RunAllPaths saying ValidateAllPathsInputs: command not found
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7.0 years ago
mafireyi ▴ 80

I am running Allpaths LG to assemble a guava genome. I have ran PrepareAllPaths.pl and it completed successfully. The PBS for PrepareAllPaths is as follows:

!/bin/bash
#PBS -N PrepareAllpaths
#PBS -q batch
#PBS -l nodes=cn01:ppn=12

cd $PBS_O_WORKDIR
mkdir -p NewGuava/data

#export PATH:/scratch/sysusers/godwin/allpaths-bin/bin:$PATH

/scratch/sysusers/godwin/allpaths-bin/bin/PrepareAllPathsInputs.pl DATA_DIR=$PBS_O_WORKDIR/NewGuava/data PLOIDY=2 IN_GROUPS_CSV=in_groups.csv IN_LIBS_CSV=in_libs.csv OVERWRITE=True

exit 0

I then ran RunAllPaths and its giving me all kinds of error messages.

My PBS file

#!/bin/bash
#PBS -N RunAllpaths
#PBS -q batch
#PBS -l nodes=cn01:ppn=12

cd $PBS_O_WORKDIR

export PATH:/scratch/sysusers/godwin/allpaths-bin/bin:$PATH

/scratch/sysusers/godwin/allpaths-bin/bin/RunAllPathsLG PRE=$PBS_O_WORKDIR DATA_SUBDIR=data RUN=firstrun REFERENCE_NAME=NewGuava TARGETS=standard OVERWRITE=True

exit 0

The error I am getting is

Unable to find optional long jumping reads (>20kb) for scaffolding.
Unable to find optional long reads for patching.
targetsToMake = 168

and

[VAPI] ValidateAllPathsInputs PRE=/scratch/sysusers/godwin DATA=NewGuava/data K=96 K_LONG=640 LONG_JUMPS=False LONG_READS=False REFERENCE=False WARN_ONLY=False
/bin/sh: ValidateAllPathsInputs: command not found

Please help debug this. Thanks

Assembly • 1.7k views
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6.9 years ago
aliceb ▴ 10

Hello,

 

I think am having the exact same problem. Did you have any luck figuring this out?

Here is the chunk of the log file before everything stops working:

"[VAPI] ValidateAllPathsInputs PRE=/cluster/scratch_xp/public/adennis/allpaths DATA=/REFERENCE/DATA K=96 K_LONG=640 LONG_JUMPS=False LONG_READS=False REFERENCE=False WARN_ONLY=False
/bin/sh: ValidateAllPathsInputs: command not found
make: *** [/cluster/scratch_xp/public/adennis/allpaths/REFERENCE/DATA/ValidateAllPathsInputs.report] Error 127"

 

I should note that I am running this on a unix computing cluster, and that I have had a few other problems not being able to find files (MergePairedFastbs, QualbStats, CacheReadsMerge, CompileAssemblyReport.pl, ParseMemMonitorOutput.pl, QualbStatsPlot.pl). My rather clumsy solution for these has been to make a symbolic link to them that is just one directory higher. However, that didn't work here!

 

Thanks!

Alice

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Do you know where the ValidateAllPathsInputs should be located? Have you tried adding this location to your path with:

export PATH=$PATH:/path/to/allpaths-bin/
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