Seems that by installing scalpel via Anaconda the "Microassembler" is not correctly installed, as you can see from below:
ls: cannot access /rds/general/user/cd3417/home/anaconda3/envs/analysis_Clara/share/scalpel-0.5.4-1/Microassembler/Microassembler: No such file or directory
Any help with this would be much appreciated.
Thanks!
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Hi, I am having the following error while trying to run sclapel somatic-discovery:
Command failure: microassembly (/rds/general/user/cd3417/home/anaconda3/envs/analysis_Clara/share/scalpel-0.5.4-1/Microassembler/Microassembler -R -I -C -F 1000000 -k 25 -K 90 -M 3 -l 25 -c 5 -x 0.01 -d 2 -u 10000 -b 1 -p /outdir/main/tumor -m bamfile.bam -g readgroups.txt -r regions-0-401215.fa >/outdir/main/tumor/logs/regions-0-401215.fa.log 2>&1)...
** 0 just got out of the pool [PID: 2433299 | exit code: 0 | exit signal: 0 | core dump: 0]
Merge DBs...
Load reference coverage...
Load loc2keys DB...
Computing hom/het state...
Num. Homozygous: 0
Num. Heterozygous: 0
Seems that by installing scalpel via Anaconda the "Microassembler" is not correctly installed, as you can see from below:
ls: cannot access /rds/general/user/cd3417/home/anaconda3/envs/analysis_Clara/share/scalpel-0.5.4-1/Microassembler/Microassembler: No such file or directory
Any help with this would be much appreciated.
Thanks!
Hi Clara, I had the same issue which is more related to the bioconda recipe than the Scalpel tool itself.
You should try again now. See this issue for more:
https://github.com/bioconda/bioconda-recipes/issues/19844