When trying to create a SummarizedExperiment object from approx. 50 bam files GenomicAlignments::summarizeOverlaps, I get the following error:

Error in result[[njob]] <- value :
  attempt to select less than one element in OneIndex
Calls: <Anonymous> ... bplapply -> bplapply -> bplapply -> bploop -> bploop.lapply
In addition: Warning message:
In parallel::mccollect(wait = FALSE, timeout = 1) :
  1 parallel job did not deliver a

This error doesn't occur if I restrict to only 5 bam files. I am running the following code on our HPC as a slurm job with 250GB of memory and 12 cores assigned to it:

# Create a transcript data base
txdb = GenomicFeatures::makeTxDbFromGFF(gtf_file)

# Collapse gene models into counting bins
exonic_parts = GenomicFeatures::exonicParts(txdb, linked.to.single.gene.only = TRUE)

# Create references to BAM files
bam_filelist = Rsamtools::BamFileList(bam_files, index=character(), yieldSize=100000, obeyQname=TRUE)

# Count the reads overlapping the bins
ese = GenomicAlignments::summarizeOverlaps(exonic_parts, bam_filelist, mode="Union", singleEnd=FALSE, ignore.strand=TRUE, inter.feature=FALSE, fragments=TRUE)

sessionInfo( )

R version 4.0.2 (2020-06-22)
Platform: x86_64-conda_cos6-linux-gnu (64-bit)
Running under: Debian GNU/Linux 10 (buster)

Matrix products: default
BLAS/LAPACK: /opt/conda/envs/rnaseq/lib/libopenblasp-r0.3.10.so

locale:
[1] C

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
 [1] GenomicAlignments_1.24.0    Rsamtools_2.4.0
 [3] Biostrings_2.56.0           XVector_0.28.0
 [5] SummarizedExperiment_1.18.1 DelayedArray_0.14.0
 [7] matrixStats_0.58.0          GenomicFeatures_1.40.0
 [9] AnnotationDbi_1.50.0        Biobase_2.48.0
[11] GenomicRanges_1.40.0        GenomeInfoDb_1.24.0
[13] IRanges_2.22.1              S4Vectors_0.26.0
[15] BiocGenerics_0.34.0         dplyr_1.0.5

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.6             lattice_0.20-41        prettyunits_1.1.1
 [4] assertthat_0.2.1       utf8_1.2.1             BiocFileCache_1.12.0
 [7] R6_2.5.0               RSQLite_2.2.4          httr_1.4.2
[10] pillar_1.5.1           zlibbioc_1.34.0        rlang_0.4.10
[13] progress_1.2.2         curl_4.3               rstudioapi_0.13
[16] blob_1.2.1             Matrix_1.3-2           BiocParallel_1.22.0
[19] stringr_1.4.0          RCurl_1.98-1.3         bit_4.0.4
[22] biomaRt_2.44.0         compiler_4.0.2         rtracklayer_1.48.0
[25] pkgconfig_2.0.3        askpass_1.1            openssl_1.4.3
[28] tidyselect_1.1.0       tibble_3.1.0           GenomeInfoDbData_1.2.4
[31] XML_3.99-0.6           fansi_0.4.2            crayon_1.4.1
[34] dbplyr_2.1.0           bitops_1.0-6           rappdirs_0.3.3
[37] grid_4.0.2             lifecycle_1.0.0        DBI_1.1.1
[40] magrittr_2.0.1         stringi_1.4.6          cachem_1.0.4
[43] ellipsis_0.3.1         generics_0.1.0         vctrs_0.3.6
[46] tools_4.0.2            bit64_4.0.5            glue_1.4.2
[49] purrr_0.3.4            hms_1.0.0              fastmap_1.1.0
[52] memoise_2.0.0
[1] "gtf_file: /local/1385061/tmp.N2RyL48FNO/by_id/arpez-4zz18-y930zhe7xllejrh/gencode.v35.annotation.gtf.gz"
[1] "bam_dir: /local/1385061/tmp.N2RyL48FNO/by_id/arpez-j7d0g-hhwwhnva9l5xsu4/Hisat2"
[1] "meta_dir: /local/1385061/tmp.N2RyL48FNO/by_id/arpez-j7d0g-hhwwhnva9l5xsu4/Metadata"
[1] "output_dir: /pstore/scratch/u/munzm1/rnaseq-myopathay-small/bash_online/dexseq_preprocOutputxyz"
[1] "multiqc_file: /local/1385061/tmp.N2RyL48FNO/by_id/arpez-j7d0g-hhwwhnva9l5xsu4/MultiQC/multiqc_data/multiqc_general_stats.txt"