Hi, everybody. I have FASTQ headers of the form

@FCC3KD2ACXX:6:1101:1545:2184#ATCACGATC/1

The "ATCACGATC" portion of these older-style headers is supposed to be the "index sequence", or the molecular barcode of a multiplexed sample, according to the Wikipedia article. But I know what the barcodes are, and that isn't one of them. All the barcodes for this project are 6-8bp, not 9, and there are "only" about 300 legitimate barcodes in the lane.

Overall, there are over 255,000 different individual ones of these index sequences on various different reads, out of about 178M reads in the file. Some of them even contain Ns, but they're all exactly 9bp long. And this particular sequence (ATCACGATC) is by far the most prevalent -- it's on 90% of the reads, so it can't be succeeding at separating anything out very specifically.

I'm coming in late to a project, and all I have to go on is the FASTQ files, the list of barcodes, and some wet-lab protocol docs that I'm not particularly qualified to interpret. Any idea what this odd extraneous-looking sequence is? If so, thanks in advance!
Your sequence string 'ATCACGATC' is a perfect match to the TruSeq adapter index 1. The length (9bp) is atypical but not unheard-of. The length of the index read is often index-length-plus-one (i.e., seven cycles for a 6mer), so it appears that the sequencer was programmed for nine index cycles (8mer+1). The last nucleotide is typically trimmed from the data by default (--use-bases-mask = I8n), but the full length can be specified by the user (I9).

As @igor indicates, the amount of data suggests that the file was not demultiplexed. However, given that 90% of your data are a perfect match, it's also unlikely to contain multiple libraries. Best guess is that some other lanes of this flow cell did contain 8mer indices, and CASAVA doesn't allow lane-specific BCL-to-FASTQ conversion (so the data in all lanes have identical formats).