comprna
ERROR:lib.tools:16862, in line 16863. Skipping line...
while running your demo codes with your demo data, i came across the following error, did i get the correct answer?
$ python $SUPPA2_HOME/suppa.py psiPerEvent \
-i /home/hcauser/suppa2/ensembl_hg19.events.ioe
-e /home/hcauser/suppa2/iso_tpm_formatted.txt
-o TRA2_events INFO:lib.tools:File /home/hcauser/suppa2/iso_tpm_formatted.txt opened in reading mode. INFO:psiCalculator:Buffering transcript expression levels. INFO:lib.tools:File /home/hcauser/suppa2/iso_tpm_formatted.txt closed. INFO:lib.tools:File /home/hcauser/suppa2/ensembl_hg19.events.ioe opened in reading mode. INFO:psiCalculator:Calculating PSI from the ioe file. ERROR:lib.tools:16862, in line 16863. Skipping line... ERROR:lib.tools:32514, in line 32515. Skipping line... ERROR:lib.tools:108063, in line 108064. Skipping line... ERROR:lib.tools:126805, in line 126806. Skipping line... ERROR:lib.tools:131920, in line 131921. Skipping line... ERROR:lib.tools:138695, in line 138696. Skipping line... INFO:lib.tools:File /home/hcauser/suppa2/ensembl_hg19.events.ioe closed. INFO:psiCalculator:Generating output TRA2_events.psi INFO:psiCalculator:Done
Hi,
these must be transcripts in the annotation that are not expressed and do not have an entry in the expression file. Did you check that your PSI file is not empty?
Thanks
Eduardo
On Wed, 2 Dec 2020 at 02:29, Sigit [email protected] wrote:
while running your demo codes with your demo data, i came across the following error, did i get the correct answer?
$ python $SUPPA2_HOME/suppa.py psiPerEvent \
-i /home/hcauser/suppa2/ensembl_hg19.events.ioe -e /home/hcauser/suppa2/iso_tpm_formatted.txt -o TRA2_events INFO:lib.tools:File /home/hcauser/suppa2/iso_tpm_formatted.txt opened in reading mode. INFO:psiCalculator:Buffering transcript expression levels. INFO:lib.tools:File /home/hcauser/suppa2/iso_tpm_formatted.txt closed. INFO:lib.tools:File /home/hcauser/suppa2/ensembl_hg19.events.ioe opened in reading mode. INFO:psiCalculator:Calculating PSI from the ioe file. ERROR:lib.tools:16862, in line 16863. Skipping line... ERROR:lib.tools:32514, in line 32515. Skipping line... ERROR:lib.tools:108063, in line 108064. Skipping line... ERROR:lib.tools:126805, in line 126806. Skipping line... ERROR:lib.tools:131920, in line 131921. Skipping line... ERROR:lib.tools:138695, in line 138696. Skipping line... INFO:lib.tools:File /home/hcauser/suppa2/ensembl_hg19.events.ioe closed. INFO:psiCalculator:Generating output TRA2_events.psi INFO:psiCalculator:Done
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