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kundajelab / atac_dnase_pipelines

ATAC-seq and DNase-seq processing pipeline
BSD 3-Clause "New" or "Revised" License
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sbatch: error: unable to open file [account] #110

Closed odegoede closed 6 years ago

odegoede commented 6 years ago

Hi,

I'm trying to run the ATAC-Seq pipeline on SCG, and am hitting an error at the adapter trimming step: 'sbatch: error: Unable to open file smontgom ' (smontgom is my PI/account name). My command (from an interactive node, in the appropriate working directory) is:

bds_scr atac_Fl_unstim $HOME/atac_dnase_pipelines/atac.bds -q smontgom -species mm10 -nth 3 -auto_detect_adapter -pe -fastq1_1 [fastq_R1_file] -fastq1_2 [fastq_R2_file]

Attached is the log file. Any thoughts on why I'm receiving this error would be much appreciated! Thanks!

atac_Fl_unstim.BDS.log

leepc12 commented 6 years ago

Check md5sum of some BDS files.

$ md5sum ~/.bds/clusterGeneric/run.pl
fa575eef24c50ce3d53d8d4dce7b7ead  /home/leepc12/.bds/clusterGeneric/run.pl

If it's not fa575eef24c50ce3d53d8d4dce7b7ead then update BDS files with the following commands:

$ wget https://github.com/leepc12/BigDataScript/blob/master/distro/bds_Linux.tgz?raw=true -O bds_Linux.tgz
$ rm -rf $HOME/.bds/
$ mv bds_Linux.tgz $HOME && cd $HOME && tar zxvf bds_Linux.tgz
odegoede commented 6 years ago

Here's what I got for the initial md5sum check:

$ md5sum ~/.bds/clusterGeneric/run.pl
c8131abb7299be0a5a54e4b15d07e786  /home/odegoede/.bds/clusterGeneric/run.pl

So I updated with the commands you provided and got:

$ md5sum ~/.bds/clusterGeneric/run.pl
5618e799e16b02be8c459d91ef5fb66d  /home/odegoede/.bds/clusterGeneric/run.pl

This isn't the md5sum that you said, but I've restarted the pipeline and it has progressed into the adapter trimming step with no errors, so things are looking good. Thanks for your help!

leepc12 commented 6 years ago

@odegoede sorry, you are right. it should be 5618e799e16b02be8c459d91ef5fb66d. thanks. I am closing this.