hey, i bumped into this error now:
2016-08-17 14:45:59,543 rMATS version: 3.2.4
2016-08-17 14:45:59,543 Start the program with [RNASeq-MATS.py -s1 testData/231ESRP.25K.rep-1.R1.fastq:testData/231ESRP.25K.rep-1.R2.fastq,testData/231ESRP.25K.rep-2.R1.fastq:testData/231E$
2016-08-17 14:45:59,597 ################### folder names and associated input files #############
2016-08-17 14:45:59,598 SAMPLE_1\REP_1 testData/231ESRP.25K.rep-1.R1.fastq:testData/231ESRP.25K.rep-1.R2.fastq
2016-08-17 14:45:59,598 SAMPLE_1\REP_2 testData/231ESRP.25K.rep-2.R1.fastq:testData/231ESRP.25K.rep-2.R2.fastq
2016-08-17 14:45:59,598 SAMPLE_2\REP_1 testData/231EV.25K.rep-1.R1.fastq:testData/231EV.25K.rep-1.R2.fastq
2016-08-17 14:45:59,599 SAMPLE_2\REP_2 testData/231EV.25K.rep-2.R1.fastq:testData/231EV.25K.rep-2.R2.fastq
2016-08-17 14:45:59,599 #########################################################################
2016-08-17 14:45:59,599 start mapping..
2016-08-17 14:45:59,599 mapping the first sample
2016-08-17 14:45:59,611 mapping sample_1, rep_1 is done with status 26112
2016-08-17 14:45:59,612 error in mapping sample_1, rep_1: 26112
2016-08-17 14:45:59,612 error detail:
EXITING: FATAL INPUT ERROR: unrecoginzed parameter name "alignEndsType" in input "Command-Line-Initial"
SOLUTION: use correct parameter name (check the manual)
Aug 17 14:45:59 ...... FATAL ERROR, exiting
2016-08-17 14:45:59,612 There is an exception in mapping
2016-08-17 14:45:59,612 Exception: <type 'exceptions.Exception'>
2016-08-17 14:45:59,612 Detail:
Are you sure you provided a BAM file with alignments? It's complaining because the first alignment in the BAM file you provided has fewer than 10 columns (there should always be at least 11). What's the output of
samtools view alignments.bam | head -n 1
(n.b., replacealignments.bam
with the file you're using as input)?this is the output :
Odd. Maybe modify the source code to add a
print(output.strip().split('\t'))
, just to see what it's getting.I have tried it before, doesnt work. But now a new error arises. Index exception error.
Can you post the full command? This would make the most sense if you specified having paired-end data when you don't.
sry for the late reply, here is the command
python RNASeq-MATS.py -s1 /mnt/d/sratoolkit.2.7.0-win64/Output_sra/SRR1035213.fastq -s2 /mnt/d/sratoolkit.2.7.0-win64/Output_sra/SRR1035214.fastq -gtf /mnt/d/STARindex/hg19-GTF -bi /mnt/d/STARindex/hg19 -o ~/test_run -t paired -len 50 -a 8 -c 0.0001
You don't have paired-end data, don't use
-t paired
.my bad, i am new to bioinfo. this is my first sem at school. sry fr this..
python RNASeq-MATS.py -s1 testData/231ESRP.25K.rep-1.R1.fastq:testData/231ESRP.25K.rep-1.R2.fastq,testData/231ESRP.25K.rep-2.R1.fastq:testData/231ESRP.25K.rep-2.R2.fastq -s2 testData/231EV.25K.rep-1.R1.fastq:testData/231EV.25K.rep-1.R2.fastq,testData/231EV.25K.rep-2.R1.fastq:testData/231EV.25K.rep-2.R2.fastq -gtf ~/tools/hg19-GTF -bi ~/tools/STARindex/hg19 -o out_test -t paired -len 50 -a 8 -c 0.0001 -analysis P
Please use
ADD COMMENT/ ADD REPLY
to answer to earlier posts in the thread, to keep everything logically structured and easy to follow. In addition, it would be nice if you would approve (up-vote) answers here to show they helped you.What version of STAR do you have installed? This appears to be a bug in whatever version of it you have.
I am using STARv3. samtoolsv1.2 rMATSv3.2.4
STARv3 doesn't exist, the most recent version is 2.5.2a.
Edit: The option that's causing an error was introduced in version 2.3.1v, so if you're using anything older then you need to upgrade.