Dear all,
I used a matrix generated from multiBamSummary to run plotCorrelation but the error message below was generated:
Fatal error: Exit code 1 () Traceback (most recent call last): File "/galaxy-repl/main/jobdir/014/089/14089566/conda-env/bin/plotCorrelation", line 7, in <module> main() File "/galaxy-repl/main/jobdir/014/089/14089566/conda-env/lib/python2.7/site-packages/deeptools/plotCorrelation.py", line 172, in main skip_zeros=args.skipZeros) File "/galaxy-repl/main/jobdir/014/089/14089566/conda-env/lib/python2.7/site-packages/deeptools/correlation.py", line 32, in __init__ self.load_matrix(matrix_file) File "/galaxy-repl/main/jobdir/014/089/14089566/conda-env/lib/python2.7/site-packages/deeptools/correlation.py", line 72, in load_matrix _ma = np.load(matrix_file) File "/galaxy-repl/main/jobdir/014/089/14089566/conda-env/lib/python2.7/site-packages/numpy/lib/npyio.py", line 392, in load fid.seek(-N, 1) # back-up IOError: [Errno 22] Invalid argument
Could anyone help please?
Many thanks, Alfred
That's a new one. What's the size of the item in your history? My only guess is that it's ~0 bytes.
Hi Devon, it is 0 bytes indeed. Any advice on how to get over this would be much appreciated !
That suggests that something went wrong with
multiBamSummary. I would normally expect that to have produced an error message (perhaps on "stderr" if you click on the info button on the history item). Can you (A) see if there's any apparent error message thatmultiBamSummaryproduced and (B) post the settings you used?Hi Devon, I just double checked and you're right, the multiBamSummary file was actually an empty file with 0 byte of data ! I should have checked before assuming it was okay and put it into plotCorrelation. There is however no error message from the multiBamSummary.
When I ran mBS, my input files were TopHat Bam files, generated using alignment to the mm10 reference genome. I have four samples that I wanted to compare, so my mBS were generated using all 4 TopHat files as inputs. I used all the mBS default settings as below: 1. Computational mode = Bin 2. Bin size in bp = 10,000 3. Distance between bins = 0 4. Region of the genome to limit the operation to = Left blank 5. Show advanced options = No 6. Save raw counts (coverages) to file = No
Many thanks !
Hmm, I don't have any good guesses then. What version of deepTools are you using in Galaxy? Can you somehow provide me with the BAM files? I can then track this down. I'm planning the next deepTools release in a couple weeks, so if this is a bug I'd like to get it resolved beforehand :)
Hi Devon, it is Galaxy Version 2.3.5.0. What would be the best way to send you those BAM files? Many thanks for looking into it. I would really like to analyse these data before the end of the week if possible
Depending on their size, you might be able to:
The fewer files the better, just for the sake of speed, so if you have the same problem just using 2 BAM files then just upload those two.
We are getting the same error on the public Galaxy server http://usegalaxy.org. Same DeepTools version. Am looking at it to see if there is a problem with inputs now. Also interested in what happens here - if true tool issue, DeepTools is updated, etc. Thanks! Jen, Galaxy team
It's weird, the history was shared with me and when I run this from the command line with the files used I get output. I'll upload the files to our Galaxy server and see if I can reproduce the issue.
Cool - thanks. Can share history with me directly if can reproduce error - use the bx address. Tx!
Will do.
It should be shared now.
OK, I can reproduce this on our Galaxy instance too, which suggests that it's a wrapper bug. I'll try to figure that out and have Björn push out the updated wrapper tomorrow.