Comments (5)
Hello @mhfk ,
The assembler crashed because the abyss-map
aligner expects the mates to be in opposite orientations, i.e.
----> <----
So, you should use the original reads as input to Trans-ABySS.
Different
in the log refers to the number of read pairs that are aligned to different unitigs.
The read orientations (i.e. FF
, RF
, and FR
) are tallied based on the mates aligned to single unitigs. I am actually quite surprised that there are only 112 reads for this.
Ka Ming
from transabyss.
Hi @kmnip ,
Apologies for the late follow-up. I have tried to run the alignment using the original reads and the same issue persisted. My workstation froze so I couldn't get the screenshot but the same error message prompted. I wonder if the assembler identified my reads as unstranded and couldn't proceed with assembly.
from transabyss.
Can you verify that the read names have the suffixes /1
and /2
within your read files?
from transabyss.
I think the file names might be the issue. The names of the files were :
Paired-end
91_1.paired.fq.gz & 91_2.paired.fq.gz
92_1.paired.fq.gz & 92_2.paired.fq.gz
93_1.paired.fq.gz & 93_2.paired.fq.gz
94_un-conc-mate.1.paired.fq.gz & 94_un-conc-mate.2.paired.fq.gz
95_un-conc-mate.1.paired.fq.gz & 95_un-conc-mate.2.paired.fq.gz
96_un-conc-mate.1.paired.fq.gz & 96_un-conc-mate.2.paired.fq.gz \
Single-end
91_1.unpaired.fq.gz & 91_2.unpaired.fq.gz & 92_1.unpaired.fq.gz & 92_2.unpaired.fq.gz & 93_1.unpaired.fq.gz & 93_2.unpaired.fq.gz
94_un-conc-mate.1.unpaired.fq.gz & 94_un-conc-mate.2.unpaired.fq.gz
95_un-conc-mate.1.unpaired.fq.gz & 95_un-conc-mate.2.unpaired.fq.gz & un-singleton.trimmed.fq.gz
96_un-conc-mate.1.unpaired.fq.gz & 96_un-conc-mate.1.unpaired.fq.gz & un-singleton.trimmed.fq.gz
I am changing the file names to names with strand information at the back (*_1.fq.gz or *_2.fq.gz) instead of having them in the middle as seen above. Will let you know if this works!
from transabyss.
@kmnip
The error persisted with similar error prompt. Perhaps there is something wrong with my command. I have both PE and SE reads to be assembled. SE reads belong to SE library and residual data from Trimmomatic. Here are the commands :
`transabyss --SS --threads 16 --pe \
./axenic/SRR8432491/91.paired_1.fq.gz ./axenic/SRR8432491/91.paired_2.fq.gz
./axenic/SRR8432492/92.paired_1.fq.gz ./axenic/SRR8432492/92.paired_2.fq.gz
./axenic/SRR8432493/93.paired_1.fq.gz ./axenic/SRR8432493/93.paired_2.fq.gz
./inplanta/SRR8432494/94_un-conc-mate.paired_1.fq.gz ./inplanta/SRR8432494/94_un-conc-mate.paired_2.fq.gz
./inplanta/SRR8432495/95_un-conc-mate.paired_1.fq.gz ./inplanta/SRR8432495/95_un-conc-mate.paired_2.fq.gz
./inplanta/SRR8432496/96_un-conc-mate.paired_1.fq.gz ./inplanta/SRR8432496/96_un-conc-mate.paired_2.fq.gz
--se
./axenic/SRR8432491/91.unpaired_1.fq.gz ./axenic/SRR8432491/91.unpaired_2.fq.gz ./axenic/SRR8432492/92.unpaired_1.fq.gz ./axenic/SRR8432492/92.unpaired_2.fq.gz ./axenic/SRR8432493/93.unpaired_1.fq.gz ./axenic/SRR8432493/93.unpaired_2.fq.gz
./inplanta/SRR8432494/94_un-conc-mate.unpaired_1.fq.gz ./inplanta/SRR8432494/94_un-conc-mate.unpaired_2.fq.gz
./inplanta/SRR8432495/95_un-conc-mate.unpaired_1.fq.gz ./inplanta/SRR8432495/95_un-conc-mate.unpaired_2.fq.gz ./inplanta/SRR8432495/un-singleton.trimmed.fq.gz
./inplanta/SRR8432496/96_un-conc-mate.unpaired_1.fq.gz ./inplanta/SRR8432496/96_un-conc-mate.unpaired_2.fq.gz ./inplanta/SRR8432496/un-singleton.trimmed.fq.gz `
from transabyss.
Related Issues (20)
- Memory problem? HOT 19
- Conda problems, instalation HOT 4
- Library conflict HOT 3
- Update conda version HOT 4
- Correct specification of paired-end reads HOT 5
- awk files not found HOT 2
- Transabyss default param setting issue HOT 4
- disable running mpi HOT 14
- Can't get the sample dataset to work HOT 14
- ERROR: CMD ended with status code 2 HOT 2
- ABYSS-P called instead abyss-pe HOT 5
- Trans-ABySS not compatible with icu=67.1 on bioconda, downgrade to 58.* to use HOT 2
- Assembly strategy for large datasets HOT 5
- Trimming of polyA tails HOT 2
- Question: no abyss-pe.Makefile in ( .../miniconda3/bin) HOT 6
- ERROR: CMD ended with status code 2 HOT 3
- Errorneusly posted
- ERROR: CMD ended with status code 1 HOT 4
- dirname: missing operand
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from transabyss.