Unexpected BAM File Reference in TEtranscripts: [E::idx_find_and_load] Could not retrieve index file for '.1735078030.51.bam'

[844464]

Hello,

I encountered an issue while running TEtranscripts. During execution, the program generated the following error message:

[E::idx_find_and_load] Could not retrieve index file for '.1735078030.51.bam'

However, I did not specify this BAM file in my input, and it does not exist in my working directory or input files. Despite this error, the program continued running, and the results appear to have been generated successfully.

Here are the details of my command

TEtranscripts --sortByPos --format BAM --mode multi
-t N-1.accepted_hits.sorted.bam N-2.accepted_hits.sorted.bam N-3.accepted_hits.sorted.bam
-c UT-1.accepted_hits.sorted.bam UT-2.accepted_hits.sorted.bam UT-3.accepted_hits.sorted.bam
--GTF zs11_agat.gtf --TE zs11TE_JH.gtf --project 2vs1 --outdir 2vs1

• Treatment BAM files:
N-1.accepted_hits.sorted.bam, N-2.accepted_hits.sorted.bam, N-3.accepted_hits.sorted.bam
• Control BAM files:
UT-1.accepted_hits.sorted.bam, UT-2.accepted_hits.sorted.bam, UT-3.accepted_hits.sorted.bam
• Annotation files:
GTF file: zs11_agat.gtf、TE file: zs11TE_JH.gtf

What I’ve tried:

1. Checked all input BAM files and their headers—no reference to .1735078030.51.bam was found.
2. Verified that all required input files and index files (e.g., .bam.bai) were provided.

My questions:
1. Why is the program attempting to load this unexpected BAM file?
2. Is it safe to ignore this error if the results seem correct?
3. How can I resolve or suppress this error to avoid confusion?

Thank you for your help!

[olivertam]

Hi,

Thank you for your interest in the software.

1. This "unexpected" BAM file is from the re-sorting of your input BAM file, as you provided the --sortByPos parameter.
2. The warning message comes from pysam, and appears to have no impact on the running of the software (see Could not retrieve index file for '.1606144755.39.bam' #82 and [E::idx_find_and_load] Could not retrieve index file for '.1712579023.8525763.bam' #185) where others have also seen this warning)
3. I believe that there could be a workaround proposed for this where we tell pysam to suppress all warnings, but we have opted against implementing this as it could also suppress the error messages too. We have pinned this [E::idx_find_and_load] Could not retrieve index file for '.1712579023.8525763.bam' #185 on our Github issues page as a compromise solution.

Thanks.

[844464]

Thank you very much for your response. The results have now been successfully generated. I truly appreciate TEtranscript’s contribution to TE research.