BioInf-Wuerzburg / proovread

PacBio hybrid error correction through iterative short read consensus
MIT License
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Binary '~/proovread/bin/../util/bwa/bwa-proovread' neither in PATH nor executable #150

Closed Hulanyue closed 5 years ago

Hulanyue commented 5 years ago

Hi! I install 'proovread' again,and when I run make sample ,it show me the error:

hly@linux:~/biosoft/proovread$ make sample bin/proovread --sample --pre sample-results -o --threads 1 [Tue Oct 8 15:14:42 2019] Running proovread-2.14.1 under Perl 5.28.1 [Tue Oct 8 15:14:42 2019] Reading core config [Tue Oct 8 15:14:42 2019] Reading command line options [Tue Oct 8 15:14:42 2019] Logging parameter to sample-results/sample-results.p arameter.log [Tue Oct 8 15:14:42 2019] Checking short read files

F.antasticus_short.fq Detected FASTQ format Estimated short read length: 100 +-0 Estimating approximate number of short reads: 50.0k

[Tue Oct 8 15:14:42 2019] Checking required binaries

[ok] samtools-1.9 /usr/bin

------------------------------------------------------------------------------

[Tue Oct 8 15:14:42 2019] Binary '/home/hly/biosoft/proovread/bin/../util/bwa/b wa-proovread' neither in PATH nor executable Exited at 'main' 'bin/proovread', line 2057 Last call 'main::check_binary' 'bin/proovread', line 668 make: *** [Makefile:32:sample] Error 255

I set up the path : ncbi-blast-2.9.0+,it shows as follows:

declare -x PATH="/home/hly/biosoft/blast/bin:/home/biosoft/samtools-1.9/bin:/home/hly/perl5/bin:/home/hly/biosoft/blast/bin:/home/biosoft/blast/bin:/home/biosoft/samtools-1.9/bin:/home/hly/perl5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/home/hly/biosoft/blast/bin"

but when I run which blast,it show nothing!! And I run make sample,it show me the error.and in /proovread/util/bwa,there is nothing! is it normal?