Having problems in make.contig step

Commands in mothur
1

Hi guys,

I have downloaded a bunch of 16S sequence data sets from NCBI in SRA format. I have used NCBI SRA toolkit to convert them into fastq format for further analysis with mothur. When try to merge the both R1 and R2 fastq files by using make.contig command, i am getting this following error.

“St_3_1M_young_sound_2015.1.1 is in your forward fastq file and not in your reverse file, please remove it using the remove.seqs command before proceeding.”

When i use my own dataset for merging i never had any issue. Can some one assist me, how to rectify this issue.

many thanks
Venkat

2

Hi Venkat,

Can you find that sequence in the reverse file? If not, it may be that the person that deposited the data did not provide all of the sequence data.

Pat

3

Thanks Pat. I have checked the reverse files, it was fine. It seems some issues with SRA toolkit, i have downloaded the same data-sets in fastQ format directly from ENA and it worked fine now.

regards
venkat

4

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