unable to run on mac #530
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I don't have a mac to reproduce your issue but it looks like your |
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THanks- here is what i have tried, which seems to take things forward a bit, but didnt solve it conda install time didnt seem to help i installed gnu-time and gnu-getopt through "brew install" then added them to path which is now /usr/local/opt/gnu-getopt/bin:/usr/local/opt/gnu-time/libexec/gnubin:/Users/christos/miniconda3/bin:/Users/christos/miniconda3/condabin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/ncbi/blast/bin:/Library/TeX/texbin:/opt/X11/bin then used again gridss\
The underlying error message can be found in ./gridss.full.20210929_112123.Christoss-giant-Mac.local.17274.log here is the log Wed Sep 29 11:21:23 BST 2021: Full log file is: ./gridss.full.20210929_112123.Christoss-giant-Mac.local.17274.log I realise the gnu-time is actually called gtime Christoss-giant-Mac:~ christos$ gtime --version so i wonder if the gridss script needs to be edited to look for gtime rather than time? Let me know if you think this makes sense thanks again |
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FWIW, i had run v1.5 using java -jar command when i try now using the same command structure java -jar gridss-2.12.1-gridss-jar-with-dependencies.jar O=/Volumes/LaCie_rugged/P70_06/IlluminaWGS_P70_06/gridss.vcf ASSEMBLY=/Volumes/LaCie_rugged/P70_06/IlluminaWGS_P70_06/D5-78408_gridss.bam I=/Volumes/LaCie_rugged/P70_06/IlluminaWGS_P70_06/D5-78408_merged.bam REFERENCE_SEQUENCE=/Volumes/Toshiba4Tb/GenomeReferences/hg38.fa i get not sure if this easier to solve? |
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Rereading the error message I see:
Which means my
But I'm still trying to get the
This is the root cause: you are unable to set the your file handle ulimit (maybe different args on macOS?) I've fixed this issue (in dev) by ignoring the result of the ulimit. Your current ulimit might already be sufficient so there's no reason to die this early. If you want to test this yourself, edit your |
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thanks- there is a problem in mac apparently- i have tried setting the max open files to 1000000, and editing gridss, but still no luck Using working directory "." The underlying error message can be found in ./gridss.full.20211001_112529.Christoss-giant-Mac.local.43823.log Log file Fri Oct 1 11:25:29 BST 2021: Full log file is: ./gridss.full.20211001_112529.Christoss-giant-Mac.local.43823.log here is my edited script, does it look correct? ulimit -n $(ulimit -Hn) || true # Reduce likelihood of running out of open file handles |
Looks like the reason your change failed was that you changed the |
Hi, it is possible i am doing something very stupid, so i apologise in advance.
I compiled with conda (miniconda3) on a Mac Mojave.
I am trying to run as follows
gridss\
and i get
--
WARNING: "getopt --test"` failed in this environment.
WARNING: The version of getopt(1) installed on this system might not be compatible with the GRIDSS driver script.
Using working directory "."
Tue Sep 28 12:06:47 BST 2021: Full log file is: ./gridss.full.20210928_120647.Christoss-giant-Mac.local.7821.log
Tue Sep 28 12:06:47 BST 2021: Found /usr/bin/time
/usr/bin/time: illegal option -- -
usage: time [-lp] command.
/usr/bin/time: illegal option -- a
usage: time [-lp] command.
Tue Sep 28 12:06:47 BST 2021: Unexpected /usr/bin/time version. Not logging timing information.
Tue Sep 28 12:06:47 BST 2021: Unable to find gridss jar. Specify using the environment variant GRIDSS_JAR, or the --jar command line parameter.
"gridss_jar=$(find_jar GRIDSS_JAR gridss)" command completed with exit code 66.
The underlying error message can be found in ./gridss.full.20210928_120647.Christoss-giant-Mac.local.7821.log
log file
Tue Sep 28 12:06:47 BST 2021: Full log file is: ./gridss.full.20210928_120647.Christoss-giant-Mac.local.7821.log
Tue Sep 28 12:06:47 BST 2021: Found /usr/bin/time
Tue Sep 28 12:06:47 BST 2021: Unexpected /usr/bin/time version. Not logging timing information.
Tue Sep 28 12:06:47 BST 2021: Unable to find gridss jar. Specify using the environment variant GRIDSS_JAR, or the --jar command line parameter.
so it can't find the .jar, although i thought my command is pointing to it?
Any help welcome!
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