quickdb.bash

[ashafik1]

Hi there,

When I try to run the bash script I get the following errors:

node04:[bin] % ./quickdb.bash mm10 /rnadb Generating GTF ./quickdb.bash: line 92: /rnadb/genes.gtf: No such file or directory Generating GTF Done Generating gtRNAdb /rnadb/tse.tar.gz: No such file or directory tar (child): /rnadb/tse.tar.gz: Cannot open: No such file or directory tar (child): Error is not recoverable: exiting now tar: Child returned status 2 tar: Error is not recoverable: exiting now rm: cannot remove ‘/rnadb/tse.tar.gz’: No such file or directory Generating gtRNAdb Done Generating Fasta /rnadb/genome.2bit: No such file or directory mustOpen: Can't open /rnadb/genome.fa to write: No such file or directory Generating Fasta Done Starting TRAX makernadb ./quickdb.bash: line 126: maketrnadb.py: command not found

Thanks

[alba1735]

Hello,

You need to specify a folder you want to build the db into otherwise it defaults to /rnadb (for docker compatibility reasons) which probably doesn’t exist or you don’t have access to on your system. If you try running the command "./quickdb.bash mm10 rnadb” instead it should create a folder called rnadb with files in it from wherever you run the command. If you still receive an error, try running “mkdir rnadb” first to create the directory for the files then try running again. Sorry for the inconvenience I will update the documentation accordingly. Please let me know if you have any other issues.

-Alex Bagi

On May 13, 2021, at 7:43 AM, ashafik1 @.***> wrote:

Hi there,

When I try to run the bash script I get the following errors:

node04:[bin] % ./quickdb.bash mm10 /rnadb Generating GTF ./quickdb.bash: line 92: /rnadb/genes.gtf: No such file or directory Generating GTF Done Generating gtRNAdb /rnadb/tse.tar.gz: No such file or directory tar (child): /rnadb/tse.tar.gz: Cannot open: No such file or directory tar (child): Error is not recoverable: exiting now tar: Child returned status 2 tar: Error is not recoverable: exiting now rm: cannot remove ‘/rnadb/tse.tar.gz’: No such file or directory Generating gtRNAdb Done Generating Fasta /rnadb/genome.2bit: No such file or directory mustOpen: Can't open /rnadb/genome.fa to write: No such file or directory Generating Fasta Done Starting TRAX makernadb ./quickdb.bash: line 126: maketrnadb.py: command not found

Thanks

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[ashafik1]

Thank you, looks like that solved the problem. I appreciate the fast response!

[ashafik1]

I'm not sure if this may be a specific error on my end, but I get another error message:

Generating GTF Generating GTF Done Generating gtRNAdb Generating gtRNAdb Done Generating Fasta Generating Fasta Done Starting TRAX makernadb Traceback (most recent call last): File "maketrnadb.py", line 188, in getmaturetrnas.main(trnascan=[scanfile], genome=genomefile,gtrnafa=gtrnafafile,namemap=namemapfile, bedfile=dbdirectory+dbname+"-maturetRNAs.bed",maturetrnatable=dbdirectory+dbname+"-trnatable.txt",trnaalignment=transcriptstk,locibed=dbdirectory+dbname+"-trnaloci.bed",maturetrnafa=dbdirectory+dbname+"-maturetRNAs.fa",cmmodel = maturemodel, prokmode = prokmode) File "/mnt/icebreaker/data2/home/ashafik/trax/tRAX-master/getmaturetrnas.py", line 125, in main seqfile = tempmultifasta(((currtrans.name, currtrans.getmatureseq(addcca = not prokmode)) for currtrans in alltrnas)) File "/mnt/icebreaker/data2/home/ashafik/trax/tRAX-master/trnasequtils.py", line 88, in tempmultifasta fafile = tempfile.NamedTemporaryFile(suffix=".fa") NameError: global name 'tempfile' is not defined