Incorrect permissions on annotation GTF file cause segfault

[alanhoyle]

Is the bug primarily related to salmon (bulk mode) or alevin (single-cell mode)?

Only tested in bulk mode

Describe the bug If the annotation GTF file exists but the running user does not have read permissions, Salmon dies with an opaque segfault or SYSSEGV

To Reproduce Steps and data to reproduce the behavior:

Run Salmon using an annotation.gtf file that exists but the user does not have read permissions on the file. Salmon runs almost to completion but then dies with a SYSSEGV or segfault.

Specifically, please provide at least the following information:

• Which version of salmon was used? Same error on Salmon 1.4.0 and 1.10.3
• How was salmon installed (compiled, downloaded executable, through bioconda)? Apptainer through a local docker image and a quay.io Biocontainers image.
• Which reference (e.g. transcriptome) was used? Gencode V36.
• Which read files were used?
• Which which program options were used?

Expected behavior

A permissions issue on an input file should gracefully fail and let the user know that the file is inaccessible.

Screenshots

From the command line output of the Salmon process:

Freeing memory used by read queue . . .
Joined parsing thread . . . "Aligned.toTranscriptome.out.bam"
Closed all files . . .
Emptied frag queue. . .
Emptied Alignemnt Group Pool. .
Emptied Alignment Group Queue. . . done
Command terminated by signal 11

from strace:

open("gencode.v36.annotation.gtf", O_RDONLY) = -1 EACCES (Permission denied)
--- SIGSEGV {si_signo=SIGSEGV, si_code=SEGV_MAPERR, si_addr=NULL} ---
+++ killed by SIGSEGV (core dumped) +++
[[...redacted...]@[...redacted...] ~]$ ls -l [...redacted_path...]F/gencode.v36.annotation.gtf
-rwxr-x--x. 1 [...redacted_user...] [...redacted_group...] 1383072363 Apr 14  2022 [...redacted_path...]/gencode.v36.annotation.gtf*

Desktop (please complete the following information):

• OS: Rocky Linux 9
• Version: Rocky Linux release 9.3 (Blue Onyx)

Additional context Add any other context about the problem here.