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Problem in running circrna #81

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FeiLiuEM opened this issue Oct 18, 2023 · 2 comments
Closed

Problem in running circrna #81

FeiLiuEM opened this issue Oct 18, 2023 · 2 comments
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bug Something isn't working

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@FeiLiuEM
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Description of the bug

Nextflow is an excellent standardized pipeline tool and helps me a lot.

When I use the circrna, it always report error:

Execution cancelled -- Finishing pending tasks before exit
WARN: Got an interrupted exception while taking agent result | java.lang.InterruptedException
ERROR ~ Error executing process > 'NFCORE_CIRCRNA:CIRCRNA:PREPARE_GENOME:HISAT2_EXTRACTSPLICESITES'

Caused by:
  Not a valid path value: 'null'

Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line

 -- Check '.nextflow.log' file for details
ERROR ~ Unexpected error [ClosedByInterruptException]

 -- Check '.nextflow.log' file for details
ERROR ~ Unexpected error [ClosedByInterruptException]

 -- Check '.nextflow.log' file for details

It doesn't seem to have read the file yet. But when I change the code to run eccdna, it works well.

Could you please tell me why?

Command used and terminal output

$nextflow run nf-core/circrna --input samplesheet_1.csv --outdir '/media/super/Hard_Disk_1/USING/circdna/HCMV/HCMV/fastq/result' --genome GRCh38 -profile docker

Relevant files

.nextflow.log

System information

N E X T F L O W ~ version 23.10.0
Hardware: Desktop
Executor: local
Container engine: Docker
OS: Ubuntu 22.04
version of circrna: revision: 18e580e [master]

@FeiLiuEM FeiLiuEM added the bug Something isn't working label Oct 18, 2023
@nictru
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nictru commented Nov 18, 2023

Could you retry this using the dev branch? You just have to add "-r dev" to the command.

@nictru
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nictru commented Jan 13, 2024

Closing this for now, feel free to re-open if the problems persist

@nictru nictru closed this as completed Jan 13, 2024
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