Re: Regarding LoRTIA
Dear Shruti,
On Sun, Nov 01, 2020 at 10:29:26PM +0530, shruti gupta wrote:
> With your support I am able to install and run the LoRTIA package
I think we should settle with some common terminology. In Debian
terminology "package" refers to a "Debian package". While for instance
GNU R calls those R code distributed at CRAN also "packages" the meaning
is different. I guess you want to express you was able to install the
LoRTIA *software* successfully - but you did not created a Debian package
from this software. Or did I miss something and you really installed
LoRTIA from some lortia*.deb package?
> I have run one test file which is generating this output
>
> shruti@debian:~/LoRTIA$ LoRTIA -5 AGAGTACATGGG --five_score 16
> --check_in_soft 15 -3 AAAAAAAAAAAAAAA --three_score 18 -s poisson -f True
> ./test/test.sam ./output/ ./test/test_reads.fasta
> Sorting ./test/test.sam...
> Iterating over ./test/test.sam...
> Generating statistics...
> Sorting and indexing output...
> Counting coverage...
> Processed files saved to ./output/
>
> Calculating l3 feature statistics...
> Calculating r3 feature statistics...
> Calculating r5 feature statistics...
> Feature file ./output//test_r5.tsv is empty. There is nothing to do here.
> Calculating l5 feature statistics...
> Feature file ./output//test_l5.tsv is empty. There is nothing to do here.
> Calculating in feature statistics...
> ERROR: The specified reference file does not contain contigs
> from the references used for mapping. Supply the same reference
> that was used for the mapping and try again.
>
> Could you all please suggest what I have to do next in this package.
Could you please confirm that you have read and understood
https://salsa.debian.org/med-team/community/MoM/-/wikis/home
I think there is some advise given there. Please ask here
about details on this page if something remains unclear.
Thanks a lot for your effort on LoRTIA in any case
Andreas.
--
http://fam-tille.de
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