JBerthelier
commented
4 years ago Dear wangj,
According to the error, it seems that your MySql database of PASTEC no more existe in your PiRATE-VM. You need this MySql database to stock data while you are using PASTEC.
You can re-create it by running this code in the konsol:
mysql -u root --password=jeremy07 -e "create database PASTEC_galaxy"
This should solve your problem for PASTEC
Other users have also somes problems with Helsearch and MGEScan-nonLTR, which seem not working on every genome assembly.
TEdenovo should work, please be careful to submit a fasta file with 60 bp in lenght and with headers containing only letters (a to z), numbers (0-9) and underscore ( _ ) Example= Contig_1
Best,
Jeremy
Dear Jeremy, The PiRATE could run RepeatScout, SINE-finder, LTRharvest, TE-hmmer, RepeatMasker. But It could not run TEdenovo, Helsearch, MITE-Hunter, MGEScan-nonLTR. When I run PASTEC, it have errors as following, even if I logged in as administrator@pba.fr.
2019-11-23 03:24:26 - PASTEClassifier - INFO - START PASTEClassifier parallelized 2019-11-23 03:24:26 - PASTEClassifier - INFO - Fasta file name: genome.fa 2019-11-23 03:24:26 - PASTEClassifier - INFO - Running STEP 1 of PASTEClassifier parallelized: DetectTEFeatures START DetectTEFeatures_parallelized Fasta file name: genome.fa split the sequences in batches Homogeneous in size 20kbp launch the programs on each batch 2019-11-23 03:24:35 - DbMySql - ERROR - ERROR 1049: Unknown database 'PASTEC_galaxy'
Fatal error: Exit code 1 () ERROR 1008 (HY000) at line 1: Can't drop database 'PASTEC_galaxy'; database doesn't exist Traceback (most recent call last): File "/home/jeremy/Pipeline/REPET_2.5/bin/PASTEClassifier.py", line 405, in
iPASTEClassifier.run()
File "/home/jeremy/Pipeline/REPET_2.5/bin/PASTEClassifier.py", line 384, in run
iDF.run()
File "/home/jeremy/Pipeline/REPET_2.5/commons/tools/DetectTEFeatures_parallelized.py", line 226, in run
iDb = DbFactory.createInstance()
File "/home/jeremy/Pipeline/REPET_2.5/commons/core/sql/DbFactory.py", line 37, in createInstance
return DbMySql(cfgFileName = configFileName, verbosity = verbosity)
File "/home/jeremy/Pipeline/REPET_2.5/commons/core/sql/DbMySql.py", line 166, in init
raise DatabaseError(msg)
_mysql_exceptions.DatabaseError: ERROR: failed to connect to the MySQL database