Not able to run Contrail assembler with fasta and fastq file formats...

Question

[saranpons3]

Hello All, I'm trying to run contrail on sample fasta and fastq data sets(Example: Ba10k.sim1.fq) in Hadoop single node cluster environment. But hadoop throws the following error messages

            Build Initial:  job_201612131400_0067 239 sException in thread "main" java.io.IOException: No good reads
        at contrail.Contrail.buildInitial(Contrail.java:218)
        at contrail.Contrail.run(Contrail.java:1097).

             Could anybody answer this?

Answer 1

[saranpons3]

As i didn't get any replies in Biostars and find any manual for Contrail online, i mailed to the developer of Contrail, Michael Schatz who replied me the following

"Thank you for your interest but I discourage you from trying to use this code -- it is several years out of date, is not compatible with current version of Hadoop, and quite frankly there are better approaches for assembling large genomes today using succinct graph structures and other recent developments."

I felt it would be helpful to someone to produce his reply here,