bismark align fails with "java.net.SocketTimeoutException: Read timed out"

[trum994]

Description of the bug

I believe this is an intermittent issue since I was able to run this workflow before but it's crashing now. I do see a BismarkIndex directory created under the stage-xxx directory but there's not a working directory created yet for the actual bismark align step.

Here's more information from the .nextflow.log file:

Feb-06 11:47:19.101 [Actor Thread 23] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=NFCORE_METHYLSEQ:METHYLSEQ:FASTQ_ALIGN_DEDUP_BISMARK:BISMARK_ALIGN (1); work-dir=null
  error [com.amazonaws.SdkClientException]: Unable to complete multipart download. Individual part download failed.
Feb-06 11:47:19.423 [Actor Thread 23] ERROR nextflow.processor.TaskProcessor - Error executing process > 'NFCORE_METHYLSEQ:METHYLSEQ:FASTQ_ALIGN_DEDUP_BISMARK:BISMARK_ALIGN (1)'

Caused by:
  java.net.SocketTimeoutException: Read timed out


com.amazonaws.SdkClientException: Unable to complete multipart download. Individual part download failed.
        at com.amazonaws.services.s3.transfer.internal.CompleteMultipartDownload.call(CompleteMultipartDownload.java:54)
        at com.amazonaws.services.s3.transfer.internal.CompleteMultipartDownload.call(CompleteMultipartDownload.java:29)
...
        at java.base/java.lang.Thread.run(Thread.java:1583)
Caused by: java.util.concurrent.ExecutionException: java.net.SocketTimeoutException: Read timed out
...
        at com.amazonaws.services.s3.transfer.internal.CompleteMultipartDownload.call(CompleteMultipartDownload.java:47)
        ... 5 common frames omitted
Caused by: java.net.SocketTimeoutException: Read timed out
        at java.base/sun.nio.ch.NioSocketImpl.timedRead(NioSocketImpl.java:278)
        at java.base/sun.nio.ch.NioSocketImpl.implRead(NioSocketImpl.java:304)
...
        ... 4 common frames omitted
Feb-06 11:47:19.546 [Actor Thread 23] DEBUG nextflow.Session - Session aborted -- Cause: Unable to complete multipart download. Individual part download failed.
Feb-06 11:47:19.616 [Actor Thread 23] DEBUG nextflow.Session - The following nodes are still active:
[process] NFCORE_METHYLSEQ:METHYLSEQ:FASTQ_ALIGN_DEDUP_BISMARK:BISMARK_ALIGN
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (value) bound ; channel: -
  port 2: (value) bound ; channel: -
  port 3: (cntrl) -     ; channel: $

Command used and terminal output

nextflow run nf-core/methylseq --input samplesheet1.csv --outdir out7 --genome GRCh38 -profile singularity -c custom.config -resume

Relevant files

my config file:

process {
  resourceLimits = [
    cpus: 32,
    memory: 238.GB,
    time: 24.h
  ]
}

System information

N E X T F L O W ~ version 24.10.4

Launching https://github.com/nf-core/methylseq [dreamy_coulomb] DSL2 - revision: 4415e90 [master]

------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/methylseq 3.0.0
------------------------------------------------------
Input/output options
  input              : samplesheet1.csv
  outdir             : out7

Reference genome options
  genome             : GRCh38
  fasta              : s3://ngi-igenomes/igenomes//Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa
  fasta_index        : s3://ngi-igenomes/igenomes//Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa.fai
  bismark_index      : s3://ngi-igenomes/igenomes//Homo_sapiens/NCBI/GRCh38/Sequence/BismarkIndex/
  bwameth_index      : s3://ngi-igenomes/igenomes//Homo_sapiens/NCBI/GRCh38/Sequence/BwamethIndex/

Generic options
  trace_report_suffix: 2025-02-06_10-42-43

Core Nextflow options
  revision           : master
  runName            : dreamy_coulomb
  containerEngine    : singularity
  launchDir          : /xxx/methseqtest
  workDir            : /xxx/nxf_workdir
  projectDir         : /xxx/.nextflow/assets/nf-core/methylseq
  userName           : xxx
  profile            : singularity
  configFiles        :