IndexError: list index out of range

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kaydee

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Feb 10, 2022, 3:34:30 AM2/10/22

to EMIRGE users

Dear Emirge support

Kindly assist in how best this can be solved I ran emirge through the following command lineemirge_amplicon.py output -1 S345_L001_R1_001.fastq -2 S345_L001_R2_001.fastq -f SILVA_138.1_SSURef_tax_silva_trunc.fasta -b SILVA_138.1_SSURef_tax_silva_trunc -i 500 -s 500 -l 151 --phred33

and I got the error

OOPS, we didn't get number of reads from bowtie:
Time loading reference: 00:00:02
Time loading forward index: 00:00:07
Time loading mirror index: 00:00:08
Seeded quality full-index search: 00:00:15
# reads processed: 38067
# reads with at least one reported alignment: 0 (0.00%)
# reads that failed to align: 38067 (100.00%)
No alignments
Time searching: 00:00:39
Overall time: 00:00:39

[]
Traceback (most recent call last):
File "/apps/chpc/bio/python/2.7.15/bin/emirge_amplicon.py", line 1580, in <module>
main()
File "/apps/chpc/bio/python/2.7.15/bin/emirge_amplicon.py", line 1549, in main
options.mapping = do_initial_mapping(em, working_dir, options)
File "/apps/chpc/bio/python/2.7.15/bin/emirge_amplicon.py", line 1257, in do_initial_mapping
em.n_alignments = em.get_n_alignments_from_bowtie(stderr_string)
File "/apps/chpc/bio/python/2.7.15/bin/emirge_amplicon.py", line 1104, in get_n_alignments_from_bowtie
if r[0][1] != '': # "paired-end" string matched -- two lines in samfile per paired-end aln
IndexError: list index out of range