Error: too many arguments

[raquelsanzmar]

Hi,

I was trying your tool and I managed to get the output, but I always get this message in the end: "Error: too many arguments" However, I get the expected output and it seems that everything is working fine. I just wanted to make sure whether there is something that I am missing.

Thank you very much in advance! This is very helpful :)

Raquel

[SchulzLab]

Hi Raquel, could you provide some example program call and with which data you get the error? Otherwise it is hard to comment whether your result would be expected.

Thanks, Marcel

[raquelsanzmar]

Hi Marcel, Thanks a lot for your answer. This is how I call it: STARE_ABCpp -b $bed_file -n 4-6 -a $gene_annotation -o Output

• $bed_file refers to a bed file with the ATAC peaks and the counts for 3 different columns
• $gene_annotation is a Gencode gtf-format file

When I run it, I get this message: Reading annotation and intersecting peaks 31s ABCpp: intersected genes and peaks 763ms; 1 processed and written 569ms; 2 processed and written 478ms; 3 processed and written 304ms; 4 processed and written 379ms; 5 processed and written 394ms; 6 processed and written 376ms; 7 processed and written 312ms; 8 processed and written 312ms; 9 processed and written 326ms; 10 processed and written 492ms; 11 processed and written 448ms; 12 processed and written 159ms; 13 processed and written 331ms; 14 processed and written 314ms; 15 processed and written 353ms; 16 processed and written 535ms; 17 processed and written 162ms; 18 processed and written 476ms; 19 processed and written 184ms; 20 processed and written 110ms; 21 processed and written 203ms; 22 processed and written 243ms; X processed and written 58ms; Y processed and written Compressing files 6861ms compression 46s ABCpp in total Error: too many arguments.

However, I do get the Output_ABCpp_scoredInteractions and Output_GeneInfo txt.gz files for each of the columns

Thanks a lot again!

[DennisHeck]

Dear Raquel,

Happy to hear that you find it useful! I couldn't reproduce your error when using the same flags. The last message from the STARE_ABCpp function itself is the reported runtime, in your case '46s ABCpp in total'. To me it looks like a message from the shell, but I'm not sure what causes it. As long as the output files are written and compressed, I think it should be fine.

Best wishes, Dennis

[raquelsanzmar]

Hi Dennis,

Thanks a lot! You are right, now I've been able to fix it and it was not coming from your program :) Again, thank you very much, this is very helpful!!

Best, Raquel