bs3-align printing version only

[nsmackler]

Hi, I built the genome without any issues and am now trying to align some reads. Unfortunately, bs3-align is just printing the version and exiting. Is there a verbose option to see what is happening?

Here are my commands: bs3-build -f Mmul_8.0.1_chrom_only.fa --rrbs --cut-site=MspI

bs3-align -g Mmul_8.0.1_chrom_only.fa -1 LID_100316.R1.fq.gz -2 LID_100316.R2.fq.gz -m 0.08 -o $sample.bs3 --rrbs -c C-CGG

This 2nd command returns: BS-Seeker3 beta

Any idea what is going on?

[khuang28jhu]

Hey man, Thanks for the comment. I am currently updating/re-organizing the RRBS part of the pipeline. I pulled that part down and that's why the code just exited. Sorry for the trouble will push asap.

[nsmackler]

No problem. Thanks for the response and please let me know when the working RRBS version is back up!

[SchulzLab]

Hi, I get exactly the same problem with the normal pipeline not using the --rrbs flag. Once I run (see command lines below) the bs3-align.py it returns only: BS-Seeker3 beta

In particular I am wondering that there are no files of the SNAP index in the folder where the reference file is located. To me it seems that nothing is being saved there, which may be the reason that the align routine simply terminates.

Thanks or any help, Marcel bs3-align.py -g hg19.fa -1 LNCaP_pooled_1_val_1.fq.gz -2 LNCaP_pooled_2_val_2.fq.gz -o LNCAPalignment bs3-align.py -g hg19.fa -i LNCaP_pooled_1_val_1.fq.gz -o LNCAPalignment

[SchulzLab]

Hi again, ok so I figured out what the problem is. After running the example, which worked I realised that the command line parameters of bs3-align.py are incomplete in the readme. Most importantly the -d parameter is not explained there, which points to the location of the snap index. From what is written in the readme right now, it appears that the -g parameter fulfils this role, which is misleading. I think the Readme needs to be urgently updated. The correct alignment call to what I have given above is:

bs3-align.py -g reference_genome/hg19.fa -d reference_genome/ -1 LNCaP_pooled_1_val_1.fq.gz -2 LNCaP_pooled_2_val_2.fq.gz -o LNCAPalignment

Also I was not able to run the bs3-align.py from anywhere else than the original folder (see the other issue I opened in the GitHub forum). However, once I gave in and ran everything within the bs3 folder it worked.

Bests, Marcel

[nsmackler]

@khuang28jhu Any progress on this? I still can't get it to run -- even after trying @SchulzLab 's solution

[nsmackler]

@khuang28jhu Are there any updates/pushes to the RRBS portion of this? If not, then I don't think the mapper will work for my needs. Please let me know.

Thanks, Noah

[DolapoA]

I am also interested to know if the RRBS option is up and running.