[E::bwa_idx_load_from_disk] fail to locate the index files
xxYaaoo opened this issue · comments
Hi,
If you correctly indexed the human genome and TE consensus sequences, the error from the very early bwa alignment step may be because no chimeric/split reads were identified.
may I get a list of intermediate output files through "ls -lh" under your output folder?
Best,
Xun
yes, when you prepared the reference files before running ERVcaller.pl, you need to run the "bwa index" command for both human and TEs. You could try it first and then let me know if you still have the same issue.
Best,
Xun
Hi,
Have you also indexed your TE consensus sequences? Can you also share the log file and the file sizes under the temp folder?
Xun
I can't find any problem with your log and temp files.
Could you try using the BAM file or the TE_seq fastq file as the inputs? (not TE_seq2 which may not contain simulated insertions and used for testing separate FASTQ inputs)
Best,
Xun
Hi,
I am glad that it works!
I don't know what is included in your slurm.err file, but sometimes it is just the log BWA or samtools running which should be fine.
Sure, let me know if you have other questions. As I suggested, TE_seq files contacted the simulated integration sites but TE_seq2 may not, which could be the potential issue.
Best,
Xun
Dear Dr. Chen,
I have run my own data successfully using ERVcaller! You really make my these days! Thank you so much! Appreciate~
Best wishes,
Yaaoo