when i use GNU Parallel to analyze data, something goes wrong

[TaoBern]

when i follow the script on the https://mixcr.com/mixcr/guides/generic-multiplex-bcr/
For the one sample analysis, it's okay. Successfully aligned reads: 5053118 (95.13%)

The script i used as below:
mixcr analyze generic-bcr-amplicon
--species mmu
--rna
--rigid-left-alignment-boundary
--rigid-right-alignment-boundary
--tag-pattern '^N{4}ccctcctttaattcccN{22}(R1:)^N{4}gaggagagagagagagN{26}(R2:)' \
--assemble-clonotypes-by {CDR1Begin:FR4End}
raw/M1_4T1_replica1_BM_R1.fastq.gz
raw/M1_4T1_replica1_BM_R2.fastq.gz
results/M1_4T1_replica1_BM

but when I run the samples together using the suggested script, the results look weird.
The script is below
module load parallel/20210622-GCCcore-10.3.0
ls raw1/R1 |
parallel -j 4
'mixcr analyze generic-bcr-amplicon -f
--species mmu
--rna
--rigid-left-alignment-boundary
--rigid-right-alignment-boundary
--tag-pattern "^N{4}ccctcctttaattcccN{22}(R1:)^N{4}gaggagagagagagagN{26}(R2:)"
--assemble-clonotypes-by {CDR1Begin:FR4End}
{}
{=s:R1:R2:=}
{=s:./:results1/:;s:_R.::=}'

But the Successfully aligned reads are all 0%. But the sample under the analysis of the first script is good. It's really weird. I will really appreaciate it if someone can help me find out the reason!

[mizraelson]

The command should be:

ls raw1/*R1* |
parallel -j 4 \
'mixcr analyze generic-bcr-amplicon -f \
--species mmu \
--rna \
--rigid-left-alignment-boundary \
--rigid-right-alignment-boundary \
--tag-pattern "^N{"4"}ccctcctttaattcccN{"22"}(R1:*)\^N{"4"}gaggagagagagagagN{"26"}(R2:*)" \
--assemble-clonotypes-by {CDR1Begin:FR4End} \
{} \
{=s:R1:R2:=} \
{=s:./:result1/:;s:_R.*::=}'

Did you use double quotes inside {} in the pattern : {"4"} etc.