Use of uninitialized value $decompression_path in concatenation (.) or string at /home/sli1/miniconda3/envs/atac3/bin/trim_galore line 2671.

[shl129]

I used trim_galore for sequence trimming with the command below: `$ trim_galore -q 25 --phred33 -e 0.1 --stringency 4 --paired -o clean/ raw/S1-1.fastq.gz raw/S1-2.fastq.gz

The terminal returned this:

Multicore support not enabled. Proceeding with single-core trimming. Path to Cutadapt set as: 'cutadapt' (default) Cutadapt seems to be working fine (tested command 'cutadapt --version') Cutadapt version: 1.18 single-core operation. Use of uninitialized value $decompression_path in concatenation (.) or string at /home/sli1/miniconda3/envs/atac3/bin/trim_galore line 2671. Proceeding with '' for decompression. at /home/sli1/miniconda3/envs/atac3/bin/trim_galore line 2671. To decrease CPU usage of decompression, please install 'igzip' and run again

Output will be written into the directory: /home/sli1/project/atac/BMDM/1212/clean/ Use of uninitialized value $decompression_path in concatenation (.) or string at /home/sli1/miniconda3/envs/atac3/bin/trim_galore line 2101. Can't exec "-d": No such file or directory at /home/sli1/miniconda3/envs/atac3/bin/trim_galore line 2101. Failed to read from file '/home/sli1/project/atac/BMDM/1212/raw/S1-1.fastq.gz' to perform sanity check: No such file or directory

But gzip has been installed and the gzip version is 1.12.

Can anyone help me?

[FelixKrueger]

Thanks for reporting this, this is indeed an oversight, caused by the fact that no default value was specified for cases when single-core operation, or when no pigz was found on the system. You now have the following options.

1. Install pigz on your system, and use -j 2 or more (optionally, install igzip in addition to pigz)
2. Clone the current dev version, in which I have tried to fix the bug: https://github.com/FelixKrueger/TrimGalore/tree/dev
3. Edit your trim_galore file, find the line https://github.com/FelixKrueger/TrimGalore/blob/a3c6a64ae71657f1a282e01134293e424177a7d5/trim_galore#L2440 and add my $decompression_path = 'gzip'; # default

I will in the next hours make a new release to fix this, and try to get it updated on Bioconda as well..

Apologies for the inconvenience, I hope this will be sorted out soon.

[FelixKrueger]

Just to quickly say, I have now made a new release (v0.6.10, a new Bioconda Pull-Request is ongoing. Best, Felix

[FelixKrueger]

The following command should hopefully fix everything by updating to the latest version v0.6.10:

conda update trim-galore

[shl129]

Thank you very much! I updated the package to the latest version, and it works!!!