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)
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?
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.
