Aligned Annihilation

   Sam Nicholls    No Comments yet    AU-PhD

This afternoon in a coffee fueled fugue, I nuked every directory containing output for any attempt to align the limpet contigs to any form of database so far. Here’s why, and what I did next.

I awoke in the morning knowing I was too far down the rabbit hole to truly know which outputs belonged to what job, which sets of outputs were now supposed to be appended to the ends of other truncated outputs, whether I was even supposed to be looking at hydrolases or taxonomy and did I try hitting on TrEMBL or SwissProt (or both, or neither)? Not that the database matters given my copies of both are now heavily redundant anyway.

As you might imagine, the obliteration was a briefly cathartic experience interrupted too soon by an intense realisation that I am definitely behind in producing interesting data. But it is refreshing to have a grasp on what we have so far, even if it is now very little1. It was also easy to work out where to go from here: generate some damn data.

Recently I sidelined BLAST in favour of rapsearch for performing searches over contigs for “interesting sequences” as the cluster simply appears unable to cope with such scale: once both the limpet assembly contigs had been sharded into 250 bite-size pieces and hit against say, 30 shards of TrEMBL v2015_03, you’re already looking at 7,500 jobs — which as seen previously is potentially problematic.

Having re-stocked my hydrolase-specific databases after the latest release of Uniprot, with bacterial and archaeal2 hydrolases, Wayne suggested to grab those from fungi too — as they are an expected taxonomic group in the dataset and we’d like to not miss them out. The table below summarises the databases for future reference:

Taxonomy Reviewed #Records DB Size (MB) Failed
Bacteria N (Tr) 1,069,711 2,700~ X
Bacteria Y (SP) 42,027 108 X
Archaea N (Tr) 20,456 59
Archaea Y (SP) 2,132 20 X
Fungi N (Tr) 61,521 243 X
Fungi Y (SP) 5,546 37

Thanks to the speed of rapsearch, one does not need to perform any sharding on the contig queries or the database, which is lovely. Additionally, my work in progress: Sunblock, takes some of the pain out of working with the cluster, prompting a few questions before automatically generating the job script and submitting it to SGE3 for execution.

Unfortunately the smooth sailing stopped shortly after scheduling and four of the six jobs terminated given a non-zero exit (as configured) from the rapsearch command and dumping the following familiar library error4:

A quick search offers no concrete solution. The disk isn’t full5 and the accounting file indicates that both the RAM and time allocated to the jobs were sufficient. You may recall my encountering this boost error recently when client nodes had been upgraded in an attempt to address the “recent” kernel NFS bug disaster.

node012 is part of the large.q and so I thought perhaps this heavily utilised big-job queue was yet to receive (or yet to reboot following) such an update. After resubmitting the jobs to other queues with Sunblock6 and found the behaviour repeated on another node, my hunch was proven incorrect. Grr.

Of the two successful jobs, the only link appears to be their small database size (see table). Yet the smallest database still met the same fateful error regardless, thus it appears the behaviour is unpredictable. I can only guess the trouble is related to a particular compute node rather than a bug in rapsearch or an error in my job submission scripts (which have had at least six PhD candidate grade eyes on them now) and so I’ve escalated my confusion and ruined the bank holiday weekend of our trusty sysadmin.

Update: The following morning

I spoke to Tom about the rapsearch jobs he’s running right now and all is apparently well on node009 and node010. So I figured I’d resubmit the previously failed fungi TrEMBL job to node010 and wait for a result: it completed sucessfully in just over 40 minutes.

Unhelpfully, the fungi SwissProt job (which admittedly was previously successful) was able to finish on the suspicious node003. So the problem is unpredictable and transient? The plot thickens.

I’ll try out the bacterial and failed archaea tasks on node010.

Update: Mostly still morning

The archaeal task was a success on node007, taking just shy of 20 minutes. One of the bacterial re-resubmissions has already failed with the same error as before. I decided to have a nose around the rapsearch repository to try and track down where calls to boost archive serialization functionality even reside. Instead I’m sat here confused as to why there is a boost/ directory included in the source that hasn’t been updated for two years, whilst the project’s Makefile still links against a local installation of boost with -lboost_serialization as a sane person would? Wat? I’m not even sure what the consequences of this are, does this old directory get used during building? I’ll have to ask our sysadmin how he managed to build it as a module but this does not sit well with me.

My good friend and resident expert in all things C(++), Dan located some manual pages that I should have read regarding boost serialization exceptions. The boost::archive_exception object holds an exception_code that maps to an enum to tell you exactly what went wrong, which is awesomely thought out and very useful. Unfortunately for me, the error isn’t caught by rapsearch which is why I have an upset stderr. My options are probably either to re-compile rapsearch with my own attempt at error handling, or re-enabling core dumps and inspecting the steaming remains with gdb. I’m opting for the latter because quite frankly, screw spending my weekend messing around trying to diagnose and fix poorly documented C-based bioinformatics tools again.

Update: A few days later

The drama continues.


  • I deleted everything that hasn’t quite worked and it felt good for a short time.
  • The cluster continues to fail in an unexpected and unpredictable fashion.
  • If a library you include gives you nice exception objects, please try to catch them and use them for good.

  1. I kept my first and only successful BLAST job which completed over Christmas, that was against a heavily outdated SwissProt. I doubt at this point it is even of any use but it is all I have to show for myself. 
  2. Is that right? 
  3. Especially useful for quickly re-submitting the jobs I sent with a missing database file extension. 
  4. At least the core wasn’t dumped this time. This also shows that my no error tolerance configuration works correctly, we caught the failure! 
  5. Tom and I can’t believe it either. It’s the most free space I’ve seen since I started here:

  6. I can’t help but name drop my tool here. It just makes my life so much easier. Instead of messing around editing job submission scripts to change queues and parameters, I can just resubmit by answering a few prompts from the comfort of my terminal!