error during Compressing corrected reads (with gzip) about spades HOT 5 CLOSED

Well, it seems that gzip failed on your system due to some reason. Most probably there was some I/O error (e.g. lack of free disk space).

from spades.

Hi!

I have a similar issue! And here's the thing!

When I execute this command by a .sh file it's ok. However, when I do it as a SLURM job, i get this error here:

'''
== Error == system call for: "['gzip', '-f', '-7', '/mnt/testingSingularity/3.correct_by_BayesHammer/ERR1906853/corrected/filtered_max_ERR1906853_2.fastq.gz.2P.fastq.00.0_0.cor.fastq']" finished abnormally, err code: 127
'''

It 's really weird as it is the exact same thing!! I do have gzip on my environment and its permissions are fine. From command line it works, as a job it doesn't!

Do you have any idea what could be wrong?

Thank you very much for all your time and help,
Haris

from spades.

You may want to ask the administrators of your server. You may want to check your environment, etc. as error code 127 is usually returned by shell when a command / program is not found.

from spades.

Is there a specific path where spades is looking for gzip?

If I try to install in on my own, where is the best to do so?

Thank you very much for the quick reply!

from spades.

Nothing special. SPAdes uses your operating system facilities to run sub-tasks. We have no idea about the specifics of your cluster, so please contact your system administrator for this.

from spades.