unknown flag issues

[jeremysutherland]

Error msg:
unknown flag refData/sino_mel.snpTable

input:

./HAFpipe-line/HAFpipe_wrapper.sh -t 1,2,3,4 \
-l HAF-pipe.log \
-d HAFpipe-line/ \
-o exptData \
-v sino_mel.vcf \
-c NC_020527.1\
-s refData/sino_mel.snpTable \
-i simpute \
-b exptData/sino_mel_export.bam \
-e sanger \
-g 15 \
-r $REF

Doesn't matter if I take out that line "-s refData/sino_mel_export.bam" because then another flag gives the same error. Any suggestions?

harp 1.20.2 py311h3638109_0 conda-forge
r-base 4.3.2 h93585b2_0 conda-forge
tabix 1.11 hdfd78af_0 bioconda
py-bgzip 0.4.0 py311hdcc4c9d_4 conda-forge

[greensii]

Try adding a space between `-c NC_020527.1` and `\`

…

On Fri, Nov 17, 2023 at 8:36 AM Jeremy Sutherland ***@***.***> wrote: Error msg: unknown flag refData/sino_mel.snpTable input: ./HAFpipe-line/HAFpipe_wrapper.sh -t 1,2,3,4 \ -l HAF-pipe.log \ -d HAFpipe-line/ \ -o exptData \ -v sino_mel.vcf \ -c NC_020527.1\ -s refData/sino_mel.snpTable \ -i simpute \ -b exptData/sino_mel_export.bam \ -e sanger \ -g 15 \ -r $REF Doesn't matter if I take out that line "-s refData/sino_mel_export.bam" because then another flag gives the same error. Any suggestions? harp 1.20.2 py311h3638109_0 conda-forge r-base 4.3.2 h93585b2_0 conda-forge tabix 1.11 hdfd78af_0 bioconda py-bgzip 0.4.0 py311hdcc4c9d_4 conda-forge — Reply to this email directly, view it on GitHub <#10>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AGBIBT7B66AGJJN7EMUH7QDYE6G7NAVCNFSM6AAAAAA7QBTL3KVHI2DSMVQWIX3LMV43ASLTON2WKOZRHE4TSNJRGM2DSOI> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>