Closed acesnik closed 4 years ago
Here's a chunk of the refflat file:
gene:ENSG00000172288 transcript:ENST00000306609 Y + 25622161 25624902 25622442 25624527 2 25622161,25624454, 25624034,25624902,
gene:ENSG00000172288 transcript:ENST00000361963 Y + 25622161 25624338 25622442 25624065 1 25622161, 25624338,
gene:ENSG00000185894 transcript:ENST00000602680 Y - 25043990 25062548 25043990 25044023 5 25043990,25048473,25051675,25052150,25062392, 25044064,25048610,25051798,25052219,25062548,
gene:ENSG00000185894 transcript:ENST00000618574 Y - 25038097 25044023 25038097 25044023 4 25038097,25038808,25041768,25043945, 25038116,25038914,25041886,25044023,
gene:ENSG00000185894 transcript:ENST00000382287 Y - 25030900 25052104 25038097 25044023 9 25030900,25031316,25037991,25038808,25041768,25043945,25048473,25051675,25052073, 25031222,25031441,25038116,25038914,25041886,25044064,25048610,25051798,25052104,
gene:ENSG00000205916 transcript:ENST00000382296 Y + 24834126 24905240 24834126 24901175 26 24834126,24840730,24841151,24841803,24842291,24842444,24851578,24851999,24852651,24853139,24853292,24854832,24857275,24859665,24862061,24864445,24866841,24869218,24871598,24873975,24883763,24893302,24895687,24896504,24901111,24905183, 24834129,24840877,24841243,24841855,24842355,24842584,24851725,24852091,24852703,24853203,24853432,24854904,24857347,24859737,24862133,24864517,24866913,24869290,24871670,24874047,24883835,24893374,24895759,24896539,24901210,24905240,
Okay, it turns out I didn't follow this step. I didn't make the experimental_design.txt file or run the Rscript.
After doing that, it ran through the end.
Ideally, it should check for the files and throw an error if they're not there. That'd have saved some time. :)
Hi again,
I ran into another road block. I'm getting the scripts to run, but there are perl errors in both the outputs from JUM_B and JUM_C. I'll attach the logs here.
jum_b.log
The jum_c.log was too big to attach. This is the gist of it:
^ that times 200M lines
Here are the commands I used:
JUM_B.sh command
cd output/JUM_Analysis/JUM_diff && (../../../tools/JUM_2.0.2/JUM_B.sh --Folder $(readlink -f ../../../tools/JUM_2.0.2/) --Test pvalue --Cutoff 1 --TotalFileNum 6 --Condition1SampleName G1_1.,G1_2.,G1_3. --Condition2SampleName S_1.,S_2.,S_3. --Condition1_fileNum_threshold 2 --Condition2_fileNum_threshold 2) 2> ../../jum_b.log && cd ../../..
JUM_C command
cd output/JUM_Analysis/JUM_diff/FINAL_JUM_OUTPUT_pvalue_1 && (../../../../tools/JUM_2.0.2/JUM_C.sh --Folder $(readlink -f ../../../../tools/JUM_2.0.2/) --Test pvalue --Cutoff 1 --TotalCondition1FileNum 3 --TotalCondition2FileNum 3 --REF ../../../../ensembl/Homo_sapiens.GRCh38.96.gff3.refflat.fi x.txt) 2> ../../../jum_c.log && cd ../../../..
Some of the output files have weird stuff like
__ARRAY(0x7fffebd2d1e0)___
written in them:AS_differential_JUM_output_cassette_exon_events_pvalue_1_final_detailed.txt