MBoemo
commented
4 years ago Hi David,
You have to specify values with the -p, -z, and -l flags. So a command like this should work, for instance:
DNAscent regions -p 0.1 -z 1 -d output/${FILE} -o output/${FILE}.regions
(Note that I just made up some numbers here as an example.) I'm surprised the third one didn't work though - that should be a valid command. I just tried it on some test data and wasn't able to reproduce the issue. Can you let me know which commit you're using?
Cheers, Mike
Hi.
We are using DNAscent to analyze DNA sequences of a culture with 0% of BrdU. DNAscent works well with the following commands, but it returns positive BrdU scores, which is undesirable for a culture that has no BrdU at all.
================================================================================================= # Making DNAscent index. DNAscent index -f ${RAW_READS} -s ${SEQ_SUMMARY}
# Detection of BrdU analog. for FILE in
ls input | grep '.bam$'do DNAscent detect -b input/${FILE} -r input/giaLam3.fasta -i index.dnascent -o output/${FILE}.detect -t 100 done# Call regions of analogue incorporation. for FILE in
ls output | grep '.detect$'do DNAscent regions --replication -d output/${FILE} -o output/${FILE}.regions done================================================================================================
With the option "--replication" above, the program runs smootly. In the case of 0% of BrdU, it is recommended to make use of the options "-p", "-z" and "-l". But each of the following variants below returns the same error:
================================================================================================= DNAscent regions --replication -p -z -d output/${FILE} -o output/${FILE}.regions DNAscent regions -p -z -d output/${FILE} -o output/${FILE}.regions DNAscent regions -l 2.0 -d output/${FILE} -o output/${FILE}.regions
=================================================================================================
The following is the error that is returned by any of the options above, independent of the input file: terminate called after throwing an instance of 'std::invalid_argument' what(): stof
Searching on internet, it seems that the error is related to trying to read a file that had its end already reached. We could not find the use of the method "eof" in the source code, but we have a limited knowledge about C++.
What do you think could possibly be the problem?
Thanks in advance for any help.
-- David da Silva Pires