IndexError: list index out of range about syri HOT 5 CLOSED

Duplicate #48 #176

Try using https://github.com/schneebergerlab/fixchr

from syri.

Duplicate #48 #176

Try using https://github.com/schneebergerlab/fixchr

Hi,
I have met the same problem as Diego. So I try to use fixchr to solve my problem, however, I met new problem like this:

I use the code as follow:
fixchr -c a1.THrd.txt -r /172.16.0.2/NFSSharedFiles/01.genome_seq/no_CTG/12.mgy.genome.chr.fasta -q /172.16.0.2/NFSSharedFiles/01.genome_seq/no_CTG/a1.genome.chr.fasta -F T --prefix a1 --nc 10

the first 5 columns of a1.THrd.coords is provided as below:
a1.THrd.txt

I got the file a1.THrd.txt using mummer, function ncmer,delta-filter and show-coords -THrd. I think the main problem is the chromosomes from different strands of two genome I use. But I am not sure where my problem is when I try to use fixchr, it seems I lack one column?
Any way to solve this issue??
Thanks, Zhou

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Solved: schneebergerlab/fixchr#6

from syri.

Solved: schneebergerlab/fixchr#6

Thank you so much for your effort, your revision works well, and i can got result from syri using following code.
syri -c ../01.108.i90_l100_m.filter.THrd.coords -d ../01.108.i90_l100_m.filter.delta -r ../ref.filtered.fa -q ../qry.filtered.fa --prefix 108 --nc 10

But please forgive me, i still got some questions which i was quite confused.

1. when i use the code above it seems to get this WARNING. Does this means that the chromosome is still not reversed or i use the wrong file?
   

2. In order to solve this problem, i replaced input file of -c -r -q with original and the new one generated by fixchr, but the warning still exsist. Following are the result generate from fixchr. Is there any ideas which file should i use? Which should be original one, which should be new file produced by fixchr?
   

Thanks again for your reply.
Zhou

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As this issue is not related to the original issue here, I am starting a new issue. Please, start new issues for different questions.

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