Entering edit mode
6.9 years ago
timo.metz
•
0
Hey there,
I used LoRDEC to correct my PacBio reads and would now like to see if the error correction actually worked. There is an error correction tool coming with LoRDEC [http://www.lirmm.fr/~rivals/lordec/FAQ/#orgheadline45] but it does not work for me, I always encounter the same error: ValueError: invalid literal for int() with base 10: 'CC_10000' Has anybody experience with this program and could maybe help me out? And if not, are there any other good ways in order to assess the quality of error corrected pacbio reads?
kind regards
Have you made lordec-stat work? I have tried many times, always got the following error. (Anyone ever got it run? I don't see anything when googled this subject) The error was thrown after the graph was built. This program didn't read existing graph (the .h5 file) and always rebuild the graph. However, lordec-correct works for me. Any suggestion on other tools to access the correction of PB reads?
terminate called after throwing an instance of 'gatb::core::system::Exception' /var/spool/torque/mom_priv/jobs/12817844.torque01.util.production.int.aci.ics.psu.edu.SC: line 25: 187869 Aborted (core dumped) lordec-stat -2 oCelfastp.fa,o7625_fastp.fa,o7884_fastp.fa -k 71 -s 9 -a 120 --thread 100 -i okaPB1_correct.fa -S ./stats/okaPB1_crt.stats