schlosslab / schloss_pacbio16s_peerj_2015 Goto Github PK

Hi,

thank you for posting the article. It seems an interesting work. In particular, for me, the results about potential bias in error randomness are noteworthy and I am looking forward to future studies on that point. However, I am missing some qualification here. The chemistry used is P4-C2. P6-C4 is now available and seems to be a significant improvement. While technically totally different, the quality differences observed by using a different chemistry with ONT MinION is striking. And while the differences will probably not be that pronounced with PacBio, I nevertheless find the statement "[...] the error rates we observed with the PacBio platform were nearly 5-fold higher than what has previously been reported. It appears that the promise offered by the PacBio platform has not been realized." in the conclusion somewhat too strong in light of the new chemistry. Accordingly, I think readers might benefit from including a respective reference/sentence to clarify that the chemistry might potentially have an effect and might reduce the error rate. In any case, the 5-fold higher error rate is something that I find of interest too...

Looking forward to your comments.

Best,

Cedric

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()

Missing V1-V5 in listing of regions that were analyzed