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how to completely uninstall masurca #2
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Just delete the entire MaSuRCA folder |
Dear Zimin,
I have this problem during the assembly :
[jeudi 12 avril 2018, 13:00:47 (UTC+0200)] Processing pe library reads
[jeudi 12 avril 2018, 13:00:47 (UTC+0200)] Average PE read length 151
MIN_Q_CHAR: 33
Estimated genome size: 1157137089
[jeudi 12 avril 2018, 13:00:47 (UTC+0200)] Computing super reads from PE
Using linking mates
Running mega-reads correction/assembly
Using mer size 15 for mapping, B=17, d=0.029
Estimated Genome Size 1157137089
Estimated Ploidy 1
Using 50 threads
Output prefix mr.41.15.17.0.029
Pacbio coverage <30x, using the longest subreads
Coverage of the mega-reads less than 5 -- using the super reads as well
Coverage threshold for splitting unitigs is 45 minimum ovl 115
Running assembly
/home1/software/masurca/MaSuRCA-3.2.4/bin/mega_reads_assemble_cluster.sh:
line 586: CA.mr.41.15.17.0.029.log: Read-only file system
Assembly stopped or failed, see CA.mr.41.15.17.0.029.log
[jeudi 12 avril 2018, 13:15:45 (UTC+0200)] Assembly stopped or failed, see
CA.mr.41.15.17.0.029.log
you find in the attachement the log file
Thank you in davance for your help.
…On 7 March 2018 at 19:37, Aleksey Zimin ***@***.***> wrote:
Just delete the entire MaSuRCA folder
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Hi, please check your disk mount -- the assembler could not write log file to disk. Then re-generate assemble.sh and re-run. |
Thank you Aleksey Zimin, it's a problem of space, I'll will fix that,
have a nice day.
…On 12 April 2018 at 14:48, Aleksey Zimin ***@***.***> wrote:
Hi, please check your disk mount -- the assembler could not write log file
to disk. Then re-generate assemble.sh and re-run.
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<#2 (comment)>,
or mute the thread
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Dear Zimin,
I have launched masurca with the config file bellow :
PARAMETERS
#set this to 1 if your Illumina jumping library reads are shorter than 100bp
EXTEND_JUMP_READS=0
#this is k-mer size for deBruijn graph values between 25 and 127 are
supported, auto will compute the optimal size based on the read data and GC
content
GRAPH_KMER_SIZE = auto
#set this to 1 for all Illumina-only assemblies
#set this to 1 if you have less than 20x long reads (454, Sanger, Pacbio)
and less than 50x CLONE coverage by Illumina, Sanger or 454 mate pairs
#otherwise keep at 0
USE_LINKING_MATES = 1
#specifies whether to run mega-reads correction on the grid
USE_GRID=0
#specifies queue to use when running on the grid MANDATORY
GRID_QUEUE=all.q
#batch size in the amount of long read sequence for each batch on the grid
GRID_BATCH_SIZE=300000000
#coverage by the longest Long reads to use
LHE_COVERAGE=30
#this parameter is useful if you have too many Illumina jumping library
mates. Typically set it to 60 for bacteria and 300 for the other organisms
LIMIT_JUMP_COVERAGE = 300
#these are the additional parameters to Celera Assembler. do not worry
about performance, number or processors or batch sizes -- these are
computed automatically.
#set cgwErrorRate=0.25 for bacteria and 0.1<=cgwErrorRate<=0.15 for other
organisms.
CA_PARAMETERS = cgwErrorRate=0.15
#minimum count k-mers used in error correction 1 means all k-mers are
used. one can increase to 2 if Illumina coverage >100
KMER_COUNT_THRESHOLD = 1
#whether to attempt to close gaps in scaffolds with Illumina data
CLOSE_GAPS=1
#auto-detected number of cpus to use
NUM_THREADS = 50
#this is mandatory jellyfish hash size -- a safe value is
estimated_genome_size*estimated_coverage
JF_SIZE = 8000000000
#set this to 1 to use SOAPdenovo contigging/scaffolding module. Assembly
will be worse but will run faster. Useful for very large (>5Gbp) genomes
from Illumina-only data
SOAP_ASSEMBLY=0
END
It is taking until today 5 days ,
Its is normal to take this long time runining?
I have Illumina data with about 180X (2X150) and Pacbio reads with 5X in
covrage.
Estimated genome size is 850Mb
thank you,
…On 12 April 2018 at 15:01, Slimane khayi ***@***.***> wrote:
Thank you Aleksey Zimin, it's a problem of space, I'll will fix that,
have a nice day.
On 12 April 2018 at 14:48, Aleksey Zimin ***@***.***> wrote:
> Hi, please check your disk mount -- the assembler could not write log
> file to disk. Then re-generate assemble.sh and re-run.
>
> —
> You are receiving this because you authored the thread.
> Reply to this email directly, view it on GitHub
> <#2 (comment)>,
> or mute the thread
> <https://github.com/notifications/unsubscribe-auth/AVm1zJhvSZeKgMoXIo5_cdV1zluvZTQRks5tn1tIgaJpZM4R-QGy>
> .
>
|
180x Illumina may be too much, I would use 120x. Depending on your system it could take a week or so. |
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how to completely uninstall masurca?
thank you
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