TEdenovo Blaster step 2 raise an error :Exception: ERROR when launching 'LaunchBlasterInParallel.py
Entering edit mode
15 months ago
mthm ▴ 40

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 (2021-02-03 14:11:26)
version 3.0
project name = monCan3F9
project directory = /home/centos/Dmontana/TEdenovo
beginning of step 2
self-alignment with Blaster
The copy option is: True 
submitting job(s) with groupid 'monCan3F9_TEdenovo_S2_Blaster' (2021-02-03 14:11:27)
waiting for 198 job(s) with groupid 'monCan3F9_TEdenovo_S2_Blaster' (2021-02-03 14:11:29)
all jobs with groupid 'monCan3F9_TEdenovo_S2_Blaster' are finished (2021-02-03 14:59:47)
start cleaning cluster nodes (2021-02-03 14:59:47)
sh: qhost: command not found
ERROR with qhost
Traceback (most recent call last):
  File "/usr/local/REPET_linux-x64-3.0/bin/TEdenovo.py", line 2130, in <module>
  File "/usr/local/REPET_linux-x64-3.0/bin/TEdenovo.py", line 294, in main
  File "/usr/local/REPET_linux-x64-3.0/bin/TEdenovo.py", line 919, in selfAlign
    raise Exception("ERROR when launching '%s'" % cmd)
Exception: ERROR when launching 'LaunchBlasterInParallel.py -q /home/centos/Dmontana/TEdenovo/monCan3F9_db/batches -s /home/centos/Dmontana/TEdenovo/monCan3F9_db/monCan3F9_chunks.fa -a -o monCan3F9.align.not_over -C /home/centos/Dmontana/TEdenovo/monCan3F9_Blaster/blaster.cfg -g monCan3F9_TEdenovo_S2_Blaster -v 0'

I wouldn't expect it to be the software installation fault cause I have not done it myself, unless there is a bug, or could it be related to my input data? I preprocessed my fasta file before running the analysis to create the 60 nt per line format:

PreProcess.py -S 1 -i input.fa -v 3

should I have done anything else that I didn't?

te docker TEdenovo REPET • 390 views
Entering edit mode
15 months ago
mthm ▴ 40

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.


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