Error in creating annotation.refFlat

[KaiWu-Umich]

Hi there. Thanks a lot for building up this wonderful package which greatly helped biologist with limited basis for coding like me.

I am trying to run my first test sample, but I met this error:

Error in rule create_refFlat: jobid: 51 output: /home/coffeelover/NGStools/Reference_Files/annotation.refFlat

RuleException: CalledProcessError in line 51 of /home/coffeelover/sc-experiment/4-cell-lines/dropSeqPipe/rules/generate_meta.smk: Command ' set -euo pipefail; /home/coffeelover/NGStools/Drop-seq_tools-1.13 -m 80g -p ConvertToRefFlat ANNOTATIONS_FILE=/home/coffeelover/NGStools/Reference_Files/annotation.gtf OUTPUT=/home/coffeelover/NGStools/Reference_Files/annotation.refFlat SEQUENCE_DICTIONARY=/home/coffeelover/NGStools/Reference_Files/genome.dict ' returned non-zero exit status 126. File "/home/coffeelover/sc-experiment/4-cell-lines/dropSeqPipe/rules/generate_meta.smk", line 51, in __rule_create_refFlat File "/home/coffeelover/miniconda3/lib/python3.6/concurrent/futures/thread.py", line 56, in run

I downloaded GTF from Ensembl and re-named as annotation.gtf as required. I am not sure what exactly caused this error nor how to troubleshoot it. Could you please help me with this issue?

Thanks a million, Kai

[Hoohm]

Hello @KaiWu-Umich I would need the error message from the tool and not the one from snakemake.

What species are you using? There are some known issues with arabidopsis.

[Hoohm]

Closing this for now, feel free to reopen