Simon Andrews

We don't calculate that value. It's taken from the TLEN field in the BAM file, so it's whatever the read mapper puts in there. It should be the full inferred...

It shouldn¹t differ for different aligners - the docs are pretty specific about what it¹s supposed to mean. I know that we did have problems when we were using this...

There is. samtools view [file] | head -100000 > small.sam ..and then import that. :-)

What do you get if you extract the tlen values and plot a histogram though?

It¹s a tab delimited file. Just do it in excel!

I did. SAM files are tab delimited files.

It's more likely to be a screw up on our end. Let me take a look.

Just for the record - in our `php.ini` file the correct syntax for this was just: ``` max_input_vars = 100000 ``` ..none of the other variables needed to be changed.

To get a more definitive answer to this I'd need to know * The version of fastqc you were running * The command you used to launch the analysis *...

OK so you have the latest version which shouldn't have the problem with the stalling upon failure. If all of the files are there then something else must be causing...