JoinStar only joins first particle stack and ignores the rest

[AGMMGA]

Describe your problem

When using a JoinStar job on particles.star coming from 2D classification / Select job, only the first star file is added to the output. The issue happens on multiple, unrelated projects.

Toy example (command below): From the same 2D job, select half of the classes to one job, half to another. stack 1 has ~44250 particles; stack2 has ~61197 particles. joinstar contains 44250 particles if joining stack1 to stack2, 61197 if joining stack2 to stack1

When using particles stack coming from Extract jobs, the join works as expected.

Environment:

• OS: Ubuntu 20
• MPI runtime: N/A
• RELION version ver4.0 commit 86fe8da5d06329e89ed7cf2648a7cdc38cefa079 (bug was present in muche earlier commit)
• Memory: 256 Gb
• GPU: N/A

Dataset:

• Bug applies to multiple projects, with differently sized particle stacks and particles.
• Particle stacks come from project that used only relion4 (i.e. they are not from relion 3.1.x)

Job options:

• Type of job: JoinStar
• Number of MPI processes: 1
• Number of threads: 1
• Full command (see note.txt in the job directory):

  `which relion_star_handler` --combine --i " Select/job066/particles.star Select/job067/particles.star "  --check_duplicates rlnImageName  --o JoinStar/job068/join_particles.star  --pipeline_control JoinStar/job068/

Error message:

run.err is empty

[AGMMGA]

Sorry, it turns out that the issue was with our slurm script improperly handling the command. We fixed that.