Issue with NF output for `calculate_ld` process

[mckeowr1]

Even with commits, no output files are saved to the output directory.

May-04 17:55:40.079 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1110438; id: 2; name: calculate_ld; status: COMPLETED; exit: 0; error: -; workDir: /scratch4/eande106/Ryan/89/16c993d83f9898e172d737f4bf5730 started: 1746395715076; exited: 2025-05-04T21:55:38.482269796Z; ]

Workdir: /scratch4/eande106/Ryan/89/16c993d83f9898e172d737f4bf5730

Contents of the workdir:

errlog.txt  finemap.vcf.gz  ld_output

Contents of ld_output file in the workdir

II:12658388_II:5392976.log  II:12658388_II:5392976.nosex

Contents of the log file

[rmckeow1@login03 ld_output]$ cat II:12658388_II:5392976.log
PLINK v1.9.0-b.7.7 64-bit (22 Oct 2024)
Options in effect:
  --allow-extra-chr
  --biallelic-only
  --ld II:12658388 II:5392976
  --maf 0.05
  --out ld_output/II:12658388_II:5392976
  --set-missing-var-ids @:#
  --snps-only
  --threads 5
  --vcf finemap.vcf.gz

Hostname: c423
Working directory: /scratch4/eande106/Ryan/89/16c993d83f9898e172d737f4bf5730
Start time: Sun May  4 17:55:10 2025

Random number seed: 1746395710
193096 MB RAM detected; reserving 96548 MB for main workspace.
--vcf: ld_output/II:12658388_II:5392976-temporary.bed +
ld_output/II:12658388_II:5392976-temporary.bim +
ld_output/II:12658388_II:5392976-temporary.fam written.
1714358 out of 1992465 variants loaded from .bim file.
1714358 missing IDs set.
195 people (0 males, 0 females, 195 ambiguous) loaded from .fam.
Ambiguous sex IDs written to ld_output/II:12658388_II:5392976.nosex .
Using 1 thread (no multithreaded calculations invoked).
Before main variant filters, 195 founders and 0 nonfounders present.
Calculating allele frequencies... done.
Total genotyping rate is exactly 1.
1609987 variants removed due to minor allele threshold(s)
(--maf/--max-maf/--mac/--max-mac).
104371 variants and 195 people pass filters and QC.
Note: No phenotypes present.

--ld II:12658388 II:5392976:

   R-sq = 0.0106935      D' = 0.175317

   Haplotype     Frequency    Expectation under LE
   ---------     ---------    --------------------
          AA      0.030769                0.018777
          TA      0.184615                0.196607
          AG      0.056410                0.068402
          TG      0.728205                0.716213

   In phase alleles are AA/TG


End time: Sun May  4 17:55:38 2025