hisat2-align died with signal 6 (ABRT) about hisat2

[roryk]

I think your files are corrupt-- that error is telling you there are less reads in your read 2 file than in the read 1 file. If you do a wc -l on those two files, are they different lengths?

[akhilpampana]

ya they are different length, and basically they are of same locus and 2 are continuous

[akhilpampana]

basically the files are split 2 two parts taken from same sample, so thats the reson for difference in length, can u please suggest me how to deal with this error??

[roryk]

Just concatenate the two files together. -1 and -2 are for paired end reads. Concatenate both files together into a file called combined.fq or something similar and call hisat2 with -r combined.fq instead of using -1 and -2.

[akhilpampana]

is it possible to write in the code itself ??

[akhilpampana]

and how to concatenate using hisat2??

[roryk]

You can just concatenate the two files together with the unix command cat:

http://man7.org/linux/man-pages/man1/cat.1.html

[akhilpampana]

ya if thats the case i will try thank you. if i got any errors i will ask thanks for the help

[akhilpampana]

thank you its running

[roryk]

Sweet!

[akhilpampana]

now i am getting this error, please help me out

[tianfree]

@akhilpampana Is your fastq data generated from Solid (colorspace)? Please show some reads.

[akhilpampana]

this is the format of the data

[roryk]

One of your files is probably truncated, if you do a tail on the two files you were trying to use originally, does it look like it is chopped off?

[akhilpampana]

hmmmm no i used cat to merge file it worked for around 20 samples not for thi what should i do????

[roryk]

It is hard to answer your questions because you aren't giving very much information.

Ignore combining the files with cat for now since things aren't working. Go back to the original files. For each of those original files, if it is single end, align it with hisat2 using -r, not -1 and -2.

This error is telling you that one of your files is corrupted and there are more bases than quality measurements. Usually this happens because the file is truncated. If you go back and align each file one by one the file that fails is the one that is corrupted. If it is truncated that means it is ending before it should, so if you look at the last lines of the file, you should see that the last read is truncated.

[akhilpampana]

k i will try again thank you

[akhilpampana]

i worked thank you very on, my file problem, i redone it

[infphilo]

Thanks to @roryk for your help to answer the questions!