Error with bowtie2

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#1

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-

Screenshot from 2021-08-30 14-48-23
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Error in de novo assembly of RNAseq using Trinity
#2

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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#3

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.

#4

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”

#5

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

#6

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

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