Error using Masurca 3.2.6 assembler

[Grendel26]

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]

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

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

[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:

/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.

[dodo1981]

Masurca, failed to create mega-reads frg file

Hi Guys,
I need your help.
Tried to solve alone by changing and avoiding some parameters, however still I am getting the same error.

I am running Masurca with config file (see below).

Analysis of asembly PE illumina with nanopore stoped on the "Generating assembly input files step"

Error type:

error reading mega-reads file at /bioappl/src/MaSuRCA/MaSuRCA-3.3.3/bin/find_contained_reads.pl line 33, <FILE> line 23780.
[Mon Jun 10 18:27:32 CEST 2019] failed to create mega-reads frg file
[Mon Jun 10 18:27:32 CEST 2019] mega-reads exited before assembly

Could someone help me what to do now? where is the problem?

Thank you in advance, a lot!!!!
D

DATA
#Illumina paired end reads supplied as <two-character prefix> <fragment mean> <fragment stdev> <forward_reads> <reverse_reads>
#if single-end, do not specify <reverse_reads>
#MUST HAVE Illumina paired end reads to use MaSuRCA
PE= il 75 11 /bioinf/proj_data_chestnut/dorota_b/Illumina/R1.fastq /bioinf/proj_data_chestnut/dorota_b/Illumina/R2.fastq
#pacbio OR nanopore reads must be in a single fasta or fastq file with absolute path, can be gzipped
NANOPORE=/bioinf/proj_data_chestnut/dorota_b/Nanopore/nanopore.fastq
END

PARAMETERS
#PLEASE READ all comments to essential parameters below, and set the parameters according to your project
#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 0 if you have more than 15x coverage by long reads (Pacbio or Nanopore) or any other long reads/mate pairs (Illumina MP, Sanger, 454, etc)
USE_LINKING_MATES = 0
#specifies whether to run the assembly on the grid
USE_GRID=0
#specifies grid engine to use SGE or SLURM
GRID_ENGINE=SGE
#specifies queue (for SGE) or partition (for SLURM) 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=500000000
#use at most this much coverage by the longest Pacbio or Nanopore reads, discard the rest of the reads
#can increase this to 30 or 35 if your reads are short (N50<7000bp)
LHE_COVERAGE=25
#set to 0 (default) to do two passes of mega-reads for slower, but higher quality assembly, otherwise set to 1
MEGA_READS_ONE_PASS=1
#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 = 60
#these are the additional parameters to Celera Assembler. do not worry about performance, number or processors or batch sizes -- these are computed automatically.
#CABOG ASSEMBLY ONLY: set cgwErrorRate=0.25 for bacteria and 0.1<=cgwErrorRate<=0.15 for other organisms.
CA_PARAMETERS = cgwErrorRate=0.15
#CABOG ASSEMBLY ONLY: whether to attempt to close gaps in scaffolds with Illumina or long read data
CLOSE_GAPS=1
#auto-detected number of cpus to use, set this to the number of CPUs/threads per node you will be using
NUM_THREADS = 20
#this is mandatory jellyfish hash size -- a safe value is estimated_genome_size*20
JF_SIZE = 160000000
#ILLUMINA ONLY. Set this to 1 to use SOAPdenovo contigging/scaffolding module. Assembly will be worse but will run faster. Useful for very large (>=8Gbp) genomes from Illumina-only data
SOAP_ASSEMBLY=0
#Hybrid Illumina paired end + Nanopore/PacBio assembly ONLY. Set this to 1 to use Flye assembler for final assembly of corrected mega-reads. A lot faster than CABOG, at the expense of some contiguity. Works well even when MEGA_READS_ONE_PASS is set to 1. DO NOT use if you have less than 15x coverage by long reads.
FLYE_ASSEMBLY=0
END