abyss-todot error

[Salim B]

Hi,

I am trying to do this large assembly but the process has come to standstill at the abyss-todot stage. It produced the following error:

abyss-todot  --dist -e indica-3.fa pe1-3.dist pe2-3.dist pe3-3.dist pe4-3.dist pe5-3.dist pe6-3.dist pe7-3.dist pe8-3.dist pe9-3.dist pe10-3.dist pe11-3.dist pe12-3.dist pe13-3.dist pe14-3.dist pe15-3.dist pe16-3.dist pe17-3.dist pe18-3.dist pe19-3.dist pe20-3.dist pe21-3.dist pe22-3.dist pe23-3.dist pe24-3.dist pe25-3.dist pe26-3.dist pe27-3.dist pe28-3.dist pe29-3.dist pe30-3.dist pe31-3.dist pe32-3.dist pe33-3.dist pe34-3.dist pe35-3.dist pe36-3.dist pe37-3.dist pe38-3.dist pe39-3.dist pe40-3.dist pe41-3.dist pe42-3.dist pe43-3.dist pe44-3.dist pe45-3.dist pe46-3.dist pe47-3.dist pe48-3.dist pe49-3.dist pe50-3.dist pe51-3.dist pe52-3.dist pe53-3.dist pe54-3.dist pe55-3.dist pe56-3.dist pe57-3.dist pe58-3.dist pe59-3.dist pe60-3.dist pe61-3.dist pe62-3.dist pe63-3.dist pe64-3.dist pe65-3.dist pe66-3.dist pe67-3.dist pe68-3.dist pe69-3.dist pe70-3.dist pe71-3.dist pe72-3.dist pe73-3.dist pe74-3.dist pe75-3.dist pe76-3.dist pe77-3.dist pe78-3.dist pe79-3.dist pe80-3.dist pe81-3.dist pe82-3.dist pe83-3.dist pe84-3.dist pe85-3.dist pe86-3.dist pe87-3.dist pe88-3.dist pe89-3.dist pe90-3.dist pe91-3.dist pe92-3.dist pe93-3.dist pe94-3.dist pe95-3.dist pe96-3.dist pe97-3.dist pe98-3.dist pe99-3.dist pe100-3.dist pe101-3.dist pe102-3.dist pe103-3.dist pe104-3.dist pe105-3.dist pe106-3.dist pe107-3.dist pe108-3.dist pe109-3.dist pe110-3.dist pe111-3.dist pe112-3.dist pe113-3.dist pe114-3.dist pe115-3.dist pe116-3.dist pe117-3.dist pe118-3.dist pe119-3.dist pe120-3.dist pe121-3.dist pe122-3.dist pe123-3.dist pe124-3.dist pe125-3.dist pe126-3.dist pe127-3.dist pe128-3.dist pe129-3.dist pe130-3.dist >indica-3.dist

 

abyss-todot: AdjIO.h:167: std::istream& read_adj(std::istream&, ContigGraph<G>&, BetterEP) [with Graph = DirectedGraph<ContigProperties, DistanceEst>; BetterEP = BetterDistanceEst; std::istream = std::basic_istream<char>]: Assertion `in.good()' failed.

/bin/bash: line 1: 18331 Aborted                 abyss-todot --dist -e indica-3.fa pe1-3.dist pe2-3.dist pe3-3.dist pe4-3.dist pe5-3.dist pe6-3.dist pe7-3.dist pe8-3.dist pe9-3.dist pe10-3.dist pe11-3.dist pe12-3.dist pe13-3.dist pe14-3.dist pe15-3.dist pe16-3.dist pe17-3.dist pe18-3.dist pe19-3.dist pe20-3.dist pe21-3.dist pe22-3.dist pe23-3.dist pe24-3.dist pe25-3.dist pe26-3.dist pe27-3.dist pe28-3.dist pe29-3.dist pe30-3.dist pe31-3.dist pe32-3.dist pe33-3.dist pe34-3.dist pe35-3.dist pe36-3.dist pe37-3.dist pe38-3.dist pe39-3.dist pe40-3.dist pe41-3.dist pe42-3.dist pe43-3.dist pe44-3.dist pe45-3.dist pe46-3.dist pe47-3.dist pe48-3.dist pe49-3.dist pe50-3.dist pe51-3.dist pe52-3.dist pe53-3.dist pe54-3.dist pe55-3.dist pe56-3.dist pe57-3.dist pe58-3.dist pe59-3.dist pe60-3.dist pe61-3.dist pe62-3.dist pe63-3.dist pe64-3.dist pe65-3.dist pe66-3.dist pe67-3.dist pe68-3.dist pe69-3.dist pe70-3.dist pe71-3.dist pe72-3.dist pe73-3.dist pe74-3.dist pe75-3.dist pe76-3.dist pe77-3.dist pe78-3.dist pe79-3.dist pe80-3.dist pe81-3.dist pe82-3.dist pe83-3.dist pe84-3.dist pe85-3.dist pe86-3.dist pe87-3.dist pe88-3.dist pe89-3.dist pe90-3.dist pe91-3.dist pe92-3.dist pe93-3.dist pe94-3.dist pe95-3.dist pe96-3.dist pe97-3.dist pe98-3.dist pe99-3.dist pe100-3.dist pe101-3.dist pe102-3.dist pe103-3.dist pe104-3.dist pe105-3.dist pe106-3.dist pe107-3.dist pe108-3.dist pe109-3.dist pe110-3.dist pe111-3.dist pe112-3.dist pe113-3.dist pe114-3.dist pe115-3.dist pe116-3.dist pe117-3.dist pe118-3.dist pe119-3.dist pe120-3.dist pe121-3.dist pe122-3.dist pe123-3.dist pe124-3.dist pe125-3.dist pe126-3.dist pe127-3.dist pe128-3.dist pe129-3.dist pe130-3.dist > indica-3.dist

make: *** [indica-3.dist] Error 134

make: *** Deleting file `indica-3.dist'

Many thanks,

/SB

[Ben Vandervalk]

Hi Salim,

The most likely explanation is that you are hitting the limit for open file descriptors on your system.

To see what your current limit for open file descriptors is, do (example output from my system is shown):

$ ulimit -a
-t: cpu time (seconds)              unlimited
-f: file size (blocks)              unlimited
-d: data seg size (kbytes)          unlimited
-s: stack size (kbytes)             10240
-c: core file size (blocks)         0
-m: resident set size (kbytes)      unlimited
-u: processes                       1031455
-n: file descriptors                1024
-l: locked-in-memory size (kbytes)  32
-v: address space (kbytes)          unlimited
-x: file locks                      unlimited
-i: pending signals                 1031455
-q: bytes in POSIX msg queues       819200
-e: max nice                        0
-r: max rt priority                 0

The `-n` line tells you the limit on open file descriptors.   Try increasing it with `ulimit -n <new_limit>` before running your assembly your job.

- Ben

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[Salim Bougouffa]

Hi Ben,

That was not the problem in this particular run.

I suspected that perhaps some of the files were corrupt or incomplete or something. I run abyss-todot on each peXX-3.dist individually and only one of them produced the error so I removed the problematic file and rerun. It has assembled the contigs and is now scaffolding.

Many thanks for your help.

Best,

/SB

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[Shaun Jackman]

Hi, Salim. I suspect you have 130 sequencing files, but not 130 different paired-end libraries. You'll want to put all your sequencing files in one library, with the file names separated by spaces. For example:

abyss-pe lib=pe pe='pe1_1.fq.gz pe1_2.fq.gz pe2_1.fq.gz pe2_2.fq.gz pe3_1.fq.gz pe3_2.fq.gz'

How many paired-end libraries do you have?

Cheers,

Shaun