ERROR ~ Error executing process > 'RAMDAQ:READCOVERAGE (RAM_0001)'

[WillDeGroat]

executor >  slurm (29)
[69/083dfe] RAMDAQ:GET_SOFTWARE_VERSIONS   | 1 of 1 ✔
[6d/34d5e3] RAMDAQ:UNTAR_HISAT2_IDX        | 1 of 1 ✔
[40/534586] RAMDAQ:UNTAR_HISAT2_RRNA_IDX   | 1 of 1 ✔
[a8/251cf7] RAMDAQ:UNTAR_RSEM_ALLGENE_IDX  | 1 of 1 ✔
[f0/07213a] RAMDAQ:FASTQC_RAW (RAM_0001)   | 1 of 1 ✔
[97/589a0e] RAM…RGE_SUMMARYFILE_FASTQC_RAW | 1 of 1 ✔
[1c/ab1e02] RAMDAQ:FASTQMCF (RAM_0001)     | 1 of 1 ✔
[a1/5f3a67] RAMDAQ:FASTQC_TRIM (RAM_0001)  | 1 of 1 ✔
[f0/5c18d4] RAM…Q:HISAT2_GENOME (RAM_0001) | 1 of 1 ✔
[e3/893515] RAM…Q:MERGE_SUMMARYFILE_HISAT2 | 1 of 1 ✔
[71/32b476] RAMDAQ:HISAT2_RRNA (RAM_0001)  | 1 of 1 ✔
[cb/b7c4ad] RAM…AM2WIG_ALLGENES (RAM_0001) | 3 of 3 ✔
[68/825653] RAMDAQ:ADJUST_BED_NONCODING    | 1 of 1 ✔
[93/1d9869] RAMDAQ:RSEQC (RAM_0001)        | 3 of 3 ✔
[-        ] RAM…MERGE_SUMMARYFILE_READDIST -
[ab/bc8989] RAMDAQ:READCOVERAGE (RAM_0001) | 3 of 3, failed: 3 ✘
[7a/1f1c8b] RAM…ECOUNTS_ALL_GTF (RAM_0001) | 1 of 1 ✔
[-        ] RAM…ERGE_FEATURECOUNTS_ALLGENE -
[84/0fb58a] RAM…RECOUNTS_MT_GTF (RAM_0001) | 1 of 1 ✔
[43/34e2f9] RAMDAQ:MERGE_FEATURECOUNTS_MT  | 1 of 1 ✔
[0f/d57b30] RAM…NTS_HISTONE_GTF (RAM_0001) | 1 of 1 ✔
[fc/6d5c8c] RAM…ERGE_FEATURECOUNTS_HISTONE | 1 of 1 ✔
[88/4831c2] RAM…OWTIE2_ALLGENES (RAM_0001) | 0 of 1
[61/58af4d] RAM…C_FEATURECOUNTS_MAPRATE_MT | 1 of 1 ✔
[93/2f7108] RAM…TURECOUNTS_MAPRATE_HISTONE | 1 of 1 ✔
Plus 11 more processes waiting for tasks…
ERROR ~ Error executing process > 'RAMDAQ:READCOVERAGE (RAM_0001)'

Caused by:
  Missing output file(s) `*.txt` expected by process `RAMDAQ:READCOVERAGE (RAM_0001)`

Command executed:

  julia /opt/run.jl relcov RAM_0001.R1.bam gencode.vM26.primary_assembly.annotation.bed RAM_0001.R1

Command exit status:
  0

Command output:
  (empty)

Command error:
  ERROR: LoadError: IOError: unlink: read-only file system (EROFS)
  Stacktrace:
   [1] uv_error at ./libuv.jl:97 [inlined]
   [2] unlink(::String) at ./file.jl:781
   [3] #rm#9(::Bool, ::Bool, ::typeof(rm), ::String) at ./file.jl:261
   [4] #rm at ./none:0 [inlined]
   [5] create_expr_cache(::String, ::String, ::Array{Pair{Base.PkgId,UInt64},1}, ::Base.UUID) at ./loading.jl:1165
   [6] compilecache(::Base.PkgId, ::String) at ./loading.jl:1274
   [7] _require(::Base.PkgId) at ./loading.jl:1024
   [8] require(::Base.PkgId) at ./loading.jl:922
   [9] require(::Module, ::Symbol) at ./loading.jl:917
   [10] include at ./boot.jl:328 [inlined]
   [11] include_relative(::Module, ::String) at ./loading.jl:1105
   [12] include(::Module, ::String) at ./Base.jl:31
   [13] exec_options(::Base.JLOptions) at ./client.jl:287
   [14] _start() at ./client.jl:460
  in expression starting at /opt/run.jl:1

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

Hello, maintainers! There seems to be an error stemming from the Julia script in yuifu/readcoverage.jl:0.1.2-workaround Singularity container. This issue interrupts the READCOVERAGE module. Any insight into this problem would be greatly appreciated. The file system that this script is run in is not read-only.

[WillDeGroat]

I was able to circumvent this locally using a Julia installation and limiting submissions of the READCOUNTS script.

[myoshimura080822]

Hi @WillDeGroat, Thank you for reporting this issue. We appreciate your detailed error log and information.

We have not encountered this error in our development environment. We are investigating this issue in collaboration with the developer of this tool and container. We will share any findings as soon as we have more details, so please bear with us.

[yuifu]

@WillDeGroat Thanks so much for sharing the information!

Could you provide a bit more detail about your setup? Specifically, we’d love to know the following:

1. What is your computing environment (e.g., OS)?
2. What command did you run (including any options)?
3. Does your current host's file system have an /opt directory?

Looking forward to your response! Thanks a ton! 🚀