User: mthm
mthm • 10
- Reputation:
- 10
- Status:
- New User
- Location:
- Last seen:
- 7 hours ago
- Joined:
- 1 month, 2 weeks ago
- Email:
- m************@gmail.com
Posts by mthm
<prev
• 8 results •
page 1 of 1 •
next >
1
vote
0
answers
54
views
0
answers
... I have tried to run `CreateGFF3sForClassifFeatures.py` in REPET pipeline once before. then,for some reason I removed the whole directory and tried to re-run the script, but because I ran it before, the data files have already been created in mysql and apparently are not re-writable! problem is that ...
written 2 days ago by
mthm • 10
0
votes
0
answers
49
views
0
answers
... I have already ran one whole cycle of TEdevono (S1-S8) on one of my samples successfully, when starting to run the second sample, the `-S 3 -s Blaster -c Recon` gets stuck at this step, without returning an error or any output file, last time I let it be for almost 3 days but it was still at the
...
written 8 days ago by
mthm • 10
0
votes
1
answer
3.3k
views
1
answers
... thanks I realized my mistake after posting it, but was too late:)
I thought this issue is too minor to be posted separately, sorry. ...
written 14 days ago by
mthm • 10
0
votes
1
answer
3.3k
views
1
answers
... Hi,
I tried to run this script but it returns this error:
fasta_file = sys.argv[1] # Input fasta file
IndexError: list index out of range
should the fasta file be of special format?
mine starts like this:
>monCan3F9-B-G1013-Map20
ATACAACCACTAACCAAACAACATATAGACTG ...
written 14 days ago by
mthm • 10
0
votes
1
answer
147
views
1
answers
... since this is a very new approach, I am going to explain it here, it might help others in future.
the new version of RepeatMasker-4.1.1 doesn't have the old "queryRepeatDatabase" option instead you should use "famdb.py"
first you need to enter the singularity shell; navigate to the directory where ...
written 26 days ago by
mthm • 10
2
votes
1
answer
98
views
1
answers
... I think the reason was the "copy" option inside the TEdenovo.cnfg file which was "yes", although I had defined the tempdir path for it, apparently it didn't work properly, once I changed the copy option on "no" the step 2 of Blaster analysis was finished successfully. ...
written 26 days ago by
mthm • 10
2
votes
1
answer
98
views
1
answer
... I am running a TEdenovo analysis in the docker container where the REPET pipeline is installed on it with all the dependencies. when running the step 2 sequence blasting analysis;
TEdenovo.py -P DmelChr4 -C TEdenovo.cfg -S 2 -s Blaster
I receive this error at the end:
START TEdenovo.py (2 ...
written 27 days ago by
mthm • 10
0
votes
1
answer
147
views
1
answer
... I have installed the Repeatmodeler v2 singularity container as a Dfam TE Tools which includes RepeatMasker and I have merged the RepBase library to the RMasker library using below instruction:
> # Navigate to an appropriate directory that is persistent outside the container $ cd /work
& ...
written 29 days ago by
mthm • 10
Latest awards to mthm
Scholar
26 days ago,
created an answer that has been accepted.
For A: TEdenovo Blaster step 2 raise an error :Exception: ERROR when launching 'LaunchB
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 2805 users visited in the last hour