mkfifo failed error and change $temp_dir

[pxchen110]

Hi,

Recently I ran hisat2 and found this error:

Caused by:
  Missing output file(s) `H1975_D_7_summary.log` expected by process `preprocess_illumina:hisat2 (2)`

Command executed:
  hisat2 -x reference -1 H1975_D_7.R1.trimmed.fastq.gz -2 H1975_D_7.R2.trimmed.fastq.gz -p 1 --new-summary --summary-file H1975_D_7_summary.log  | samtools view -bS | samtools sort -o H1975_D_7.sorted.bam -T tmp --threads 1

Command exit status:
  0

Command output:
  (empty)

Command error:
  INFO:    Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred
  INFO:    Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred
  INFO:    Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred
  (ERR): mkfifo(/tmp/41.inpipe1) failed.
  Exiting now ...

This error was caused by mkfifo(/tmp/41.inpipe1) failed I have checked the available space of my /tmp directory and all settings (availaible space or permission) was normal.

So I tried to change the temp directory to mkfifo the pipe file. However, I read the hisat2 code (https://github.com/DaehwanKimLab/hisat2/blob/master/hisat2) and found the temp directory is unchangeable:

241 my $temp_dir = "/tmp";

Do you have any suggestion on how to solve this mkfifo error or how to change the temp directory while running hisat2 ? thank you