Wrong Species Selected

[juliana-chu]

Hello there!
I ran into an error saying that "wrong species selected" on Scinet which needs access from terminal. I tried the same sample on my local terminal, it ran just fine. The sample I use is from specie araTha10.
this is the command I used on both terminal:
vast-tools align D7K60W2_190919_NextSeq.fastq -sp araTha10
this is the error I received:
[vast align]: Set tmp directory to /gpfs/fs0/scratch/n/nprovart/julianac/vast-ww60/tmp! sh: bowtie: command not found Too few first reads (<500) could be mapped to mRNA library for detecting strand-orientation of reads. Maybe wrong species selected? at /gpfs/fs1/home/n/nprovart/julianac/vast-tools/bin/RunDBS_1.pl line 599.
Also, In the system they have bowtie 2.3.4.3, instead of bowtie 1.0. so I used 2, should I switch to bowtie 1.0?

[mirimia]

Hello,

Yes, I think this is an issue with bowtie, since it says no read has been mapped. Please use bowtie1 and let me know if that works.

thanks
Manu

[juliana-chu]

Hello,Manu

After I changed to bowtie 1, it worked! Thank you!