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SchlossLab / Schloss_PacBio16S_PeerJ_2015

Repository to accompany "Sequencing 16S rRNA gene fragments using the PacBio SMRT DNA sequencing system"
MIT License
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shell script #3

Open kemin711 opened 9 years ago

kemin711 commented 9 years ago

I am new to this field, so forgive me if I sounds stupid.

In running the write.paper shell script, I am seeing the following error. It is looking for a reference file: v4/HMP_MOCK.filter.fasta that is not in my system. /references/HMP_MOCK.fasta was found in the current directory of the project. So what is the best way to fix this issue?

mothur > get.groups(fasta=v4/v4.trim.unique.good.filter.unique.fasta, name=v4/v4.trim.unique.good.filter.names, group=v4/v4.good.groups, groups=mock1.v4-mock2.v4-mock3.v4) Unable to open v4/v4.trim.unique.good.filter.unique.fasta. Trying default /remote/RSU/sw-cache/metag/bin/v4.trim.unique.good.filter.unique.fasta Unable to open /remote/RSU/sw-cache/metag/bin/v4.trim.unique.good.filter.unique.fasta Unable to open v4/v4.trim.unique.good.filter.names. Trying default /remote/RSU/sw-cache/metag/bin/v4.trim.unique.good.filter.names Unable to open /remote/RSU/sw-cache/metag/bin/v4.trim.unique.good.filter.names Unable to open v4/v4.good.groups. Trying default /remote/RSU/sw-cache/metag/bin/v4.good.groups Unable to open /remote/RSU/sw-cache/metag/bin/v4.good.groups You have no current groupfile, designfile, countfile or sharedfile and one is required. You must provide at least one of the following: fasta, name, taxonomy, group, shared, design, count or list. [ERROR]: did not complete get.groups.

mothur > seq.error(fasta=current, name=current, reference=v4/HMP_MOCK.filter.fasta, processors=8) [WARNING]: no file was saved for fasta parameter. [WARNING]: no file was saved for name parameter. You have no current fasta file and the fasta parameter is required. Unable to open v4/HMP_MOCK.filter.fasta. Trying default /remote/RSU/sw-cache/metag/bin/HMP_MOCK.filter.fasta Unable to open /remote/RSU/sw-cache/metag/bin/HMP_MOCK.filter.fasta

Using 8 processors. [ERROR]: did not complete seq.error.

mothur > quit()

pschloss commented 9 years ago

Thanks for the question. Aside from this problem, I hope you're finding the repository helpful. I think it should work fine with just using the HMP_MOCK.filter.fasta file that is in the main directory. I need to come back to this project and finish it up with some new data that we've gotten using the newer chemistry.