Question: abyss fixmate error (but read IDs seem appropriate)
0
gravatar for jdoyle30724
2.4 years ago by
jdoyle307240 wrote:

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 • 728 views
ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by jdoyle307240

Huh! Thanks! I'll give it a go now...

ADD REPLYlink written 2.4 years ago by jdoyle307240

This worked like a charm, thanks!

ADD REPLYlink written 2.4 years ago by jdoyle307240

Please use ADD COMMENT or ADD REPLY to answer to previous reactions, as such this thread remains logically structured and easy to follow. I have now moved your post but as you can see it's not optimal. Adding an answer should only be used for providing a solution to the question asked.

If an answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted. Upvote|Bookmark|Accept

Interesting guidelines for posting can be found in the following posts:

ADD REPLYlink written 2.4 years ago by WouterDeCoster41k
2
gravatar for benv
2.4 years ago by
benv710
Canada
benv710 wrote:

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
ADD COMMENTlink written 2.4 years ago by benv710
1

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'.

ADD REPLYlink written 2.4 years ago by benv710
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