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lindaszabo / KNIFE

Known and Novel IsoForm Explorer. Statistically based splicing detection for circular and linear isoforms
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Error in predictJunctions GLM while running KNIFE #5

Closed ShobanaSekar closed 6 years ago

ShobanaSekar commented 7 years ago

Hi,

I am trying to run KNIFE_v1.4 on some of our samples and am running into a few errors for some of them. I am getting these during the call to predictJunctions_tableData.r

Error 1:

Error in rbindlist(list(linear_reads, decoy_reads)) : Item 2 has 7 columns, inconsistent with item 1 which has 6 columns. If instead you need to fill missing columns, use set argument 'fill' to TRUE. Execution halted

Error 2 (for a different sample):

Error in fread(classFile, header = TRUE, sep = "\t") : File '/scratch/ssekar/circRNA/fastqs_n_tools/ADCC/KNIFE/ADCC_0019_PC_Whole_C1_OV2TD_L02544.proj/ADCC_0019_PC_Whole_C1_OV2TD_L02544.proj/circReads/ids/ADCC_0019_PC_Whole_C1_OV2TD_L02544.proj_R1__output.txt' does not exist. Include one or more spaces to consider the input a system command.

The file fread() complains to be missing is actually present and not empty. I am not sure what else is causing this error. This is all going through fine for 15/20 samples I am running this on.

It will be really helpful to get your inputs on fixing these errors.

Thank you, Shobana Sekar

lindaszabo commented 7 years ago

For the first error, the only time I have seen this is if there are no decoy reads, which can either happen for very shallowly sequenced libraries or if the wrong read_id_style is used (appended vs complete).

For the second error, I am not sure why fread would give an error that the file does not exist if it does.

rfarouni commented 7 years ago

Hi @ShobanaSekar @lindaszabo

I am not sure, but for the second error, the culprit could be the double underscore in "R1__output.txt". The code sometimes adds an underscore to the file name using 'join', like in this line and sometimes it doesn't, but rather includes it hardcoded in the suffix, just like in this line.

ShobanaSekar commented 6 years ago

Sorry this is late, but I was able to resolve this issue by changing the file names of those files that contained an extra "_1" somewhere in its name.

Best Shobana