Problem in running Celescope for RNA

[AndreaGhiroldi]

I've installed Celescope and run the test_script and everything worked. I've tried to run an analysis on one sample but I've got this error:

(celescope) andrea@Precision-7920-Tower:/hdd_a/andrea/Celescope$ sh run.sh
: not foundmulti_rna
run.sh: 2: --mapfile: not found
run.sh: 3: --genomeDir: not found
run.sh: 4: --thread: not found
run.sh: 5: --mod: not found

This is my run.sh file:
multi_rna
--mapfile ./my.mapfile
--genomeDir /hdd_a/andrea/Celescope/hs_ensembl_99
--thread 16
--mod shell\

Any suggestion? Thank you

[zhouyiqi91]

You forgot to add backslash at end of each line.
https://unix.stackexchange.com/questions/368753/what-does-this-command-with-a-backslash-at-the-end-do#:~:text=A%20backslash%20escapes%20the%20next,command%20to%20span%20multiple%20lines.

[AndreaGhiroldi]

Thank you for the response. However the \ was present at the end of each line. I've added a space between the last character of a line and the \ and this is the error occured.

(celescope) andrea@Precision-7920-Tower:/hdd_a/andrea/Celescope$ sh run.sh
usage: rna multi-samples [-h] --mapfile MAPFILE [--mod {sjm,shell}] [--queue QUEUE] [--rm_files] [--steps_run STEPS_RUN] [--outdir OUTDIR] [--thread THREAD] [--use_R3] [--debug] [--wells WELLS]
[--chemistry {auto,scopeV1,scopeV2.0.0,scopeV2.0.1,scopeV2.1.0,scopeV2.1.1,scopeV2.2.1,scopeV3.0.1,flv_rna,flv,bulk_vdj,bulk_rna,customized}] [--pattern PATTERN]
[--whitelist WHITELIST] [--adapter_3p ADAPTER_3P] [--outFilterMatchNmin OUTFILTERMATCHNMIN] [--soloCellFilter SOLOCELLFILTER] [--starMem STARMEM]
[--STAR_param STAR_PARAM] [--SAM_attributes SAM_ATTRIBUTES] [--soloFeatures SOLOFEATURES] --genomeDir GENOMEDIR
rna multi-samples: error: the following arguments are required: --mapfile, --genomeDir
run.sh: 2: --mapfile: not found
run.sh: 3: --genomeDir: not found
run.sh: 4: --thread: not found
run.sh: 5: --mod: not found

this is the run.sh file:
multi_rna
--mapfile /hdd_a/andrea/Celescope/my.mapfile
--genomeDir /hdd_a/andrea/Celescope/hs_ensembl_99
--thread 16
--mod shell \

Thanks

[zhouyiqi91]

It seems that the backslash was not properly added. You can try move all the arguments in one line to avoid this issue.
For example

multi_rna --mapfile /hdd_a/andrea/Celescope/my.mapfile  --genomeDir ..."

[AndreaGhiroldi]

Thank you. Now it seems to work. Thank you again