I'm using the Galaxy GVL-QLD instance.
I have single reads chip-seq files from E. coli. I set up my genome as a custom build.
I groomed, mapped my reads with BWA (when I use bowtie, some rows have the sequence in the quality score column and the quality scored in the OPT columns, and other rows are fine.. I got stuck there so I choose to map with BWA).
When I perform MACS (after removing unmapped reads via Filter SAM), down to MFOLD = 5 (which I know is not recommended but I'm testing the tool), it says that it finds 11 paired peak and it is not enough to built the model. And hence if fails.
I get this error message
INFO @ Tue, 27 Oct 2015 12:24:44: # ARGUMENTS LIST: # name = chip-seq_1_POS_MERGE # format = SAM # ChIP-seq file = /mnt/galaxy/files/000/117/dataset_117174.dat # control file = None # effective genome size = 3.22e+06 # tag size = 35 # band width = 75 #
I also get this error somtimes:
Traceback (most recent call last): File "/mnt/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/macs/ae2ec275332a/macs/macs_wrapper.py", line 139, in <module> if __name__ == "__main__": main() File "/mnt/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/macs/ae2ec275332a/macs/macs_wrapper.py", line 115, in main os.rmdir( treatment_dir ) OSError: [Errno 39] Directory not empty: '/mnt/tmp/953.1.all.q/tmplrIbXB/chip-seq_1_POS_MERGE_MACS_wiggle/treat'
I have tried to tweak the tag size (my reads are 51 bp) and the bandwidth, but it only increases the number of paired peaks (up to 21) but still fails. I am expecting only 6 peaks in my treatment sample.
Any suggestion to de-bug ?
Thank you :)