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When the sample names contain spaces in the AMD, this are also included in the Sample_Name column for the nf-core/eager input table. This causes the nf-core/eager to crash when running the input table downloaded with AMDirT. See example bellow:
Error executing process > 'library_merge (Body 188)'
Caused by:
Process `library_merge (Body 188)` terminated with an error exit status (1)
Command executed:
samtools merge Body 188_udgnone_libmerged_rmdup.bam SRR6263249_rmdup.bam SRR6263255_rmdup.bam
samtools index Body 188_udgnone_libmerged_rmdup.bam
Command exit status:
1
Command output:
(empty)
Command error:
[E::hts_open_format] Failed to open file "188_udgnone_libmerged_rmdup.bam" : No such file or directory
samtools merge: fail to open "188_udgnone_libmerged_rmdup.bam": No such file or directory
Solution: spaces should be either stripped or replaced by an underscore or full stop.
The text was updated successfully, but these errors were encountered:
When the sample names contain spaces in the AMD, this are also included in the Sample_Name column for the nf-core/eager input table. This causes the nf-core/eager to crash when running the input table downloaded with AMDirT. See example bellow:
Solution: spaces should be either stripped or replaced by an underscore or full stop.
The text was updated successfully, but these errors were encountered: