abyss fixmate error (but read IDs seem appropriate)

Question

[jdoyle30724]

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

[jdoyle30724]

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

[jdoyle30724]

This worked like a charm, thanks!

[WouterDeCoster]

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.

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

• How To Ask Good Questions On Technical And Scientific Forums
• How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
• How to Use Biostars, Part II: Post types, Deleting, (Un)Subscribing, Linking and Bookmarking

Answer 1

[benv]

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

[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'.