5). Troubleshooting

Table of contents

• Possible errors

Possible errors

Nextflow errors

Unable to acquire lock

Example error message:

N E X T F L O W   ~  version 24.04.4

Launching `main.nf` [nostalgic_bell] DSL2 - revision: 1ad9e34c91

ERROR ~ Unable to acquire lock on session with ID dae0895a-e811-4779-b769-87eb7d2f530e

Common reasons for this error are:
 - You are trying to resume the execution of an already running pipeline
 - A previous execution was abruptly interrupted, leaving the session open

You can see which process is holding the lock file by using the following command:
 - lsof /PATH/TO/LOCK

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

Typically this occurs for one of two reasons:
     1). The pipeline is already running elsewhere on the system.
            - No fix required, Only one instance of the pipeline can be run at once.
     2). A run was improperly exited (for example during a disconnection from the system.
            - Can be checked with htop, either manually kill the remaining processes, wait for the processes to finish or delete the work/ directory.

Insufficient /tmp/ storage

Example error messages:

Command error:
  INFO:    Converting SIF file to temporary sandbox...
  FATAL:   while extracting /PATH/TO/*.img: root filesystem extraction failed: failed to copy content in staging file: write /tmp/rootfs-*/*: no space left on device

Java HotSpot(TM) 64-Bit Server VM warning: Insufficient space for shared memory file: /tmp/hsperfdata_user/* Try using the -Djava.io.tmpdir= option to select an alternate temp location.

Error: Could not find or load main class ___.tmp.hsperfdata_user.*

In both cases this is due to insufficient storage space in the /tmp/ directory due to unsquashfs uncompress singularity images within /tmp/.
            - Either don't use conda to install/run Nextflow/Singularity or attempt the fix here (Note: edit the conf/profile.config).