hicup2homer error in converting HiCPro bam file

[Lei-Guo]

Dear Developer,

I'm having trouble running hicup2homer to convert HiCPro bam files to Homer files. The command and errors are as below. Can you please help me? Thanks a lot.

hicup2homer BT12_hg19.bwt2pairs.bam

Processing BT12_hg19.bwt2pairs.bam

Undefined subroutine &main::get_csome_position called at hicup2homer line 104, <IN> line 2.

[re2srm]

I am having the same issue. Were you able to resolve it?

Thanks

[StevenWingett]

Hi,

Just wondering, where you using the hicup2homer script in its original location (i.e. in the HiCUP folder with the script hicup_module.pm)?

If I am remembering correctly, hicup2homer uses the subroutine get_csome_position, which is found in hicup_module.pm.

Does that resolve the issue?

STeven

[re2srm]

Thanks for replying.

I was using conda installation of hicup where everything was working fine except the hicup2homer. I wasn't specifying the script location but using conda path location automatically.

I downloaded latest version of hicup manually and used the script from the folder but still got the same error. I have now downloaded hicup version 0.8.2 manually and running the script from there is working. Not sure if it is an issue with the conda environment or something in the latest version.

[lldelisle]

Hi, The difference between the conda version and the version from download is that in conda we are using symlink to have them in the bin directory. Adding a line similarly to: https://github.com/StevenWingett/HiCUP/blob/1213d5abad05e3bf3b954e0fb32d1e18a6b7a3b1/Conversion/hicup2ncc#L11 in hicup2homer will solve the issue. @StevenWingett do you need a PR?

[StevenWingett]

Hi @lldelisle,

A PR would be great!

Thanks, Steven

[lldelisle]

For me the current version of hicup2homer does not work:

Summary of my perl5 (revision 5 version 34 subversion 0) configuration:

  Platform:
    osname=linux
    osvers=4.19.0
    archname=x86_64-linux-gnu-thread-multi
    uname='linux localhost 4.19.0 #1 smp debian 4.19.0 x86_64 gnulinux '

I have the same error as with the conda environment...

There are 2 fixes, @StevenWingett , I let you choose: https://github.com/lldelisle/HiCUP/tree/solve98_v1 https://github.com/lldelisle/HiCUP/tree/solve98_v2

[StevenWingett]

Hi,

Thanks for that! Actually, the second link appeared not work. Just to double-check, the second link should be:

https://github.com/lldelisle/HiCUP/tree/solve98v2

Is that correct?

Thanks,

Steven

[lldelisle]

Yes, sorry

[hu0002lu]

Hi, The difference between the conda version and the version from download is that in conda we are using symlink to have them in the bin directory. Adding a line similarly to:

https://github.com/StevenWingett/HiCUP/blob/1213d5abad05e3bf3b954e0fb32d1e18a6b7a3b1/Conversion/hicup2ncc#L11

in hicup2homer will solve the issue. @StevenWingett do you need a PR?

Hi I added the line to the hicup2homer script, but now it has more issues like: Use of uninitialized value $positionR in concatenation (.) or string at /home/zh381/rds/rds-acf1004-afs-lab-rds/programs/HiCUP-0.9.2/Conversion/hicup2homer line 108, line 24578. Argument "4<M-]M-vM-+e\n" isn't numeric in bitwise and (&) at project/programs/HiCUP-0.9.2/Conversion//hicup_module.pm line 1107, line 24580. (got hundreds of lines of error like this, use of unintialized error), may i know how to solve the problem? Thanks!

[StevenWingett]

Hi again,

Sorry for not responding sooner, but I've been working on other projects.

lldelisle I like fix v1 the best:

https://github.com/lldelisle/HiCUP/tree/solve98_v1

Thanks very much for helping with the HiCUP project!

Best, Steven