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abyss fixmate error (but read IDs seem appropriate)

Hi,

I am running some test jobs on ABySS 2.0.2 and could use some help trouble-shooting the dreaded "All reads are mateless" error. The names of my reads seem appropriate:

For example in IMP_MP1_u.part-01.fastq:

@SN7001234:268:C9LVEACXX:5:2301:1233:2057/1 and @SN7001234:268:C9LVEACXX:5:2301:1203:2064/1

And in IMP_MP2_u.part-01.fastq:

@SN7001234:268:C9LVEACXX:5:2301:1233:2057/2 and @SN7001234:268:C9LVEACXX:5:2301:1203:2064/2

My initial command is as follows:

for k in `seq 41 10 81`; do
mkdir k$k
abyss-pe -C k$k lib='pe' mp='mp' np=48 j=24 name=test k=$k n=2 pe='/oasis/scratch/comet/jdoyle/temp_project/IMP_ABySS/IMP_reads/IMP_PE1_u.part-02.fastq /oasis/scratch/comet/jdoyle/temp_project/IMP_ABySS/IMP_reads/IMP_PE2_u.part-02.fastq' mp='/oasis/scratch/comet/jdoyle/temp_project/IMP_ABySS/IMP_reads/IMP_MP1_u.part-01.fastq /oasis/scratch/comet/jdoyle/temp_project/IMP_ABySS/IMP_reads/IMP_MP2_u.part-01.fastq'

done

But I ended up with the following:

abyss-map   -j24 -l40     test-3.fa \
    |abyss-fixmate   -l40  -h /oasis/scratch/comet/jdoyle/temp_project/IMP_ABySS/IMP_reads/IMP_PE1_bb.part-02.fastq-3.hist \
    |sort -snk3 -k4 \
    |DistanceEst   -j24 -k51 -l40 -s1000 -n2   -o /oasis/scratch/comet/jdoyle/temp_project/IMP_ABySS/IMP_reads/IMP_PE1_bb.part-02.fastq-3.dist /oasis/scratch/comet/jdoyle/temp_project/IMP_ABySS/IMP_reads/IMP_PE1_bb.part-02.fastq-3.hist
abyss-map: missing arguments
Try `abyss-map --help' for more information.
Mateless 0
Unaligned 0 Singleton 0 FR 0 RF 0 FF 0 Different 0 Total 0


abyss-fixmate: error: All reads are mateless. This can happen when first and second read IDs do not match.

error: `/oasis/scratch/comet/jdoyle/temp_project/IMP_ABySS/IMP_reads/IMP_PE1_bb.part-02.fastq-3.hist': No such file or directory
make: *** [/oasis/scratch/comet/jdoyle/temp_project/IMP_ABySS/IMP_reads/IMP_PE1_bb.part-02.fastq-3.dist] Error 1
make: *** Deleting file `/oasis/scratch/comet/jdoyle/temp_project/IMP_ABySS/IMP_reads/IMP_PE1_bb.part-02.fastq-3.dist'
make: Leaving directory `/oasis/scratch/comet/jdoyle/temp_project/IMP_ABySS/k51'

Thoughts? Feelings?

Thanks,

Jackie

abyss benvforthewin
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written by jdoyle30724 • jdoyle30724

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written by WouterDeCoster WouterDeCoster

1 answer

Hi @jdoyle30724,

You have the right idea, but abyss-pe is getting confused because "pe" is a reserved variable. Try changing "pe" => "pet" in your command and it should work:

for k in `seq 41 10 81`; do
    mkdir k$k
    abyss-pe -C k$k lib='pet' mp='mp' np=48 j=24 name=test k=$k n=2 pet='/oasis/scratch/comet/jdoyle/temp_project/IMP_ABySS/IMP_reads/IMP_PE1_u.part-02.fastq /oasis/scratch/comet/jdoyle/temp_project/IMP_ABySS/IMP_reads/IMP_PE2_u.part-02.fastq' mp='/oasis/scratch/comet/jdoyle/temp_project/IMP_ABySS/IMP_reads/IMP_MP1_u.part-01.fastq /oasis/scratch/comet/jdoyle/temp_project/IMP_ABySS/IMP_reads/IMP_MP2_u.part-01.fastq'
done
• 0 views • link
written by benv benv

See the abyss-pe man page (available in the doc subdirectory in the source tarball) for more info about abyss-pe parameters. From the root of the ABySS source tree, you can view it by running 'man doc/abyss-pe.1'.

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written by benv benv

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