Error when using XARGS

[kabilov]

I try to use spring througth xargs.

function my_func() {
# arg1 = R1
# arg2 = options

R1=$(basename $1)
R2=${R1/_R1/_R2}
name=${R1%_R1*}
options=$2

spring -c -g $options -o $name.spring -i $R1 $R2; echo

}

export -f my_funct

options="--num-threads 8"
echo ${files[*]} |xargs -d" " -I{} -n1 -P$num bash -c 'my_func "$@"' _ {} "$options"

And for some fastq.gz files the following error is thrown:
terminate called after throwing an instance of 'std::runtime_error'
what(): Cannot create temporary directory.
environment: line 1: 25179 Aborted (core dumped) spring -c -g $options -o $name.spring -i $R1 $R2

It appears that this issue only occurs when running the script on a remote drive.
The same fastq files on the local drive don't throw the error.

[shubhamchandak94]

Hi @kabilov, can you try using the -w flag that allows you to set the working directory where Spring creates the temporary directory it works in? Any directory where you have read/write access is good (perhaps don't use /tmp/ since it's on RAM and might use too much of it).

[kabilov]

Hi @shubhamchandak94
Thank you for reply.

I tried using the -w flag to set the working folder to the local drive, but that didn't help.
I also want to add that sometimes this error does not appear.

Is there a possibility that the name of tmp folder is the same for different files?

[shubhamchandak94]

I think this is due to a race condition situation in the Spring code where it generates a random string and checks if it exists, and if not it tries to create a directory. If multiple instances are running it's possible that a directory of the same name is created between the check and the creation of the directory. I will look into this and try to fix over the next few days (will need a few more days after that to get the update into conda).

Quick question: how many files are you working with?

[kabilov]

In the test, 3 pairs of fastq files were compressed.

I usually use tmp name with nanoseconds time: tmp_$(date +%H:%M:%S:%N)

[shubhamchandak94]

I just pushed a fix attempt, can you try it out and see if it fixes the issue? If so, I will also update on bioconda. Thanks!

[kabilov]

I checked the corrected Spring, the error disappeared.
Thank you for your help.