cryptic error when running coverM genome

[nixon444]

Hi,

I've been trying to run coverM on a number of genome sets to calculate relative abundance, but I get this same error each time:

thread 'main' panicked at 'index out of bounds: the len is 0 but the index is 0', src/coverage_printer.rs:467:35 note: run with RUST_BACKTRACE=1 environment variable to display a backtrace

The command I used is:

coverm genome -1 coverM/108_1.fastq -2 coverM/108_2.fastq -d goodbins/ -x fa -t 16 -v -o 108_binabund_output.tsv

What does this mean, and what am I doing wrong here?

For info, I am running this in a container which has worked for others in my group, on our group server

Cheers, Sophie

[CHEN15623]

Hi,

I've been trying to run coverM on a number of genome sets to calculate relative abundance, but I get this same error each time:

thread 'main' panicked at 'index out of bounds: the len is 0 but the index is 0', src/coverage_printer.rs:467:35 note: run with RUST_BACKTRACE=1 environment variable to display a backtrace

The command I used is:

coverm genome -1 coverM/108_1.fastq -2 coverM/108_2.fastq -d goodbins/ -x fa -t 16 -v -o 108_binabund_output.tsv

What does this mean, and what am I doing wrong here?

For info, I am running this in a container which has worked for others in my group, on our group server

Cheers, Sophie

I have the same problem. Have you solved it？

[wwood]

Hi,

This is a strange one. Can you send the bins and reads to me e.g. via Dropbox? Thanks

[CHEN15623]

Hi,

This is a strange one. Can you send the bins and reads to me e.g. via Dropbox? Thanks

Thanks, my problem has been solved, which is probably caused by a mismatch between the version of samtools and htslib

Best Chen

[wwood]

Hi,

I believe this has been solved, so closing.