Bam files generated with STAR cause a segmentation fault core dump error when used with another tool

Question

I am mapping RNA-Seq data using STAR, using multi-sample two-pass mapping. I first mapped all samples with one-pass then concatenated their SJOut files and filtered junctions. I launched the second mapping by using this SJOut file.

To generate the genome, I used the following command:

/home/STAR-2.7.10b/bin/Linux_x86_64/STAR \
--runThreadN 10 \
--runMode genomeGenerate \
--genomeDir /home/genomeDir3 \
--genomeFastaFiles /home/Homo_sapiens.GRCh38.dna.primary_assembly.fa \
--sjdbGTFfile /home/Homo_sapiens.GRCh38.110.gtf \
--sjdbOverhang 100 \
--sjdbGTFfeatureExon exon \
--genomeSAindexNbases 14 \
--limitGenomeGenerateRAM 51200000000

then used this command to map each sample :

/home/lebechekhadidja/STAR-2.7.10b/bin/Linux_x86_64/STAR \
--genomeDir /home/genomeDir3 \
--readFilesIn "/home/Brain2/$file_name".fastq.gz \
--sjdbGTFfile /home/Homo_sapiens.GRCh38.110.gtf \
--sjdbFileChrStartEnd "/home/Human.Brain.All.SJ.out.RedunChrReadsNonCanonFilter" \
--readFilesCommand zcat \
--runThreadN 10 \
--genomeLoad NoSharedMemory \
--readFilesCommand zcat \
--outSAMtype BAM SortedByCoordinate \
--twopassMode None \
--quantMode TranscriptomeSAM GeneCounts \
--quantTranscriptomeBan Singleend \
--outSAMattrIHstart 1 \
--outSAMattributes NH HI AS nM NM MD jM jI MC ch XS \
--outSAMprimaryFlag OneBestScore \
--outSAMmapqUnique 60 \
--outSAMunmapped Within \
--outBAMsortingThreadN 10 \
--outBAMsortingBinsN 50 \
--winAnchorMultimapNmax 50 \
--limitBAMsortRAM 51200000000

when I use Multimapper resolution tool to resolve multimapped reads I get this erro message :

Parsing segment boundaries from annotation file: /home/Homo_sapiens.GRCh38.110.gtf Segmentation fault (core dumped)

The thing is that when I mapped samples using STAR in galaxy platform, using same parameters. I didn't encounter the same error. so I tried to use command line in galaxy + STAR version in galaxy (this is why I used STAR-2.7.10b) but I keep getting the same error. these are command lines for genome generation step and mapping step in galaxy :

enter image description here

when I ran MMR debgging with gdb I got this error :

[New Thread 0x7ffff7a59700 (LWP 3020)] 
[New Thread 0x7ffff7258700 (LWP 3021)] 
[New Thread 0x7ffff6a57700 (LWP 3022)] 
[New Thread 0x7ffff6256700 (LWP 3023)] 
[New Thread 0x7ffff5a55700 (LWP 3024)] 
[New Thread 0x7ffff5254700 (LWP 3025)] 
[New Thread 0x7ffff4a53700 (LWP 3026)] 
[New Thread 0x7ffff4252700 (LWP 3027)] 
[New Thread 0x7ffff3a51700 (LWP 3028)] 
[New Thread 0x7ffff3250700 (LWP 3029)] 
[New Thread 0x7ffff2a4f700 (LWP 3030)] 
[New Thread 0x7ffff224e700 (LWP 3031)] 
[New Thread 0x7ffff1a4d700 (LWP 3032)] 
[Detaching after vfork from child process 3033] 
------------ tool progres messages -------------------- 
Thread 5 "mmr" received signal SIGSEGV, Segmentation fault. [Switching to Thread 0x7ffff6256700 (LWP 3023)] 0x0000555555560569 in Alignment::fill_coverage_vector (this=0x555570139400, cov_keep=std::vector of length 0, capacity 0) at /usr/include/c++/9/bits/stl_bvector.h:237 237         { return reference(_M_p, 1UL << _M_offset); }

I tried various STAR versions, experimented with various options and still the problem persists.