Closed Nour-EddineS closed 1 year ago
Hey! This is unfortunately a known issue, see here: https://github.com/BoevaLab/FREEC/issues/106. the current work around in the pipeline is to provide a len file using this parameter: https://nf-co.re/sarek/3.1.2/parameters#cf_chrom_len
Dear @FriederikeHanssen, How can I create a len file please? Best regards,
If you click "Help" a description opens up:
Control-FREEC requires a file containing all chromosome lenghts. By default the fasta.fai is used. If the fasta.fai file contains chromosomes not present in the intervals, it fails (see: https://github.com/BoevaLab/FREEC/issues/106).
In this case, a custom chromosome length can be specified. It must be of the same format as the fai, but only contain the relevant chromosomes.
Example shown here (it is from a different genome build, so don't use this one): http://bioinfo-out.curie.fr/projects/freec/src/hg18.len
You can check your bed file, and then only keep the chromosomes from the fai of the genome build you are using that are also in the bed file. Then name it to something my_len.len and add it with the above parameter. To download the fai, either check your local igenomes installation if you ave it, or you can get from https://ewels.github.io/AWS-iGenomes/ here
Has this worked? If yes, could you close this issue?
@FriederikeHanssen Yes it works Thanks :)
Description of the bug
Dear SAREK Team, I want to use Somatic variant calling, but pipeline completed with errors. Thanks in advance for your help.
Best regards,
Command used and terminal output
Relevant files
nextflow.log samplesheet.csv tar_bla_cancer2.bed.tar.gz
System information
CPU: Intel(R) Xeon(R) CPU E5-1620 v3 @ 3.50GHz RAM: 32 GB Distribution: Ubuntu 22.04.1 LTS