Persistent velveth-63: command not found

[sebetso388]

Good day Dr Birte Kehr

I tried to follow advice given to previous submissions..

Both velvet and popins are successfully compiled. Part of what the command process is looks for a program called velveth-63 which at no point was installed during compilation.
Neither velveth README file nor its website makes any mention of it. I did search online and there is no mention of velveth-63.
I then compiled velveth with MAXKMERLENGTH=63, no dice.

Kind Regards,
G. Sebetso

[bkehr]

Dear G Sebetso,

Did you set the paths to bwa, velveth, velvetg, samtools, and sickle in the file popins.config or did you add them to your PATH variable?

In case you added them to your PATH variable, you can either replace velvetg-63 and velveth-63 by velvetg and velveth in the popins.config file or rename your binaries to velvetg-63 and velveth-63.

When compiling velvet, two binaries are created: velvetg and velveth. I rename these binaries to velvetg-63 and velveth-63 when compiling with MAXKMERLENGTH=63.

Birte

[sebetso388]

Hi,

The two binaries were renamed as advised, however I immediately ran into another error shown below: I don't know if anyone else had a similar issue.

nohup: ignoring input and appending output to ‘nohup.out’
[PopIns 2020-10-08 14:32:30] Working directory created at ./UG13S29_GS
[PopIns 2020-10-08 14:32:31] Cropping unmapped reads from UG13S29_sorted.bam
[PopIns 2020-10-08 14:32:33] Map of low quality mates has 3834 records.
[PopIns 2020-10-08 14:32:33] Unmapped reads written to ./UG13S29_GS/paired.1.fastq, ./UG13S29_GS/paired.2.fastq, ./UG13S29_GS/single.fastq
terminate called after throwing an instance of 'std::__ios_failure'
what(): basic_ios::clear: iostream error

[bkehr]

Could you send me the exact command line you used for running popins?

[sebetso388]

Hi,

Below is the command;

nohup popins assemble -s UG13S29_GS UG13S29_sorted.bam 2> UG13S29_GS.err &