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I am using hmmSplicer-0.9.5 to map reads (SRR066576.fastq) to the Pfalciparum genome (PlasmoDB-9.1) and the software is issuing the following ERROR MESSAGE:
'Could not find find any reads in "results/Pfalciparum/tmp/bowtieHalf.fastq"'
No alignments
/home/roylab/roylab_bin/hmmSplicer-0.9.5/hmmWithQuality.py:658: RuntimeWarning: invalid value encountered in divide
pi_bar /= K
The program terminates without finding any splice junctions. That is contrary to previously published results.
It looks like the software is not generating a file of half-reads for bowtie mapping?
Anyone have any insight to this error and steps to correct it?
Thanks!
'Could not find find any reads in "results/Pfalciparum/tmp/bowtieHalf.fastq"'
No alignments
/home/roylab/roylab_bin/hmmSplicer-0.9.5/hmmWithQuality.py:658: RuntimeWarning: invalid value encountered in divide
pi_bar /= K
The program terminates without finding any splice junctions. That is contrary to previously published results.
It looks like the software is not generating a file of half-reads for bowtie mapping?
Anyone have any insight to this error and steps to correct it?
Thanks!