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SystemsGenetics / KINC

Knowledge Independent Network Construction
MIT License
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How to extract KINC network with container? #190

Open feltus opened 1 year ago

feltus commented 1 year ago

Hi all.

I am unable to install KINC so I need to use the container. I can only get KINC to output EMX/CMX/CCM files but not do a network extraction. Below is what I did that results in trying to write to a read-only file system and launching MPI jobs. Please help as my students are naturally frustrated and I want to leave them with KINC instead of WGCNA. Alex

#nextflow version 22.10.7.5853
module add openjdk/11.0.15_10-gcc/9.5.0
module add openmpi/4.1.4-gcc/9.5.0-ucx
nextflow run systemsgenetics/KINC-nf -with-singularity

####Pull KINC Docker image and convert to singularity SIF
singularity pull kinc-3-4-2.sif docker://systemsgenetics/kinc:3.4.2-cpu

singularity run -B ${PWD} ./kinc-3-4-2.sif kinc run extract \
  --emx "500.merged-gtex-kirp-kich-kirp-gem.log2.quantile.emx" \
  --ccm "500.merged-gtex-kirp-kich-kirp-gem.log2.quantile.ccm" \
  --cmx "500.merged-gtex-kirp-kich-kirp-gem.log2.quantile.cmx" \
  --format "tidy" \
  --output "500.merged-gtex-kirp-kich-kirp-gem.log2.quatile.800000-gcn.txt" \
  --mincorr  0.800000 \
  --maxcorr 1

[WARN  tini (997058)] Tini is not running as PID 1 and isn't registered as a child subreaper.
Zombie processes will not be re-parented to Tini, so zombie reaping won't work.
To fix the problem, use the -s option or set the environment variable TINI_SUBREAPER to register Tini as a child subreaper, or run Tini as PID 1.
--------------------------------------------------------------------------
A call to mkdir was unable to create the desired directory:

  Directory: /local_scratch
  Error:     Read-only file system

Please check to ensure you have adequate permissions to perform
the desired operation.
--------------------------------------------------------------------------
[node0077.palmetto.clemson.edu:997090] [[30396,0],0] ORTE_ERROR_LOG: Error in file util/session_dir.c at line 106
[node0077.palmetto.clemson.edu:997090] [[30396,0],0] ORTE_ERROR_LOG: Error in file util/session_dir.c at line 382
--------------------------------------------------------------------------
It looks like orte_init failed for some reason; your parallel process is
likely to abort.  There are many reasons that a parallel process can
fail during orte_init; some of which are due to configuration or
environment problems.  This failure appears to be an internal failure;
here's some additional information (which may only be relevant to an
Open MPI developer):

  orte_session_dir failed
  --> Returned value Error (-1) instead of ORTE_SUCCESS
--------------------------------------------------------------------------
[node0077.palmetto.clemson.edu:997083] [[INVALID],INVALID] ORTE_ERROR_LOG: Unable to start a daemon on the local node in file ess_singleton_module.c at line 582
[node0077.palmetto.clemson.edu:997083] [[INVALID],INVALID] ORTE_ERROR_LOG: Unable to start a daemon on the local node in file ess_singleton_module.c at line 166
--------------------------------------------------------------------------
It looks like orte_init failed for some reason; your parallel process is
likely to abort.  There are many reasons that a parallel process can
fail during orte_init; some of which are due to configuration or
environment problems.  This failure appears to be an internal failure;
here's some additional information (which may only be relevant to an
Open MPI developer):

  orte_ess_init failed
  --> Returned value Unable to start a daemon on the local node (-127) instead of ORTE_SUCCESS
--------------------------------------------------------------------------
--------------------------------------------------------------------------
It looks like MPI_INIT failed for some reason; your parallel process is
likely to abort.  There are many reasons that a parallel process can
fail during MPI_INIT; some of which are due to configuration or environment
problems.  This failure appears to be an internal failure; here's some
additional information (which may only be relevant to an Open MPI
developer):

  ompi_mpi_init: ompi_rte_init failed
  --> Returned "Unable to start a daemon on the local node" (-127) instead of "Success" (0)
--------------------------------------------------------------------------
*** An error occurred in MPI_Init
*** on a NULL communicator
*** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,
***    and potentially your MPI job)
[node0077.palmetto.clemson.edu:997083] Local abort before MPI_INIT completed completed successfully, but am not able to aggregate error messages, and not able to guarantee that all other processes were killed!