Error running "gemBS extract"

[aszabo08]

Hi,

I had the following problem when running the extraction step, after successfully performing the indexing and calling stages.
This is the log file:

INFO - Launch:
        /usr/local/lib/gemBS/bin/mextr --loglevel info --compress --md5 --regions-file ./S0070_mextr_ctgs.bed --cpgfile ./S0070_cpg.txt.gz --noncpgfile ./S0070_non_cpg.txt.gz --bed-methyl ./S0070 --tabix --threads 40 --threshold 10 --bw-mode strand-specific ./S0070.bcf
WARN - Removing output file ./S0070_cpg.txt.gz
WARN - Removing output file ./S0070_non_cpg.txt.gz
WARN - Removing output file ./S0070_cpg.bed.gz
WARN - Removing output file ./S0070_cpg.bb
WARN - Removing output file ./S0070_chg.bed.gz
WARN - Removing output file ./S0070_chg.bb
WARN - Removing output file ./S0070_chh.bed.gz
WARN - Removing output file ./S0070_chh.bb
WARN - Removing output file ./S0070_pos.bw
WARN - Removing output file ./S0070_neg.bw
ERROR - Error received from worker thread 7
ERROR - Worker thread 3 received error: receiving on a closed channel
ERROR - Worker thread 2 received error: receiving on a closed channel
ERROR - Worker thread 1 received error: receiving on a closed channel
ERROR - Worker thread 4 received error: receiving on a closed channel
ERROR - Worker thread 5 received error: receiving on a closed channel
ERROR - Worker thread 0 received error: receiving on a closed channel
ERROR - Worker thread 6 received error: receiving on a closed channel
Error: "Exiting after error"

When running the above mextr command in the gemBS4 docker container, this is the output:

INFO - compress_bbi_thread starting up
INFO - write_bbi_thread starting up
INFO - compress_bbi_thread shutting down
thread '<unnamed>' panicked at 'attempt to divide by zero', mextr/src/bbi/tree.rs:197:21
note: run with `RUST_BACKTRACE=1` environment variable to display a backtrace
Aborted (core dumped)

I was wondering if maybe you could advise me on this issue?

Many thanks,
Anita

[seynard]

Hi, I am experiencing exactly the same issue. Did you find a solution to it?
Thanks, Sonia