plantdr430/transposableelmt

Wrapper script to identify TEs and mask genome

transposableelmt's Issues

Problems with TransposonPSI

Hi Stephen,

I am having some problems running the TransposonPSI step. Could you help me with this?

Thanks in advance,

Héctor

I am running the command

/DATOS/hoberti/Programas/TransposableELMT/TransposableELMT.py --cpus 8 -in Assembly.fasta -o TransposableELMT

and it give me this problem

Running TransposonPSI: This will take some time
Traceback (most recent call last):
File "/DATOS/hoberti/Programas/TransposableELMT/TransposableELMT.py", line 787, in
run_transposonPSI()
File "/DATOS/hoberti/Programas/TransposableELMT/TransposableELMT.py", line 648, in run_transposonPSI
with open(best_hits_gff, 'r') as best_hits, open(psi_gff3, 'w') as gff3:
IsADirectoryError: [Errno 21] Is a directory: '/DATOS/hoberti/Fungi/XX/TransposableELMT/working_directory/TransposonPSI'

The log of TransposonPSI is

processing NODE_1_length_734927_cov_85.738756.
Error, formatdb -i transposonPSI.32675.centos.tmp/NODE_1_length_734927_cov_85_738756/NODE_1_length_734927_cov_85_738756.seq -p F (ret -1) at /DATOS/hoberti/Programas/TransposonPSI/transposonPSI.pl line 115, <$filehandle> line 1.