Entering edit mode
I am using a5 Miseq pipeline but facing error while running example files of phix as well as sample files. [a5] ERROR:Unable to identify any properly paired reads [a5] ERROR: Please check that you have provided at least one library of paired-end reads with names conforming to the Illumina read pair convention.
Kindly help me out!
What is the command-line you are running?
Don't add comments as answers, add them as comments to the appropriate question / answer / comment. Could you fix this?
And what is the output of:
And
I asked for the output of the commands:
And
But anyway, the problem is with the SGA binary from A5_MiSeq:
If you are luck it is just a matter of setting sga execute permissions, but you may even have to recompile it.
yes it works. but now I am having following error [a5] Found only 3168 read pairs in library [a5] Using 3168 read pairs for mapping [a5] java -jar -Xmx512m '/home/ambrina/a5_miseq_linux_20160825/bin'/GetInsertSize.jar test.raw1.sub.pe.sam [a5] Printing preprocessed library file to test.preproc.libs [a5] Processed libraries: raw1: id=raw1 p1=test.s1/phiX_p1.fastq.split.r1.fq p2=test.s1/phiX_p1.fastq.split.r2.fq rc=0 ins=185 err=0.551 nlibs=1 libfile=test.library_1.txt [a5_s3] Scaffolding contigs from test.contigs.fasta with SSPACE [a5_s3] Scaffolding contigs from test.contigs.fasta with SSPACE [a5] Total contig length 5469 [a5] raw1: Insert 185, coverage 49.82, expected links 107 [a5] SSPACE -m 16 -n 10 -k 2 -a 0.4 -o 1 -x 0 -l test.library_1.txt -s test.contigs.fasta -b test.raw1 -d test.s3 > test.s3/test.raw1.out
Bowtie-build error; -1 at /home/ambrina/a5_miseq_linux_20160825/bin/SSPACE/bin/mapWithBowtie.pl line 43.
Bowtie-build error; -1 at /home/ambrina/a5_miseq_linux_20160825/bin/SSPACE/bin/mapWithBowtie.pl line 43. [a5_s4] Detecting and breaking misassemblies in test.crude.scaffolds.fasta with A5QC Illegal division by zero at /home/ambrina/a5_miseq_linux_20160825/bin/a5_pipeline.pl line 1556, <readfile> line 25344.