Using instructions at https://sourceforge.net/p/ngopt/wiki/A5PipelineREADME/, I am opting to specify library files for my a5miseq runs. But I am getting errors, may be someone can tell me what is wrong with my run syntax? Details below. Thanks!
2 specific questions:
1. when using a custom adapter sequence library, can the directory path for this file be my local directory, or does it have to be in the same installation directory alongside the a5_pipeline.pl Perl script?
2. Do my input files require formatting? I've used these with a5miseq itself, but specifying them directly on command line, instead of in a library file. So it's weird that I am getting an error now, but not with my earlier runs...
Thank you!
Library file content:
[LIB]
p1=/home/aksrao/FUSARIUM/Compare_Assemblers/a5pipeline/UNALTERED/EthFoc-11.S285_L007.1.txt
p2=/home/aksrao/FUSARIUM/Compare_Assemblers/a5pipeline/UNALTERED/EthFoc-11.S285_L007.2.txt
ins=400
Run syntax:
/share/apps/a5miseq-20160825/bin/a5_pipeline.pl --end=5 mylibs1 a5miseq2_EthFoc11 --adapter=/home/aksrao/FUSARIUM/Compare_Assemblers/a5miseq2/PC_adapters.fa
STDERR:
[a5] Found the following libraries:
raw1:
id=raw1
p1=/home/aksrao/FUSARIUM/Compare_Assemblers/a5pipeline/UNALTERED/EthFoc-11.S285_L007.1.txt
p2=/home/aksrao/FUSARIUM/Compare_Assemblers/a5pipeline/UNALTERED/EthFoc-11.S285_L007.2.txt
ins=400 ERROR: The file "/home/aksrao/FUSARIUM/Compare_Assemblers/a5pipeline/UNALTERED/EthFoc-11.S285_L007.1.txt " contains unsupported characters such as quotes, spaces, or &:%?*><$. Please ensure that all sequence input file names are free from unsupported characters
And the head of input file #1 (specified as p1 in the library file reads):
@J00113:201:HCK5TBBXX:7:1101:31690:1191 1:N:0:NGGAACAA
TNAGACAGATGGCCAATGGCTCCGCTCAATTGAGAAGTGCCGTGTCGGAATTGCTGGAGAGATCGGAAGAGCACACGTNTGANCTCNAGTCACTGGAACAAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAACCAACGCCCCCG
+
A#AAFFAFJJJJJJJJJJJJFJJJJJFJJJJJJ7JJJJJJJJAFAJJAFJAF7AFFFJJJJJJJJJJJJFJJJJJFAA#JJJ#JJF#JJJJJJJJ7JJJJJFAFJFF<JFJAJJ<JF-F7-A<FAJJJJJJJJAJ--------))--)--
@J00113:201:HCK5TBBXX:7:1101:32096:1191 1:N:0:NGGAACAA
CNCAAACCTTCTTTTCCCCGCCGAACAACTCGGGCAACCCTAACGCGGCCGCCCGGGTGCCTAGCGGAGCCTCGGTGGNCACNTCCNGCAACTTTCCTGGGATGCGGAGTGAGACGTCCAGCTTGAGCGGAGAGTCTGGAGAGTTATCCA
+
A#AFFFFA-AFJJAJJJAJFJJJJJJJJJJJJ<FJJJJFJJJJJ7FFJJ-AJJJJJJ<AJJJJJJJF<FJJJJFJJJJ#JJF#JJJ#JFJFJ7JJJAAJFFAF-FFFFJ<F<--A<7AFJFJ<-7F-FJAFFJJ--<FJJ)-77-<F<JJ
@J00113:201:HCK5TBBXX:7:1101:32360:1191 1:N:0:NGGAACAA
GNAACGAACTCGACACCTCCAGCTCCGATACTACCAGCACTAGCAATGTCATCAGCTACTTTTGACACATAAGCACTGNCATNCGGNAGCCAATATCGGAAGAGAGGACGCGAGGTGACAGGTGGGTTCTTGAAAGAAGTGTAGTGGTTG
