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mlin / PhyloCSF

Phylogenetic analysis of multi-species genome sequence alignments to identify conserved protein-coding regions

Home Page:http://compbio.mit.edu/PhyloCSF

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Issue with completing run

jdwheaton opened this issue · comments

commented

Mike Lin,

I have recently downloaded and successfully installed PhyloCSF on Mac OS X Mavericks, however I am having an issue running the program with FASTA alignments I have generated, which I will describe in detail below.

I am attempting to generate CSF scores for putative lncRNAs identified using RNA-seq and cufflinks. I have generated MAF alignments successfully and converted them to FASTA format. Using the mouse alignment as a reference, I have attempted to use 29mammals to score the alignment of a single exon between Mouse, Human, Rat, Cow, and Chimpanzee.

When I run the program, however, I get a blinking cursor and PhyloCSF never generates an output. I have tried several permutations of this, eventually testing alignment between Mouse and Human ONLY, with the same issue. This is particularly perplexing given that the example .fa files you provide with the package run fine and generate the exact scores you provide in the description, and my sequences are of similar length and (to my eyes) identical formatting.

Can you contribute any insight as to what may be the problem here? I'd be happy to send you a sample FASTA alignment if necessary, as I am a novice in bioinformatics and may be missing something simple.

Thanks for the help,

Josh Wheaton

phylocsf_problem

commented

I have since figured this out. Galaxy was outputting an additional blank line at the end of the FASTA file that PhyloCSF did not like. Simply removing this line has fixed the problem.