how to completely uninstall masurca

[SolayMane]

how to completely uninstall masurca?
thank you

[alekseyzimin]

Just delete the entire MaSuRCA folder

[SolayMane]

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.

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On 7 March 2018 at 19:37, Aleksey Zimin ***@***.***> 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 <#2 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AVm1zKsKbQEqcqVqDZ6CNdmnYRwoG2lIks5tcCj2gaJpZM4R-QGy> .

[alekseyzimin]

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

[SolayMane]

Thank you Aleksey Zimin, it's a problem of space, I'll will fix that, have a nice day.

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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> .

[SolayMane]

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,

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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> > . >

[alekseyzimin]

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