Please use -x option instead.
# reads processed: 1
# reads with at least one alignment: 0 (0.00%)
# reads that failed to align: 1 (100.00%)
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:Bowtie	VN:1.3.0	CL:"/builddir/build/BUILD/bowtie-1.3.0-src/bowtie-align-s-debug --wrapper basic-0 --trim5 16 -S --quiet -a .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII"
0	4	*	0	0	*	*	0	0			XM:i:0
No alignments
Cline 9 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie --debug   -s 1 -S --quiet -a .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII
Setting the index via positional argument will be deprecated in a future release. Please use -x option instead.
# reads processed: 0
# reads with at least one alignment: 0 (0.00%)
# reads that failed to align: 0 (0.00%)
No alignments
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:Bowtie	VN:1.3.0	CL:"/builddir/build/BUILD/bowtie-1.3.0-src/bowtie-align-s-debug --wrapper basic-0 -s 1 -S --quiet -a .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII"
Cline multiread 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie --debug   -u 1 -S --quiet -a .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII
Setting the index via positional argument will be deprecated in a future release. Please use -x option instead.
# reads processed: 1
# reads with at least one alignment: 1 (100.00%)
# reads that failed to align: 0 (@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:Bowtie	VN:1.3.0	CL:"/builddir/build/BUILD/bowtie-1.3.0-src/bowtie-align-s-debug --wrapper basic-0 -u 1 -S --quiet -a .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII"
0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	XA:i:0	MD:Z:16	NM:i:0	XM:i:2
0.00%)
Reported 1 alignments
Cline multiread 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie --debug   -u 2 -S --quiet -a .simple_tests.tmp -c CATCGATCAGTATCTG,ATCGATCAGTATCTG
Setting the index via positional argument will be deprecated in a future release. Please use -x option instead.
# reads processed: 2
# reads with at least one alignment: 2 (100.00@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:Bowtie	VN:1.3.0	CL:"/builddir/build/BUILD/bowtie-1.3.0-src/bowtie-align-s-debug --wrapper basic-0 -u 2 -S --quiet -a .simple_tests.tmp -c CATCGATCAGTATCTG,ATCGATCAGTATCTG"
0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	XA:i:0	MD:Z:16	NM:i:0	XM:i:2
1	0	0	4	255	15M	*	0	0	ATCGATCAGTATCTG	IIIIIIIIIIIIIII	XA:i:0	MD:Z:15	NM:i:0	XM:i:2
%)
# reads that failed to align: 0 (0.00%)
Reported 2 alignments
Cline paired 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie-build  --threads 1 --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie --debug   -s 1 -S --quiet -a .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII
Setting the index via positional argument will be deprecated in a future release. Please use -x option instead.
/usr/include/c++/12/bits/stl_queue.h:725: std::priority_queue<_Tp, _Sequence, _Compare>::const_reference std::priority_queue<_Tp, _Sequence, _Compare>::top() const [with _Tp = Branch*; _Sequence = std::vector<Branch*>; _Compare = CostCompare; const_reference = Branch* const&]: Assertion '!this->empty()' failed.
bowtie aborted with exitlevel 134
error: Bad exit status from /var/tmp/rpm-tmp.ZxOlN8 (%check)
RPM build errors:
    Bad exit status from /var/tmp/rpm-tmp.ZxOlN8 (%check)
Child return code was: 1
EXCEPTION: [Error()]
Traceback (most recent call last):
  File "/usr/lib/python3.9/site-packages/mockbuild/trace_decorator.py", line 93, in trace
    result = func(*args, **kw)
  File "/usr/lib/python3.9/site-packages/mockbuild/util.py", line 600, in do_with_status
    raise exception.Error("Command failed: \n # %s\n%s" % (command, output), child.returncode)
mockbuild.exception.Error: Command failed: 
 # bash --login -c /usr/bin/rpmbuild -bb --target riscv64 --nodeps /builddir/build/SPECS/bowtie.spec