search

alekseyzimin / masurca

GNU General Public License v3.0
239 stars 35 forks source link

how to completely uninstall masurca #2

Open SolayMane opened 6 years ago

SolayMane commented 6 years ago

how to completely uninstall masurca? thank you

alekseyzimin commented 6 years ago

Just delete the entire MaSuRCA folder

SolayMane commented 6 years ago

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 notifications@github.com wrote:

Just delete the entire MaSuRCA folder

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/alekseyzimin/masurca/issues/2#issuecomment-371239090, or mute the thread https://github.com/notifications/unsubscribe-auth/AVm1zKsKbQEqcqVqDZ6CNdmnYRwoG2lIks5tcCj2gaJpZM4R-QGy .

alekseyzimin commented 6 years ago

Hi, please check your disk mount -- the assembler could not write log file to disk. Then re-generate assemble.sh and re-run.

SolayMane commented 6 years ago

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 notifications@github.com 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 https://github.com/alekseyzimin/masurca/issues/2#issuecomment-380811485, or mute the thread https://github.com/notifications/unsubscribe-auth/AVm1zJhvSZeKgMoXIo5_cdV1zluvZTQRks5tn1tIgaJpZM4R-QGy .

SolayMane commented 6 years ago

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 slimane.khayi@gmail.com 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 notifications@github.com 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 https://github.com/alekseyzimin/masurca/issues/2#issuecomment-380811485, or mute the thread https://github.com/notifications/unsubscribe-auth/AVm1zJhvSZeKgMoXIo5_cdV1zluvZTQRks5tn1tIgaJpZM4R-QGy .

alekseyzimin commented 6 years ago

180x Illumina may be too much, I would use 120x. Depending on your system it could take a week or so.