run error

[carlferr]

hi,
I'm using nanodisco for the analysis of methylation profile.
I downloaded and built nanodisco via singularity as suggested in the manual.
here my CL:

singularity pull --name nanodisco.sif library://fanglab/default/nanodisco
singularity verify nanodisco.sif
Verifying partition: FS:
45AD365F84BDF7402CC3CA83F93AC2888FC02443
[REMOTE]  Alan Tourancheau <[email protected]>
[OK]      Data integrity verified

INFO:    Container verified: nanodisco.sif

singularity build --sandbox nd_env nanodisco.sif

Then I opened nanodisco enviroment and I run the preprocessing step

singularity run --no-home -w nd_env
root@nanodisco:~/dataset$ nanodisco preprocess -p 10 -f barcode01/ -s barcode01 -o ../analysis/preprocessed_subset -r ../reference/ref.fasta
[2022-09-09 11:28:04] Localize all fast5 files.
[2022-09-09 11:28:04]     Found 23 fast5 files.
[2022-09-09 11:28:04] Extract sequences from fast5.
 Processed fast5 [-------------------------]   0% eta:  ?s (elapsed: 00:00:00)Error in { : 
  task 1 failed - "task 2 failed - "HDF5. Object header. Can't open object.""
Calls: extract.sequence -> %dopar% -> <Anonymous>
Execution halted
HDF5: infinite loop closing library
      L,G_top,T_top,P,P,Z,FD,E,SL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL
Unexpected error during read extraction process.

This command gave me an "HDF5: infinite loop closing library" error, could you help me to solve this issue?
Thanks in advance

[touala]

Hello @carlferr,

Unfortunately, I don't know what the issue could be simply from this error message. Are you still facing this issue?

From the commands you reported, I would not recommend to use nanodisco as a sandbox (--sandbox) outside of the provided tutorial/example. You should run it as follow: singularity exec nanodisco.sif nanodisco. Please let me know if you still have issues.

Best,

Alan