Segmentation fault (core dumped) (ERR): bowtie2-align exited with value 139

[surkiim]

Hi everyone,
I’m encountering an issue with mapping filtered paired-end FASTQ files using Bowtie2. Most of my files map without any problems, but four files consistently produce the following error:

Segmentation fault (core dumped)
(ERR): bowtie2-align exited with value 139

It occured on Ubuntu with /usr/bin/bowtie2-align-s version 2.3.5.1 64-bit and on another with /usr/bin/bowtie2-align-s version 2.5.2 64-bit. I’ve tried reducing the number of threads (even down to one), but the error persists. Interestingly, unfiltered files map successfully, and the filtering was done using fastp version 0.23.4.

After dividing one problematic file, I managed to isolate the exact read pair causing the issue:
@VH01157:41:AACHKHFM5:1:1205:27472:29057 1:N:0:TAGGCATG+AGAGGATA
CCTACAATACCTCCAGCCTCCTCCCATCTCATTGCC
+
CCCCCCCCCC;CCCC-CCCCCC;---;;CCCCCCCC
@VH01157:41:AACHKHFM5:1:1205:27472:29057 2:N:0:TAGGCATG+AGAGGATA
GCAATGAGATGGGAGGAGGCTGGAGGTATTGTAGGG
+
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CC-C
You can find the FASTQ files here:
fastq-reads.zip

My bowtie2 command was:

    bowtie2 --phred33 --very-sensitive --seed 42 -p 1 -x "$index" \
    -1 "$r1_file" -2 "$r2_file" 2> "$summary_file" | \
    samtools view -hbS -@ 1 - | \
    samtools sort -@ 1 -o "$bam_file"

I’ve reviewed the problematic read pair but haven’t found anything obviously wrong. Could anyone provide insight into what might be causing this issue?
Thank you for your help!