When I assembly with minia with these command:
mkdir 1-assembly && cd 1-assembly/
cp ../reads.list reads.list
for KMER in $(cat ../kmer.list)
do
echo "Minia assembling at k=$KMER ......" | tee -a ../log.txt
$DIR_MINIA/minia -in reads.list -kmer-size $KMER -abundance-min 2 -out k$KMER -max-memory $MEMORY
test -s k$KMER.contigs.fa && echo || ($DIR_MINIA/minia -in reads.list -kmer-size $KMER -abundance-min 2 -storage-type file -out k$KMER -max-memory $MEMORY)
test -s k$KMER.contigs.fa && echo || ($DIR_MINIA/minia -in reads.list -kmer-size expr $KMER - 2 -abundance-min 2 -out k$KMER -max-memory $MEMORY)
test -s k$KMER.contigs.fa && echo || ($DIR_MINIA/minia -in reads.list -kmer-size expr $KMER - 2 -abundance-min 2 -storage-type file -out k$KMER -max-memory $MEMORY)
test -s k$KMER.contigs.fa && (echo "Finished Minia k=$KMER" | tee -a ../log.txt) || (echo "Minia assembly with k-mer value of $KMER failed......" && exit)
echo -e "\n" | tee -a ../log.txt
rm -rf dummy* unitigs h5 trashme
cp ../reads.list reads.list
for n in 1 2 3; do echo "./k$KMER.contigs.fa" >> reads.list; done
done
echo "Finished Multi-kmer Minia assembly" | tee -a ../log.txt
echo -e "\n" | tee -a ../log.txt
the linux showed an error:
inia assembling at k=121 ......
Minia 3, git commit 9c33379
Segmentation fault (core dumped)
Minia 3, git commit 9c33379
Segmentation fault (core dumped)
Minia 3, git commit 9c33379
Segmentation fault (core dumped)
Minia 3, git commit 9c33379
Segmentation fault (core dumped)
Minia assembly with k-mer value of 121 failed......
I can't solve this problem. I hope you I get help. Thank you very much.
When I assembly with minia with these command:
mkdir 1-assembly && cd 1-assembly/
cp ../reads.list reads.list
for KMER in $(cat ../kmer.list)
do
echo "Minia assembling at k=$KMER ......" | tee -a ../log.txt
$DIR_MINIA/minia -in reads.list -kmer-size $KMER -abundance-min 2 -out k$KMER -max-memory $MEMORY
test -s k$KMER.contigs.fa && echo || ($DIR_MINIA/minia -in reads.list -kmer-size $KMER -abundance-min 2 -storage-type file -out k$KMER -max-memory $MEMORY)
test -s k$KMER.contigs.fa && echo || ($DIR_MINIA/minia -in reads.list -kmer-size
expr $KMER - 2-abundance-min 2 -out k$KMER -max-memory $MEMORY)test -s k$KMER.contigs.fa && echo || ($DIR_MINIA/minia -in reads.list -kmer-size
expr $KMER - 2-abundance-min 2 -storage-type file -out k$KMER -max-memory $MEMORY)test -s k$KMER.contigs.fa && (echo "Finished Minia k=$KMER" | tee -a ../log.txt) || (echo "Minia assembly with k-mer value of $KMER failed......" && exit)
echo -e "\n" | tee -a ../log.txt
rm -rf dummy* unitigs h5 trashme
cp ../reads.list reads.list
for n in 1 2 3; do echo "./k$KMER.contigs.fa" >> reads.list; done
done
echo "Finished Multi-kmer Minia assembly" | tee -a ../log.txt
echo -e "\n" | tee -a ../log.txt
the linux showed an error:
inia assembling at k=121 ......
Minia 3, git commit 9c33379
Segmentation fault (core dumped)
Minia 3, git commit 9c33379
Segmentation fault (core dumped)
Minia 3, git commit 9c33379
Segmentation fault (core dumped)
Minia 3, git commit 9c33379
Segmentation fault (core dumped)
Minia assembly with k-mer value of 121 failed......
I can't solve this problem. I hope you I get help. Thank you very much.