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njaupan / ecc_finder

a tool to detect eccDNA using Illumina and ONT sequencing
GNU General Public License v3.0
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Problems with bedtools merge #14

Open inud3mon opened 2 years ago

inud3mon commented 2 years ago

Hi njaupan,

I am having an issue running the test Arabidopsis samples provide. It always crashes at the same point. I also tried running with my own samples and got the exact same problem at this point:

' bedtools merge -o collapse,collapse -i /tmp/.........-c 5,6'

It tells me that it that the file only has 5 columns and 6 is not there?

How can I fix this issue please?

I believe it was the same issue as raised by @nemitheasura ??

Thanks,

Jenn

njaupan commented 2 years ago

Hi Jenn, one causal issue was the scipt configuration path, now I'm updating the installation package and I'll get back to that soon! Many thanks.

liu-zhiyang commented 2 years ago

I came across the same error.

pybedtools.helpers.BEDToolsError:
Command was:

        bedtools merge -o collapse,collapse -i /tmp/pybedtools.hmysjqyo.tmp -c 5,6

Error message was:

*****
***** ERROR: Requested column 5, but database file /tmp/pybedtools.hmysjqyo.tmp only has fields 1 - 0.

The error occurred when I tried to run ecc_finder on data which was pooled from two replication while each of the replication encountered no error. It is confusing.

liu-zhiyang commented 1 year ago

@inud3mon Have you solved this problem?

TingheZhang commented 8 months ago

I met the same issue and I think the main reason is bedtools got killed or crashed. The potential reason caused this may be OOM or limit /temp space. If not these two issues, we need to wait for fix.