ceres score in crispr screen

Question

[biology_inform]

hi all, Is there anyone who can successfully run CERES pipeline in R?

https://github.com/cancerdatasci/ceres

[seidel]

Are you looking for moral support or technical support? Have you tried using it with an older version of R and bioconductor? (i.e. circa 2019?). What sorts of errors do you get?

[biology_inform]

:) technical support.

my run is giving Error: Encountered internal Bowtie 2 exception (#1) Command: /Users/sudeeris/Downloads/bowtie2-2.5.1-macos-arm64/bowtie2-align-s --wrapper basic-0 -t -p 4 -a -v 0 -f -S hg19 /var/folders/hr/0x5lrx7s2fg_0hgrw94pdt8c0000gn/T//RtmppY1ven/guides.fa /var/folders/hr/0x5lrx7s2fg_0hgrw94pdt8c0000gn/T//RtmppY1ven/guides.sam (ERR): bowtie2-align exited with value 1 sh: samtools: command not found Error in value[3L] : failed to open BamFile: file(s) do not exist: ‘/var/folders/hr/0x5lrx7s2fg_0hgrw94pdt8c0000gn/T//RtmppY1ven/guides.bam’

this error and I think there is problem with the bowtie command but i couldnt solve the problem. Edit: I am. aware of the problem with the samtools command i already solved it.

Thanks in advance

[biology_inform]

they didnt provide a good tutorial thats why i cannot determine whether i have problem in input files

ps: but i cannot run the demo files

[seidel]

I see. Well given the bowtie2 error, I would say the most straightforward thing to do is make sure you can run bowtie2. You can try this with just a few lines of fastq data (as opposed to an entire data set, and remember fastq uses 4 lines per sequence record). Many of these things are solved one small step at a time.

[biology_inform]

I solved the issue with using bowtie. But now I am experiencing this issue;

Error in makeGRangesFromDataFrame(., seqinfo = genomeinfo, keep.extra.columns = T) :
The "start" and/or "end" columns contain NAs. Use 'na.rm=TRUE' to ignore the rows with NAs. In addition: Warning message: In .normarg_seqnames2(seqnames, seqinfo) : levels in 'seqnames' with no entries in 'seqinfo' were dropped

Shouldn't it be easily working for the demo dataset?

[Sajid]

I am running into the same issue:

RRuntimeError: Error in makeGRangesFromDataFrame(., seqinfo = genomeinfo, keep.extra.columns = T) : 
  The "start" and/or "end" columns contain NAs. Use 'na.rm=TRUE' to
  ignore the rows with NAs.

My thought is that this is possibly due to old package dependencies. If anyone has this example CERES code working on their local, please to share a requirements.txt file of your R packages.. Thanks