search

bioinform / rnacocktail

Other
87 stars 48 forks source link

Error in run_editing STEP 10 #15

Closed thestarocean closed 5 years ago

thestarocean commented 5 years ago

Currently I am using RNAcocktail for RNA editing sites identification. All procedure went smoothly until STEP 10, with log showing as follows: INFO 2019-04-09 11:37:47,149 src.run_editing --------------------------STEP 9-------------------------- INFO 2019-04-09 11:37:47,150 src.run_editing Task: Rerun GIREMI for 1351 INFO 2019-04-09 11:37:47,150 src.run_editing Running "bash -c cd /cloud/data/zxcai/soft/giremi && giremi -f /cloud/data/zxcai/ref/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa -l /cloud/data/zxcai/RNAcocktail_test/giremi/1351/SNV_annotated_filtered.bed -o /cloud/data/zxcai/RNAcocktail_test/giremi/1351/giremi_out.txt /cloud/data/zxcai/RNAcocktail_test/giremi/1351/alignments.pos_sorted.bam" INFO 2019-04-09 12:28:29,244 src.run_editing Returned code 1 (3042.03 seconds) INFO 2019-04-09 12:28:29,252 src.utils Creating directory /cloud/data/zxcai/RNAcocktail_test/out/giremi/1351 INFO 2019-04-09 12:28:29,287 src.run_editing --------------------------STEP 10-------------------------- INFO 2019-04-09 12:28:29,296 src.run_editing GIREMI failed! INFO 2019-04-09 12:28:29,296 src.utils Run log is saved in /cloud/data/zxcai/RNAcocktail_test/logs/run-editing-20190409-113746.log INFO 2019-04-09 12:28:29,296 src.utils All Done!

And when I check the work dir for output files generated during the analysis, I discovered that giremi_out.txt existed, but not giremi_out.txt.res (which should be copied to output dir in STEP 10). So I try to locate where this problem comes from, and could not find where giremi_out.txt.res is generated according to run_editing.py. My guess is that when rerun Giremi to remove N variants, maybe the output should be giremi_out.txt.res?

thestarocean commented 5 years ago

I realized that according to giremi documents, giremi.pl did produce .res files. However, in defaults.py, GIREMI was assigned with "giremi". So my guess is that this value should be "giremi.pl"? So it could use the R script to predict RNA editing and output .res files?

thestarocean commented 5 years ago

OK, I figure out that I was using giremi.zip downloaded from https://www.ibp.ucla.edu/research/xiao/GIREMI.html. Apparently, it's a bit different with github version, because it uses giremi.pl while github version uses only "giremi". Sorry for bothering you.

msahraeian commented 5 years ago

@thestarocean happy to see your interest in RNACocktail. That's great that you have already resolved the issue.