When running growthpred on protein-coding ORFs of metagenomic reads (highly expressed genes were sorted out from this datset before and are uploaded as an extra file) only the optimal growth temperature but none of the other growthpred parameters is returned.
In the log file I get the following error message:
/bin/sh: line 1: 7060 Segmentation fault (core dumped) /local/gensoft2/exe/growthpred/v1.07/libexec/utilCUB -A 0.302613 -C 0.187839 -G 0.161389 -c 0 -t < ./out_file.oths
/bin/sh: line 1: 7062 Segmentation fault (core dumped) /local/gensoft2/exe/growthpred/v1.07/libexec/utilCUB -A 0.302613 -C 0.187839 -G 0.161389 -c 0 -t < ./out_file.hegs
Error in read.table(commandArgs(), header = TRUE) :
no lines available in input
this indicates me that there is a problem with the input file, but I just can’t figure out where the problem could be. My input files are recognized as fasta-files. I also don’t have problems running growthpred on other fasta-input files from assembled protein coding metagenome contigs. I was wondering if the error could be related to the short lengths of the input files (~175 bp)?
Thanks for your advices.