:
Dear Mira users,
I am trying to run Mira on paired-end Illumina reads (2x250bp) and 454
shotgun reads for denovo assembly. I wrote the following control file to
run a test on a small subset of the data (2500 reads of each) :
#################################################################
project = MyFirstAssembly
job = genome,denovo,accurate
# now the Illumina paired-end data
readgroup = DataIlluminaPairedLib
autopairing
data = ../../data/Varaldi_LbFV_TTCAGC_L001_R1_001_test.fastq
../../data/Varaldi_LbFV_TTCAGC_L001_R2_001_test.fastq
technology = solexa
template_size = 250 850 autorefine
segment_placement = ---> <---
# now the shotgun 454 data
readgroup = DataForShotgun454
data = ../../data/HADOPUC01_test.fastq
technology = 454
##################################################################
I ran it this way:
~/TOOLS/mira_4.0.2_linux-gnu_x86_64_static/bin/mira script.mira.txt > log
and in the log file, I get the following error :
Deleting old directory MyFirstAssembly_assembly ... done.
Creating directory MyFirstAssembly_assembly ... done.
Creating directory MyFirstAssembly_assembly/MyFirstAssembly_d_results ...
done.
Creating directory MyFirstAssembly_assembly/MyFirstAssembly_d_info ...
done.
Creating directory MyFirstAssembly_assembly/MyFirstAssembly_d_chkpt ...
done.
Creating directory MyFirstAssembly_assembly/MyFirstAssembly_d_tmp ... done.
WARNING WARNING WARNING!
It looks like the directory MIRA uses for temporary files
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp
is on a NFS (Network File System) mount. This will slow down MIRA
*considerably*
... by about a factor of 10!
If you don't want that, you have three possibilities:
1) RECOMMENDED! Use -DI:trt to redirect the tmp directory somewhere else
on a
local disk or even SSD.
2) ALSO POSSIBLE: put the whole project somewhere else on your file system.
3) ABSOLUTELY NOT RECOMMENDED AT ALL: use "-NW:cnfs=warn" to tell MIRA not
to stop when it finds the tmp directory on NFS.
If you do not know what NFS is and which directory to use in "-DI:trt", ask
your local system administrator to guide you.
Fatal error (may be due to problems of the input data or parameters):
********************************************************************************
* Tmp directory is on a NFS mount ... but we don't want that.
*
********************************************************************************
->Thrown: void Assembly::checkForNFSMountOnTmpDir()
->Caught: main
Aborting process, probably due to error in the input data or
parametrisation.
Please check the output log for more information.
For help, please write a mail to the mira talk mailing list.
Subscribing / unsubscribing to mira talk, see:
<//www.freelists.org/list/mira_talk>
//www.freelists.org/list/mira_talk
CWD: /pandata/varaldi/MIRA_LbFV/assemblies/test
Thank you for noticing that this is *NOT* a crash, but a
controlled program stop.
Failure, wrapped MIRA process aborted.
I suspect a problem with input data but I can’t figure out what is wrong.
I tried to run with illumina only, 454 only, but get the same message. Here
are the heads of the fastq files:
Illumina reads 1:
head ../../data/Varaldi_LbFV_TTCAGC_L001_R1_001_test.fastq
@MSQ-M01173:12:000000000-A5G1V:1:1101:13700:2421 1:N:0:TTCAGC
CTATCTCGCCGTAGGCCGCGATCGGCGAACGAATTTCACACCTCCGACGGACAGCTACCCGTGCGAGGATTGCGGCCACGGGGCTCTCTCCCCTGTACTAATTATAGCCTTTCGGTGAAAAAACGTGCGGAAAGCACAACGCCACGGCGCTTTGTCTTATACTCCCACCATAAAAACCAGGCTGCGAGGAAGGTCATGTCATTCGCTATCACCACCCGCCAGGCGGGGATCGTCGACGTCGATGCCGGGC
+
CCCCCFFFCCCCGFGGGGGGGGGGGGGGGGGGGHHHHHHHHGHGHGGGGGGGGGHHHHHHGGGGGGGGGHHHHGGGGGGGGGGGGHHHHHHHGHGHHHHHHHHHHHHHHHHHHGGCDCHHHHGGGGHHGGGGGGGGGGGGGGGGFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFDBEF;EFFFFBFAAEFFFFFFF
@MSQ-M01173:12:000000000-A5G1V:1:1101:13726:2421 1:N:0:TTCAGC
AATTATTACAAATTATTTCATTAATATTAACATTGGTTGGATTATTATATTTTTCTCTCCATTCAGAGAAATATAAAAGCACTTGATTAACTATATTATTTTTTACATTATATTCTAAATTATTTATAATATGATATTGTTGATACCAAATTTTTACAAAAGGTCTTAAAAAGAATCCTAAATTTAATTCATATTTATCAATATCATTTACATAATCAGTCAATAATATAATTTTCTCTAATGTAGTATC
+
CCCCCFFFFFFFGGGGGGGGGGHHHHHHFHHHHHHHHGGGHHHHHHHHHHHHHHHHHHHHHHHHGHHHHHHHHHHHHHHHGHHHHGHHHHHHHHHHHHHHHHHGHHHHHHHHHHHHHHHHGHHHHHHHHHHHHHHHHHHHHHHGFHFGHHHHHHHHGHHHGHGHHHHIHHHHGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGGHHHHHHHHHHHHHHGHGHHHHHHHHHHHHHHFHHFHHH
@MSQ-M01173:12:000000000-A5G1V:1:1101:12637:2422 1:N:0:TTCAGC
GATGAAAATAATGATTTGTTAATGTTATTATGGAAAGACAGAGCTCCTATATATATAATATATACTTCAGATTTTGAAATCTTTCATTATATAAAAGATGATATTAAATATTTAAAAAATATTACATTTCTTTTTTATATATTACATACGGAAAATAATAATCCTATACCTAAAAATATAAGAGAATCAAATATATTTATATTTTATTTACCAAGATTAGCAAAAACTATAGCTTTTGAAAAAGAAAAAA
Illumina reads 2
head ../../data/Varaldi_LbFV_TTCAGC_L001_R2_001_test.fastq
@MSQ-M01173:12:000000000-A5G1V:1:1101:13700:2421 2:N:0:TTCAGC
CGACGCGCGTGCGCCCCCAGCTGGCCGGATCGGCATTGGGTGCGCCGTCTTTGAACAGATCGTTGGCGAAGGTGACGCCGTGGCCGACAAAGCACGCTTCGCCGAGGGTGACGTATTCGCAGATAAAGCTGTGCGACTGAATTTTACTGCGCGCGCCGATGCTGACGTGGCGTTGGATCTCCACAAACGGCCCGACGAAGACATCGTCGCCGCGCCGGCAGCCGTACAGATTGCAGGGCTCGACAACGGT
+
CCCCCCCCCCCCGGGGGGGGGGHHGHGGGGGGGGGGHHHHEEGGGGGEFHGEHHHHHHFBHHGGFHHGGFFG3FHHGGGGDFGGHGGGG?HHHHHGG?AFGGGGGGGGCEHHGCCCFFGGFG?BFFFFGE9;CGGGGGGFFEFFFFFFFFFFFFFFFF=DDFBFFFFEFEFFD>
DFFFF0FF0FFEFFDAFFFFDFFF;DFFFFFFAEFFFF-@DADFFFAFFA..;.BF0B9F;0ACD.A;-;A;AD##
<javascript:_e(%7B%7D,'cvml','DFFFF0FF0FFEFFDAFFFFDFFF;DFFFFFFAEFFFF-@DADFFFAFFA..;.BF0B9F;0ACD.A;-;A;AD');>
@MSQ-M01173:12:000000000-A5G1V:1:1101:13726:2421 2:N:0:TTCAGC
AAATTGTTAAACCAATTTCTTTTAAACGTATAATAATATTTTTTTTTTCGTACCTTTCTTCATTAAAGAATGATGATTTATTTGTTTCCATTAAATTAAATTTAATTAAAAATGATTGTGAACGAAAGCGATTTATTGATTTTTACAGTAAATCATATACAGGTTCTTTAAAAGCCGTTTATATTATGGAAAATAATGATACTACATTAGAGAAAATTATATTATTGACTGATTATGTAAATGATATTGA
+
BBBBBFFFFFFFGGGGGGGGGGHHGHHGGHHHHGHHHFHFFGHGGGGGHCCGHGHHHEGHH5FHHHHHFHHHHHHHHGHHHHHHHHHGFFFHHHGHHGHFHHHHHHGHHGHFGHHGGHHHGHFHEFAFHG?GGGHHHHFHHHHHHHEHFFH2HHDHHHGHHGHHGGHHHGGGHHAGCCGFHHHHFGHHBFGHHHHHGFFHHHHHHGHHGHHGGFHHHHHHHHGHHHHFHEHHHFHHHGGGGGG0FGGGGB
@MSQ-M01173:12:000000000-A5G1V:1:1101:12637:2422 2:N:0:TTCAGC
CATAATTATTTTTTTCTATTTTTTCTTTTTATCAAAAAAAACCCTTATATATTCAAAACACTTGTTGTTGGATCTTGTATTCCGTTATAGATAGGACAGTTTAACAAAGTACATAAAGTAACACAACCACAATCATAAATTTTATCATCTACTTTACTATCAGATAGCGAAGCTAAACCTTTAACACTTATTATGTTATTTAATGGACCGTCAATTACGTTATTTATATAAAAAATTTTTTCTTTTTCAA
454 reads:
head ../../data/HADOPUC01_test.fastq
@HADOPUC01BU0HJ
AGACGCACTCACATAGTACATTATGTCAATTCATCCTTGATAGTATATCTATTATATATTCCTTACCATTAGATCACGAGCTTAATTACCATGCCGCGTGACACGCGAG
+HADOPUC01BU0HJ
FFFIIIIIIIIIIIIIIIIIGGDIIIIIIBBBFIIIDDDEIIIIIIIIIIIHHHIIIIIIIIFA;99>>><=BAAAFFFFFFFBE===EB@BEBGGFDEDFEA
=<AFD@HADOPUC01BXXF8
GTAATGTATACCGAATGAACGATTCAATTACACTCTTGAACAAGGCACACAGGGAGTA
+HADOPUC01BXXF8
FBBBHIIIIHEEIFFB?779BB:::77779BGIGE?<B<<<=:<<DEII>:11111=3
@HADOPUC01BST77
GATTCAATGATGCTATTCAATGGCTCACGGATCATAGAGTCATGGCTGGTGAAATCCCAAGTCAATGAATTATATTGTCGCTAAAGATTATTCTGAATCAGGAAG
I would greatly appreciate any help.
thank you all
Julien Varaldi
Biometry and Evolutionary Biology
University Lyon1
43 boulevard du 11 novembre 1918
69622 Villeurbanne
FRANCE
julien.varaldi@xxxxxxxxxxxxx
<javascript:_e(%7B%7D,'cvml','julien.varaldi@xxxxxxxxxxxxx');>
tel: 00334 72448101
fax: 00334 72431388
