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
Huh! Thanks! I'll give it a go now...
This worked like a charm, thanks!
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