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walaj / svaba

Structural variation and indel detection by local assembly
GNU General Public License v3.0
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[E::bwa_idx_load_from_disk] fail to locate the index files #125

Closed chorong5155 closed 1 year ago

chorong5155 commented 1 year ago

Hi all, I am a beginner running bwa.. I keep running into

[E::bwa_idx_load_from_disk] fail to locate the index files /var/spool/slurmd/job3476723/slurm_script: line 45: /HapIP_Mock_polysome_19215R-02-03_S67_L002.paired.sam: Permission denied

These two errors..

below is from the snap of the process..

[BWTIncConstructFromPacked] 680 iterations done. 6184442904 characters processed. [bwa_index] 2364.60 seconds elapse. [bwa_index] Update BWT... 14.77 sec [bwa_index] Pack forward-only FASTA... 13.99 sec [bwa_index] Construct SA from BWT and Occ... 1000.04 sec [main] Version: 0.7.12-r1039 [main] CMD: bwa index /projects/b1042/WalshLab/cpp4747/trial/genomes/hg38+VacV.fna [main] Real time: 3435.034 sec; CPU: 3415.497 sec [E::bwa_idx_load_from_disk] fail to locate the index files /var/spool/slurmd/job3476723/slurm_script: line 45: /HapIP_Mock_polysome_19215R-02-03_S67_L002.paired.sam: Permission denied

I found a few also ran into these issue but could not find the solution for me.. I would much appreciate if you could give me kind advice!

Thanks

walaj commented 1 year ago

Will close since not a svaba problem. Looks like an issue with permissions and indexing, should direct to a local informatician who can help with your computing environment.