Error related to cutadapt version 2.5

[xie186]

Hi,

I'm using TrimGalore 0.6.4 and cutadapt 2.5. I was given the error shown as below:

Use of uninitialized value $major_version in numeric eq (==) at /group/bioinfo/apps/apps/TrimGalore-0.6.4/trim_galore line 615.
Use of uninitialized value $major_version in numeric gt (>) at /group/bioinfo/apps/apps/TrimGalore-0.6.4/trim_galore line 632.
Cutadapt major version was not 1 or higher. Simply too old...
[Thu Mar 26 13:55:48 2020]
Error in rule trimPE:
    jobid: 0
    output: output/trim_galore/3I0/, output/trim_galore/3I0.log, output/trim_galore/3I0/3I0_val_1.fq.gz, output/trim_galore/3I0/3I0_val_2.fq.gz

It seems that the reason is that cutadapt --version output the version information to STDERR instead of STDOUT for v2.5. I checked the latest version of TrimGalore:

TrimGalore/trim_galore

Line 2311 in beca802

$cutadapt_version = `$path_to_cutadapt --version`;

Here we may need to use:

$cutadapt_version = `$path_to_cutadapt --version 2>&1`;

Thanks,
Shaojun

[FelixKrueger]

Thanks for that, could you try the current development version to see if it now works? Cheers, Felix

[xie186]

I can successfully run it with the development version. Thank you so much for your quick response.
Best,
Shaojun

[FelixKrueger]

Excellent, thanks for the quick feedback!