I have PE HiSeq4000 data that has been already trimmed using Trimmomatic, and Error Corrected using allpaths-LG. What would be my syntax for a5miseq?
My understanding is that I should use --begin=2 --end=5, since I am starting beyond pre-processing step 1, but I want fully assembled contigs and assemblies, respectively.
The STDERR message I am receiving is as follows:
Module slurm/16.05.8 loaded
Module openmpi/2.0.1 loaded
Module a5miseq/20160825 loaded
[a5] Begin: 22:57 on 8-3-2017
[a5] Found the following libraries:
raw1:
id=raw1
p1=/home/aksrao/FUSARIUM/Compare_Assemblers/Error_Correction/bbtools/bbduk_AksR_bbtoolsEC_EthFoc11_R1.fq
p2=/home/aksrao/FUSARIUM/Compare_Assemblers/Error_Correction/bbtools/bbduk_AksR_bbtoolsEC_EthFoc11_R2.fq
[a5_s2] Can't find error corrected reads bbduk_AksR_bbtoolsEC_a5miseq_EthFoc11.ec.fastq at /share/apps/a5pipeline-20130326/bin/a5_pipeline.pl line 225, <LIB> line 3.
What should be my syntax to account for pre-processed PE data (i.e. trimming & EC already completed)? i.e. how should I prevent
Can't find error corrected reads
I am using a5miseq version 20160825, described by manuscript at - https://www.ncbi.nlm.nih.gov/pubmed/25338718, and command line help prompt for the Perl script reads as follows:
user@farm:~/FUSARIUM/Compare_Assemblers/a5miseq$ perl /share/apps/a5miseq-20160825/bin/a5_pipeline.pl
A5-miseq version 20160825
Usage: a5_pipeline.pl [--begin=1-5] [--end=1-5] [--preprocessed] [--threads=4] [--debug] [--metagenome] <lib_file> <out_base>
Or: a5_pipeline.pl <Read 1 FastQ> <Read 2 FastQ> <out_base>
Or: a5_pipeline.pl <Read 1,2 Interleaved FastQ> <out_base>
<out_base> is the base file name for all output files. When assembling from
a single library, the fastq files may be given directly on the command line.
If using more than one library, a library file must be given as <lib_file>.
The library file must contain the filenames of all read files.
If --preprocessed is used, <lib_file> is expected to be the library file
created during step 2 of the pipeline, named <out_base>.preproc.libs. Note
that this flag only applies if beginning pipeline after step 2.
The executable was downloaded as a tarball from Google Archives - http://bit.ly/2wxcczQ
