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DaehwanKimLab / hisat2

Graph-based alignment (Hierarchical Graph FM index)
GNU General Public License v3.0
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Error: Encountered internal hisat exception (#1) #65

Open IsaacPonce opened 8 years ago

IsaacPonce commented 8 years ago

Hi I hope some help me I'm a newbie in bioinformatics. I already built the index and when I run the program I get this error Error: Encountered internal hisat exception (#1) Command: hisat2_home/hisat2-align-s --wrapper basic-0 -f -x -Uq -bashfiletoalign.fastq -S file.sam (ERR): hisat exited with value 1

the input was $ hisat2 -f -x $index -Uq $filetoalign.fastq -S file.sam I dont know if someone want to help me, thanks in advance.

MatteoSchiavinato commented 8 years ago

First, does it output something in the -S output.sam file? Check your writing permissions in that -S directory. Then, why do you use -Uq? -U readsfile.fq should be the proper flag. Finally, are your indexes correctly built with hisat2-build ?

IsaacPonce commented 8 years ago

Thank you for help, No output file was created, I have all permissions in that directory (-rwx) I tried -U and same happens, I tried the already built indexes provided in the HISAT2 page and still the same I even tried to run the examples and i got the error "Could not open read file ... skipping"

MatteoSchiavinato commented 8 years ago

Build your own indexes on your reference genome, that sould do the trick.