ERROR: Fail to convert seq IDs to less than 15 character

[intirules]

So i wanna run my harvest results in Retriever and 1 of 22 genomes give me this problem.

$$$ ERROR: Fail to convert seq IDs to less than 15 characters! Please provide a genome with shorter seq IDs.
In harvest i used:

gt ltrharvest -index 1.fna -seqids Yes tabout no -seed 30 -xdrop 5 -mat 2 -mis -2 -ins -3 -del -3 -minlenltr 100 -maxlenltr 7000 -mindistltr 1000 -maxdistltr 15000 -similar 80.0 -overlaps no -mintsd 4 -maxtsd 20 -motif TGCA -motifmis 1 -vic 60 > 1.harvest.scn

in Retriever:
perl LTR_retriever -genome /medicina/wocana/Tesis/Secuencias/Retriever/1/1.fna -inharvest /medicina/wocana/Tesis/Secuencias/Harvest/1/1.harvest.scn

Any idea how i can fix it?

[oushujun]

Hello, This message tells that sequence names in the genome is too long for RepeatMasker, which could only take up to 15 characters. LTR_retriever takes two approaches to convert long sequence names to fit the requirement, which is successful most of the time but could also fail occasionally (such as your 1/22 genome). In such cases, you may need to apply some command line skills to convert sequence names manually, then feed the converted genome to LTR_retriever. You may not need to rerun LTRharvest if your sequence order is not changed. For sequence name conversion, I had successful experiences using Perl one-liners such as: perl -nle 's/PATTERN//g; print $_' genome.fa > genome.fa.modified Simply replace 'PATTERN' with the shared string among long sequence names. Let me know if you have further questions. Shujun

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On Fri, May 4, 2018 at 3:58 PM, Agus ***@***.***> wrote: So i wanna run my harvest results in Retriever and 1 of 22 genomes give me this problem. $$$ ERROR: Fail to convert seq IDs to less than 15 characters! Please provide a genome with shorter seq IDs. In harvest i used: gt ltrharvest -index 1.fna -seqids Yes tabout no -seed 30 -xdrop 5 -mat 2 -mis -2 -ins -3 -del -3 -minlenltr 100 -maxlenltr 7000 -mindistltr 1000 -maxdistltr 15000 -similar 80.0 -overlaps no -mintsd 4 -maxtsd 20 -motif TGCA -motifmis 1 -vic 60 > 1.harvest.scn in Retriever: perl LTR_retriever -genome /medicina/wocana/Tesis/Secuencias/Retriever/1/1.fna -inharvest /medicina/wocana/Tesis/Secuencias/Harvest/1/1.harvest.scn Any idea how i can fix it? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#14>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AFt-NJHZf41dlAfgwT5LtDCseYiXfTKrks5tvLL5gaJpZM4TzMMh> .

[intirules]

Thx at the end we solve it with:

$vi EditFasta

File='1.fna'
OutFile = '1_fixed.fna'

f = open(File,'r')
g = open(OutFile,'w')
for line in f:
line.rstrip()
if '>' in line:
temp = line.split()
temp1 = ' '.join(temp[0:-1])
temp1 = temp1.lstrip('>')
towrite = '>'+temp[-1]+' '+temp1+'\n'
g.write(towrite)
else:
g.write(line)
f.close()
g.close()

$python EditFasta