Error with bowtie2

While mapping with bowtie2, in Galaxy I got the following error messages for each of the paired_end files. I also got alignment result. So, is my alignment result could run completely or they are just a part of the whole thing? Should I solve the problems using fastp and run again? Or I am good to go with the results?

Warning: skipping mate #1 of read 'SRR14466480.24455260 24455260 length=1' because length (1) <= # seed mismatches (0)
Warning: skipping mate #1 of read 'SRR14466480.24455260 24455260 length=1' because it was < 2 characters long
Warning: skipping mate #1 of read 'SRR14466480.24461757 24461757 length=1' because length (1) <= # seed mismatches (0)
Warning: skipping mate #1 of read 'SRR14466480.24461757 24461757 length=1' because it was < 2 characters long
Error, fewer reads in file specified with -2 than in file specified with -1
terminate called after throwing an instance of 'int'
(ERR): bowtie2-align died with signal 6 (ABRT) (core dumped)

Also got this one-

It looks like this is the actual error:

Error, fewer reads in file specified with -2 than in file specified with -1

I am not to familiar with bowtie2 errors but I guess that one of the fastq files has more reads than the other which is not expected with paired-end data. You could double check this with FastQC for example. Are you doing a step before bowtie2? And are you performing this step separately on both fastq files?

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I checked the parameter total sequences for each forward and paired files from fastqc. They were same numbers. And as they were in a collection (all the SRA_id under a collection; under the SRA id the forward and reverse read were organized), while mapping I chose paired end collection as the input parameter, but still had these error.

Now I am doing fastp before mapping again as per some suggestion this could solve the issue. I am not sure whether I did any other mistake.

Could you try to filter out those short reads of only 2 bases? With a tool that is made for paired-end data like cutadapt?

EDIT:

This is also possible with fastp but not default, you need to turn it on under “Lenght filtering options”

Okay. Thanks for your kind help. But fastp by default filters out reads that are <15 seq length

The value 15 is default yes. But the functionality to remove the <15 reads is not turned on by default.

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