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maximilianh / crisporWebsite

All source code of the crispor.org website
http://crispor.org
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Error writing primers to file #25

Closed jfreimer closed 5 years ago

jfreimer commented 5 years ago

I am trying to generate amplicon primers for guide RNAs. I am running the following command: python crispor.py hg38 sampleFiles/test/input.fa sampleFiles/test/output.tsv --satMutDir=sampleFiles/test/ -d

and getting the following error. I have looked in the primer3Out.txt file and the primers are there, but they are not getting processed and written properly in the next steps.

DEBUG:root:Running set -o pipefail; /scratch/groups/pritch/jake/crispor/crisporWebsite/bin/Linux/primer3_core /tmp/primer3In.txt > /tmp/primer3Out.txt INFO:root:Writing primers to sampleFiles/test/seq1_ontargetPrimers.tsv DEBUG:root:reading offtargets from /tmp/crisporpLUEKA/FuOwg3SoSc4U3oJnIDkt.bed.gz Traceback (most recent call last): File "crispor.py", line 8266, in <module> main() File "crispor.py", line 8264, in main mainCommandLine() File "crispor.py", line 8109, in mainCommandLine writeOntargetAmpliconFile("primers", batchId, options.ampLen, options.tm, pFh) File "crispor.py", line 5681, in writeOntargetAmpliconFile effScores = allEffScores[pamId] KeyError: 's20+'

jfreimer commented 5 years ago

Found the issue, it was doing to have NGG in the input fasta.