Two fastq files —> FASTQ Groomer —> Trimmomatic —> 2Pared files to BWE-MEN —>RmDup —> GATK happlotypeCaller
No error found (all green boxes). However, the last command returns 0 lines and there is a message in the output saying:
java: error while loading shared libraries: libjli.so: cannot open shared object file: No such file or directory galaxy
The input file used to run HaplotypeCaller looks ok
Using database hg38
EDIT:
I gave ran again the same command and now I have got another error
ERROR MESSAGE: SAM/BAM/CRAM file input.bam is malformed. Please see https://software.broadinstitute.org/gatk/documentation/article?id=1317for more information. Error details: SAM file doesn’t have any read groups defined in the header. The GATK no longer supports SAM files without read groups
ERROR ------------------------------------------------------------------------------------------
On which server does that happen? It seems we need to fix the conda package or the conda installation.
How can I see in which server I am working on?