Kevinzjy
commented
3 months ago Hi @EdWardYF7 , please make sure that the HISAT2 version is compatible with the index and that you have enough RAM to perform the alignment
Open EdWardYF7 opened 3 months ago
Kevinzjy
commented
3 months ago Hi @EdWardYF7 , please make sure that the HISAT2 version is compatible with the index and that you have enough RAM to perform the alignment
hi guys i try to use hisat2 aligning the fastq file to the index which i have built before, here is the command line:
/home/wyf/miniconda3/bin/hisat2 -x /home/wyf/Pipeline/RNA-seq/02.hisat/Eriocheir_sinensis -p 8 -1 /homRNA-seq/01.afterqc/good/SRR12616419_2.good.fq.gz -S /home/wyf/Pipeline/RNA-seq/03.bidui/SRR12616419/SRR12616419.sam
then it went wrong! it be like:
Error: Could not open alignment output file / Error: Encountered internal HISAT2 exception (#1) Command: /home/wyf/miniconda3/bin/hisat2-align-s --wrapper basic-0 -x /home/wyf/Pipeline/RNA-seq/02.hi0,106,101,92,59,134,128,120,114,112,107,99,76,70,69,54,50,139,132,124,123,122,121,118,117,108,105,103, -1 /tmp/3529138.inpipe1 -2 /tmp/3529138.inpipe2 (ERR): hisat2-align exited with value 1
i have searched many websites but i cannot find the answer, now i am reindexing my reference genome, hopefully someone will help me, i will appreciate that!!