remove_unused_barcodes.py not working after updating to qiime 1.9.1

[Santi Gallego]

I have a shell script pipeline that incorporates qiime as well as remove_unused_barcodes.py. After I updated qiime to 1.9.1, I began to get errors with remove_unused_barcodes.py. Note that remove_unused_barcodes.py did not change as it is not part of qiime. Has anyone else had this issue or have any ideas as to what might be going on?

Error:

M00934:3:000000000-A7Y81:1:2119:24545:13430 not found

M00934:3:000000000-A7Y81:1:2119:16610:13428 not found

M00934:3:000000000-A7Y81:1:2119:20151:13435 not found

M00934:3:000000000-A7Y81:1:2119:21093:13435 not found

M00934:3:000000000-A7Y81:1:2119:13250:13435 not found

M00934:3:000000000-A7Y81:1:2119:5881:13439 not found

M00934:3:000000000-A7Y81:1:2119:17817:13439 not found

M00934:3:000000000-A7Y81:1:2119:20257:13441 not found

M00934:3:000000000-A7Y81:1:2119:17354:13444 not found

M00934:3:000000000-A7Y81:1:2119:6761:13450 not found

M00934:3:000000000-A7Y81:1:2119:14431:13453 not found

M00934:3:000000000-A7Y81:1:2119:17323:13445 not found

M00934:3:000000000-A7Y81:1:2119:11773:13453 not found

M00934:3:000000000-A7Y81:1:2119:20946:13444 not found

M00934:3:000000000-A7Y81:1:2119:22010:13449 not found

M00934:3:000000000-A7Y81:1:2119:24543:13453 not found

M00934:3:000000000-A7Y81:1:2119:10645:13456 not found

M00934:3:000000000-A7Y81:1:2119:16126:13462 not found

M00934:3:000000000-A7Y81:1:2119:20441:13463 not found

M00934:3:000000000-A7Y81:1:2119:10665:13469 not found

M00934:3:000000000-A7Y81:1:2119:24268:13469 not found

M00934:3:000000000-A7Y81:1:2119:7154:13470 not found

M00934:3:000000000-A7Y81:1:2119:2045:13472 not found

M00934:3:000000000-A7Y81:1:2119:10970:13473 not found

M00934:3:000000000-A7Y81:1:2119:16106:13473 not found

M00934:3:000000000-A7Y81:1:2119:12170:13479 not found

(...)

 

[Mike Robeson]

Hi Santi,

It seems that you made use of my old clunky and quickly hacked together script from this post? If so, you probably want to switch to the more streamlined version here. I essentially pulled out the relevant code I wrote for join_paired_ends.py and use this for cases in which I want to test other paired-end merging tools.  If you are using `join_paired_ends.py`, use the  `-b` option. This will do exactly what you want.

However, if you used another tool to join / merge paired-ends, make sure that tool writes the output in the same order as the input. This will most likely not be the case if using the multi-cpu options of some merging tools (I think this may be the case for FLASH and PEAR?). That is, the order of the output will be different causing the script to fail. The script works this way to keep the code scalable for larger data sets.  This avoids the requirement of having large memory to process your data; this is what my old original script does. :-/

Finally, script `join_paired_ends.py`, and my updated stand-alone version, also expect that the fastq headers of the index reads and the final merged / joined output to be identical.

Let us know if this helps. If not, can you provide us more detail on the commands used as well as a snippet of the first few lines of your fastq files?

-Cheers!

-Mike

[Santi Gallego]

Thanks Mike! I will try it and get back with the results!