error 134...

[Arthur Pastuer]

Shaun,

   I got the same error (134) running my data set. The exact same command/data set completed without errors using ABySS 1.2.1. Do you have any advice for those of us encountering this error? There are still scaffolds in my *-contigs.fa file. What is the "dot" file used for in ABySS 1.2.3?

Best, Art

On Mon, Sep 13, 2010 at 2:41 AM, Alejandro Sanchez <arro...@gmail.com> wrote:

No space left on device means that you ran out of hard disk space...
Your /tmp partition must be full or to small.

Cheers.

On Mon, Sep 13, 2010 at 4:42 AM, Matthew King <kingd...@gmail.com> wrote:
> The first KAligner failed with this error:
> sort: write failed: /tmp/sortvPFmhl: No space left on device
> gunzip -c 200bpTotal-3.sam.gz \
>        |DistanceEst  -j24 -k64 -s200 -n10 -o 200bpTotal-3.dist
> 200bpTotal-3.hist
> DistanceEst: DistanceEst.cpp:257: void
> readContigLengths(std::istream&, std::vector<unsigned int,
> std::allocator<unsigned int> >&): Assertion `!lengths.empty()' failed.
> /bin/sh: line 1: 27810 Done                    gunzip -c
> 200bpTotal-3.sam.gz
>     27811 Aborted                 | DistanceEst -j24 -k64 -s200 -n10 -
> o 200bpTotal-3.dist 200bpTotal-3.hist
> make: *** [200bpTotal-3.dist] Error 134
> make: *** Deleting file `200bpTotal-3.dist'
> From what i could tell it may have been a full /tmp directory so I
> then ran the KAligner again using verbose and streaming the output to
> a file. KAligner -v -j24 -k64 HA0001Total_in.solexa.fastq
> 200bpTotal-3.fa --sam > retry200.log
> This time it died with the error:
> SOLEXA4:3:56:16732:10775#0/1    16      12889296        1
> 255     17S64M20S       *       0       0       *       *
> SOLEXAKAligner: KAligner.cpp:438: void* alignReadsToDB(void*):
> Assertion `cout.good()' failed.
>
> I am not sure what would cause this error but it should not have run
> out of memory.
>
> Thanks again for any help.
>
> On Sep 11, 10:34 am, Matthew King <kingdom...@gmail.com> wrote:
>> Hello,
>> I maybe having an issue with the way I setup the assemblies when the
>> pipeline gets to the KAligner step.
>> I have abyss-pe successfully running in parallel using mpich, and the
>> ABYSS-P threads all seem to run just fine. It is now at the KAligner
>> phase, and they are not running on j threads.
>>
>> There seems to be different problems with my two runs. The first run
>> has created a .sam.gz file, which is empty.
>> The second run has created the .dist file, but that is empty as well.
>> KAligner is running, just not on multiple threads.
>>
>> The final out put of the first run is:
>> Assembled 920775796 k-mer in 18121117 contigs
>> Concatenating to 200bpTotal-1.fa
>> Concatenating to 200bpTotal-bubbles.fa
>> Done.
>> AdjList  -k64 200bpTotal-1.fa >200bpTotal-1.adj
>> PopBubbles  -k64   -g 200bpTotal-3.adj 200bpTotal-1.adj>200bpTotal-1.path
>>
>> MergeContigs -k64 -o 200bpTotal-3.fa 200bpTotal-1.fa 200bpTotal-1.path
>> The minimum coverage of single-end contigs is 2.
>> The minimum coverage of merged contigs is 2.
>> awk '!/^>/ {x[">" $1]=1; next} {getline s} $1 in x {print $0 "\n" s}'
>> 200bpTotal-1.path 200bpTotal-1.fa >200bpTotal-indel.fa
>> KAligner   -j24 -k64 HA0001Total_in.solexa.fastq 200bpTotal-3.fa \
>>                 |ParseAligns  -k64 -h 200bpTotal-3.hist \
>>                 |sort -snk3 -k4 \
>>                 |gzip >200bpTotal-3.sam.gz
>>
>> The final output of the second run is:
>> Assembled 1304827904 k-mer in 25473926 contigs
>> Concatenating to SunCompTotalAss-1.fa
>> Concatenating to SunCompTotalAss-bubbles.fa
>> Done.
>> AdjList  -k64 SunCompTotalAss-1.fa >SunCompTotalAss-1.adj
>> PopBubbles  -k64   -g SunCompTotalAss-3.adj SunCompTotalAss-1.adj>SunCompTotalAss-1.path
>>
>> MergeContigs -k64 -o SunCompTotalAss-3.fa SunCompTotalAss-1.fa
>> SunCompTotalAss-1.path
>> The minimum coverage of single-end contigs is 1.21739.
>> The minimum coverage of merged contigs is 2.23611.
>> Consider increasing the coverage threshold parameter, c, to 2.23611.
>> awk '!/^>/ {x[">" $1]=1; next} {getline s} $1 in x {print $0 "\n" s}'
>> SunCompTotalAss-1.path SunCompTotalAss-1.fa >SunCompTotalAss-indel.fa
>> KAligner   -j60 -k64 /Linux/genome/illumina/500bp/
>> HA0002_620HLAAXX_1_1_trimmed101.fq /Linux/genome/illumina/500bp/
>> HA0002_620HLAAXX_1_2_trimmed101.fq /Linux/genome/illumina/500bp/
>> HA0002_620HLAAXX_4_1_trimmed101.fq /Linux/genome/illumina/500bp/
>> HA0002_620HLAAXX_4_2_trimmed101.fq /Linux/genome/illumina/500bp/
>> HA0002_620HLAAXX_5_1_trimmed101.fq /Linux/genome/illumina/500bp/
>> HA0002_620HLAAXX_5_2_trimmed101.fq /Linux/genome/illumina/500bp/
>> HA0002_620HLAAXX_6_1_trimmed101.fq /Linux/genome/illumina/500bp/
>> HA0002_620HLAAXX_6_2_trimmed101.fq /Linux/genome/illumina/500bp/
>> HA0002_620HLAAXX_7_1_trimmed101.fq /Linux/genome/illumina/500bp/
>> HA0002_620HLAAXX_7_2_trimmed101.fq /Linux/genome/illumina/500bp/
>> HA0002_620J0AAXX_2_1_trimmed101.fq /Linux/genome/illumina/500bp/
>> HA0002_620J0AAXX_2_2_trimmed101.fq SunCompTotalAss-3.fa \
>>                 |ParseAligns  -k64 -h lib1-3.hist \
>>                 |sort -snk3 -k4 \
>>                 |DistanceEst  -j60 -k64 -s200 -n10 -o lib1-3.dist lib1-3.hist
>>
>> Am I being impatient? Thanks for any help

[Shaun Jackman]

Hi Art,

The assembly is essentially complete if you have the file
${name}-contigs.fa. The dot file shows which contigs overlap with which
other contigs.

To help me troubleshoot this problem, if the files ${name}-4.adj and
${name}-4.path2 are not too big, send them my way in a private email and
I'll try to sort it out.

Cheers,
Shaun

[Shaun Jackman]

Hi Arthur,

I've found a data set that duplicates this error. I'll work on fixing
the bug now.

Cheers,
Shaun

On Mon, 2010-09-13 at 06:10 -0700, Arthur Pastuer wrote: