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ERROR: The build data not found in ... !

Open nmc-ei opened this issue 2 years ago • 1 comments

Hello, I got error.

$ fusioncatcher -d ./fusion_test/Human/ -i ./fusion_test/Sample_001/ -o ./fusion_test/Fusion_001/
Checking Python version...
  * Compatible Python version found!
Checking size of installed RAM memory ...
  * 191870 MB of RAM memory found!



ERROR: The build data not found in '/home/username/fusion_test/Human/'!



$ 

I already have done

$ fusioncatcher-build -g homo_sapiens -o ./fusion_test/Human/
WARNING: Cannot restart automatically because the previous log file '/home/username/fusion_test/Human/fusioncatcher-build.log' cannot be found!
The workflow will be restarted from the beginning with step 1!
Log of the pipeline:
.
.
.
--input_genome /home/username/fusion_test/Human/genome.fa \
--output /home/username/fusion_test/Human/
--------------------------------------------------------------------------------
+-->EXECUTING...
  * chromosome 1 has length 248956422
.
.
.
* chromosome KI270394.1 has length 970
--------------------------------------------------------------------------------
==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 30 second(s)
////////////////////////////////////////////////////////////////////////////////
  Running: step = 6   Time: 14:59   Date: 2021-11-25 (elapsed time: 0d:0h:2m)
.
.
.
+-->EXECUTING...
Starting...
Get lists of chromosomes...
Downloaded:      1.30 MB
FINISHED downloading:      1.30 MB
.
.
.
chromosome = Y
Downloaded:      0.48 MB
FINISHED downloading:      0.48 MB

End.
--------------------------------------------------------------------------------
==> Execution time: 0 day(s), 0 hour(s), 21 minute(s), and 23 second(s)
.
.
.
+-->EXECUTING...
Starting...
Downloaded:      1.30 MB
Finished downloading:      1.30 MB

chromosome = 1

IOError = timed out


ERROR: Workflow execution failed at step 16 while executing:
----------------
   get_paralogs.py \
   --organism homo_sapiens \
   --server www.ensembl.org \
   --output /home/username/fusion_test/Human/
----------------


Executing second time the same step/command in order to capture error messages (i.e. STDERR)...

-------------------------------------------
Starting...
Downloaded:      1.30 MB
Finished downloading:      1.30 MB
.
.
.
chromosome = Y
Downloaded:      0.50 MB
Finished downloading:      0.50 MB

End.


WARNING: First execution ended with error but second execution did not! Therefore cannot capture the STDERR!
################################################################################
################################################################################
TOTAL RUNNING TIME: 0 day(s), 0 hour(s), 41 minute(s), and 8 second(s) 
################################################################################
################################################################################
$

Thank you.

nmc-ei avatar Nov 25 '21 08:11 nmc-ei

Does the test.sh from FusionCatcher run fine?

ndaniel avatar Jun 01 '22 09:06 ndaniel