[E::bwa_idx_load_from_disk] fail to locate the index files when running

[NTNguyen13]

Hi, I run the script in https://github.com/humanlongevity/HLA/wiki/BAMs-compatible-with-xHLA to preprocess the file from International Genomes Sample Resource Project, which is mapped to Hg38 with HLA and alternative contigs. However, I got no output file from this, only one error:

.......[A lot of similar warning]
*****WARNING: Query A00296:45:HFMLCDSXX:4:2678:7283:5087 is marked as paired, but its mate does not occur next to it in your BAM file.  Skipping.
*****WARNING: Query A00296:45:HFMLCDSXX:4:2678:8712:11193 is marked as paired, but its mate does not occur next to it in your BAM file.  Skipping.
*****WARNING: Query A00296:45:HFMLCDSXX:4:2678:8874:30890 is marked as paired, but its mate does not occur next to it in your BAM file.  Skipping.
[E::bwa_idx_load_from_disk] fail to locate the index files

What is the problem in my case?

[PKazakova]

Hi, when I run get-reads-alt-unmap.sh ( [https://github.com/humanlongevity/HLA/wiki/BAMs-compatible-with-xHLA]) in.bam out.bam to process my data, there was an error message:

*****WARNING: Query A01013:41:HYL5YDSXX:4:2664:1072:7138 is marked as paired, but its mate does not occur next to it in your BAM file.  Skipping.
*****WARNING: Query A01013:41:HYL5YDSXX:4:2664:18484:5979 is marked as paired, but its mate does not occur next to it in your BAM file.  Skipping.
*****WARNING: Query A01013:41:HYL5YDSXX:4:2664:24975:21731 is marked as paired, but its mate does not occur next to it in your BAM file.  Skipping.
*****WARNING: Query A01013:41:HYL5YDSXX:4:2664:8901:9612 is marked as paired, but its mate does not occur next to it in your BAM file.  Skipping.
*****WARNING: Query A01013:41:HYL5YDSXX:4:2665:4146:11835 is marked as paired, but its mate does not occur next to it in your BAM file.  Skipping.
*****WARNING: Query A01013:41:HYL5YDSXX:4:2666:1362:15060 is marked as paired, but its mate does not occur next to it in your BAM file.  Skipping.
*****WARNING: Query A01013:41:HYL5YDSXX:4:2666:29107:26819 is marked as paired, but its mate does not occur next to it in your BAM file.  Skipping.
*****WARNING: Query A01013:41:HYL5YDSXX:4:2666:30418:17722 is marked as paired, but its mate does not occur next to it in your BAM file.  Skipping.
*****WARNING: Query A01013:41:HYL5YDSXX:4:2666:31873:3803 is marked as paired, but its mate does not occur next to it in your BAM file.  Skipping.
*****WARNING: Query A01013:41:HYL5YDSXX:4:2667:17933:32487 is marked as paired, but its mate does not occur next to it in your BAM file.  Skipping.
*****WARNING: Query A01013:41:HYL5YDSXX:4:2667:27561:4570 is marked as paired, but its mate does not occur next to it in your BAM file.  Skipping.
*****WARNING: Query A01013:41:HYL5YDSXX:4:2667:32750:23610 is marked as paired, but its mate does not occur next to it in your BAM file.  Skipping.
[bwt_restore_sa] SA-BWT inconsistency: primary is not the same. Abort!
[main_samview] fail to read the header from "-".
sambamba-sort: not enough data in stream

Has anyone found a solution of this problem?

[tmhmxg59]

I believe you are missing fna, as @cjieming noted.

#27
#35

[xhy1219]

I believe you are missing fna, as @cjieming noted.

#27
#35

Hi! Does the missing fna same with chr6.fa? I just changed chr6.fa extension to chr6.fna but got the same error..

[NTNguyen13]

@xhy1219 hi, you can use the chr6.fa file, just need to change the path inside the get-reads-alt-unmap.sh from chr6.fna to chr6.fa