Open jjjscuedu opened 5 years ago
I am not sure why this syntax is giving you issues. Perhaps a different bash version? Could you try removing the commented out lines and see if that works? Like this:
bwa mem -t $threads ${out}/work_files/assembly.fa $reads_1 $reads_2 \
| samtools view -@ $threads -bS - \
| samtools sort -T ${out}/work_files/tmp-samtools -@ $threads -O bam \
-o ${out}/work_files/${sample}.bam -
If that doesn't work, then mayby put them on one line:
bwa mem -t $threads ${out}/work_files/assembly.fa $reads_1 $reads_2 | samtools view -@ $threads -bS - | samtools sort -T ${out}/work_files/tmp-samtools -@ $threads -O bam -o ${out}/work_files/${sample}.bam -
Hi, @ursky ,
I met exactly the same problem as @jjjscuedu .(Shown in uploaded file) My bash version is echo "${BASH_VERSION}" 4.2.46(2)-release. And the bug has been resolved by removing the commented out lines. Thanks so much! error.txt
Thanks for the info! I had a few users contact me about this. The issue seems to be system-dependent - I cannot replicate it. This confuses me, because I have the same bash version... Nonetheless, its an easy fix, which I incorporated into metawrap v1.1.1
, which is now out.
When will this update get pushed to conda? It seems to still be on version 1.0. Updating via conda install metawrap-mg=1.1.1
gets stuck indefinitely in Solving environment
(I stopped after 40minutes in this state).
I would leave it running longer than that. Conda can take a long time depending on the system and software. MetaWRAP has so many dependencies that Conda struggles to find a configuration that satisfies all the software versions. Hence the long Solving environment
stage. The versions 1.0
that you are seeing is the one on Bioconda - which does not include the latest updates.
Dear all,
When I try to run metaWRAP for my dataset,
there are some errors like this:
Can anyone give me some suggestions?
Thanks a lot!
Jingjing