SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Masurca error - assembler deleted prior to being run AeonJeffJ Bioinformatics 2 06-05-2018 11:41 PM
MaSuRCA installation error [email protected] Bioinformatics 1 06-09-2017 11:10 PM
MaSuRCA Assembler runCA Error rafaykhan De novo discovery 3 02-23-2017 06:11 PM
MaSuRCA error bsp017 Illumina/Solexa 18 05-15-2016 10:23 PM
MaSurCa Assembler Coverage. J.David General 0 01-21-2014 09:57 AM

Reply
 
Thread Tools
Old 06-16-2018, 01:36 PM   #1
Grendel26
Junior Member
 
Location: France

Join Date: Feb 2018
Posts: 4
Default Error using Masurca 3.2.6 assembler

Hi all, I'm actually using MaSuRCA-3.2.6 to assemble my genome and a ran the fallowing script:

```
#PBS -S /bin/bash
#PBS -l nodes=1pn=8:bigmem,mem=100gb
#PBS -e /pandata/ACG-0006_0027/LOGS/ACG-006_assembly.error
#PBS -o /pandata/ACG-0006_0027/LOGS/ACG-006_assembly.out
#PBS -N ACG-006
#PBS -q q1week


DATA
PE= pe 150 22 /pandata/LEPIWASP/ACG-0006_0027/frag_1.fastq /pandata/LEPIWASP/ACG-0006_0027/frag_2.fastq

END

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 = 0
#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 = 16
#this is mandatory jellyfish hash size -- a safe value is estimated_genome_size*estimated_coverage
JF_SIZE = 200000000
#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
```

Then, I got the asemble.sh file and I ran it as well and got the following .out:

```
[Sat Jun 16 22:32:45 CEST 2018] Processing pe library reads
[Sat Jun 16 22:49:04 CEST 2018] Average PE read length 150
[Sat Jun 16 22:49:05 CEST 2018] Using kmer size of 49 for the graph
[Sat Jun 16 22:49:06 CEST 2018] MIN_Q_CHAR: 33
WARNING: JF_SIZE set too low, increasing JF_SIZE to at least 1115876884, this automatic increase may be not enough!
[Sat Jun 16 22:49:06 CEST 2018] Creating mer database for Quorum
[Sat Jun 16 23:09:23 CEST 2018] Error correct PE.
[Sat Jun 16 23:11:49 CEST 2018] Error correction of PE reads failed. Check pe.cor.log.

`and .error: `

/panhome/TOOLS/MaSuRCA-3.2.6/assemble.sh: line 102: 46750 Aborted quorum_error_correct_reads -q $((MIN_Q_CHAR + 40)
) --contaminant=/panhome/TOOLS/MaSuRCA-3.2.6/bin/../share/adapter.jf -m 1 -s 1 -g 1 -a 3 -t 16 -w 10 -e 3 -M quorum_mer_db.jf pe.re
named.fastq --no-discard -o pe.cor.tmp --verbose > quorum.err 2>&1
```

Does someone have an idea of what is going on here? Thanks for your help.

The 2 fasta files are comming from an illumina Hiseq 3000 150bp and the genome size of my specie is around 1.5 GB.
Grendel26 is offline   Reply With Quote
Old 06-17-2018, 05:11 AM   #2
Grendel26
Junior Member
 
Location: France

Join Date: Feb 2018
Posts: 4
Default

I checked on internet and tried to change the JF_Size with JF_SIZE = 25500000000 and got this error:

Code:
line 102: 25712 Aborted                 quorum_error_correct_reads -q $((MIN_Q_CHAR + 40)
) --contaminant=/panhome/bguinet/TOOLS/MaSuRCA-3.2.6/bin/../share/adapter.jf -m 1 -s 1 -g 1 -a 3 -t 16 -w 10 -e 3 -M quorum_mer_db.jf pe.re
named.fastq --no-discard -o pe.cor.tmp --verbose > quorum.err 2>&1
and the .out
Code:
[Sun Jun 17 11:40:30 CEST 2018] Processing pe library reads
[Sun Jun 17 11:50:47 CEST 2018] Average PE read length 150
[Sun Jun 17 11:50:47 CEST 2018] Using kmer size of 49 for the graph
[Sun Jun 17 11:50:48 CEST 2018] MIN_Q_CHAR: 33
[Sun Jun 17 11:50:48 CEST 2018] Creating mer database for Quorum
[Sun Jun 17 12:19:01 CEST 2018] Error correct PE.
[Sun Jun 17 12:35:01 CEST 2018] Error correction of PE reads failed. Check pe.cor.log.
and the frag.fastaq files are correct:


Code:
/pandata/LEPIWASP/ACG-0006_0027$ file -b -i frag_1.fastq
text/plain; charset=us-ascii
/pandata/LEPIWASP/ACG-0006_0027$ file -b -i frag_2.fastq
text/plain; charset=us-ascii
and I cannot check the pe.cor.log file because it does not exist.
Grendel26 is offline   Reply With Quote
Reply

Tags
assembler

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 05:50 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO