Problems with Included Example Analyses in SPLASH 2.11.6

[stevenjbark]

Hello SPLASH2,

I have been able to get SPLASH2 installed and the scripts appear to be running. However, the examples included in the GitHub repository for SPLASH2 are not working and generating errors. Neither the primary example or the 10X example are functional.

In the primary example (download.py and input.txt) I think there is a problem with generating the kmc-tmp files. The kmc-tmp directories appear to be generated in the splash-tmp directory, but there are no files in the kmc-tmp directories. There are multiple errors indicated by "stage_1_thread-XXXX.log error entries. I opened the earliest stage_1_thread-0000.log error file entry:

DATE TIME STAMP /usr/bin/time -v /mount/mills/steve/SPLASH/kmc -t16 -fq -b -cil -cs65535 -k62 -m12 SRX145...._1.fastq.gz splash-tmp-7f37.../SRX145... _1 splash-tmp-7f37..../kmc_tmp_SRX145..._1
/bin/sh: /usr/bin/time: No such file or directory

In the case of the download-10X.py and input-10X.txt example, that gives a different error.
Error: Unknown extension of S10.txt.

I am using the current SPLASH=2.11.6 version on a RedHat Linux HPC system. Would running an earlier version be better?

Regards,
Steve
Baylor College of Medicine

[kdauria]

For the first error, splash is calling the time command at /usr/bin/time, but it isn’t found at that path on your system. Try sudo yum install time.

[stevenjbark]

I have checked that /usr/bin/time is installed on our cluster. I have also added the export PATH=/usr/bin:$PATH to my .bashrc and sourced this. The errors are the same.