fusioncatcher
fusioncatcher copied to clipboard
ERROR: The build data not found in ... !
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.
Does the test.sh
from FusionCatcher run fine?