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chiulab / MSSPE-design

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Trouble running the code with the example provided #1

Open nsapoval opened 4 years ago

nsapoval commented 4 years ago

I have downloaded the repository and have tried executing the sample run using the MSA file provided.

./MSSPE-design.sh ZIKV-96seqs.fasta 13 500 250 50 0.1 2 -9000 8

I have tried running the code in two configurations of a virtual environment, and in both cases I get the same error pasted below. I am running on a x86_64 GNU/Linux 4.15.0-66-generic Ubuntu machine.

creating new files: ZIKV-96seqs.nospace.split.500mer.250overlap.fasta generating BLAST db running BLAST selecting forward primers cat: ZIKV-96seqs.nospace_first50.subtracted.13.kmers_output.txt: No such file or directory awk: cmd. line:1: fatal: division by zero attempted awk: cmd. line:1: fatal: division by zero attempted forward mean= forward stdev= filtering primers with Tm within 2 standard deviations of the mean written to ZIKV-96seqs.nospace.forward.13mers.tab selecting reverse primers cat: ZIKV-96seqs.nospace_last50_rc.13.kmers_output.txt: No such file or directory awk: cmd. line:1: fatal: division by zero attempted awk: cmd. line:1: fatal: division by zero attempted reverse mean= reverse stdev= filtering primers with Tm within 2 standard deviations of the mean

My virtual environments are as follows.

Environment 1 (Python 3.7.3):

biopython 1.74 py37h7b6447c_0
blast 2.9.0 pl526h3066fca_4 bioconda blast-legacy 2.2.26 2 biocore perl 5.26.2 h14c3975_0 primer3 2.5.0 pl526he1b5a44_0 bioconda pyfasta 0.5.2 pypi_0 pypi ...

Environment 2 (Python 2.7.16):

blast-legacy 2.2.26 2 biocore perl 5.26.2 h14c3975_0 primer3 2.5.0 pl526he1b5a44_0 bioconda pyfasta 0.5.2 pypi_0 pypi ...

ShenWei-wei commented 4 years ago

Try copy annotateTm.py, iterate_checkdimer.sh, kmer_count_fasta_top50.pl, MSSPE-design.sh, ntthal, pyfasta into /usr/bin/, It looks like the main shell call file iterate_checkdimer.sh direct does not add a path