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Hi,
I am running mhap step right now. However, I got errors for some files.
Please see below for the error information.
Is there any way to fix it? Thanks!
Opened fasta file /public4/zhangxt/project/…
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Hi,
Under LSF environment canu runs successfully at 1-overlapper stage but stopped at 2-correction without submitting more jobs. The files:
Bspecies.ovlStore.summary.err
Bspecies.ovlStore.per-read.l…
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I've got a 3.6 MB bacterial genome that has several large repeats of at least two or more copies of repeats that are approximately 25, 35, and 55 Kb. As input, I have three PacBio runs that are 7.7 K…
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Two questions related to the Falcon assembly.
(a) is there any option in the Falcon that put a limit on the read coverage limit,
(b) any idea how I can check read depth of the contigs.
I am asking th…
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I have been trying to iterate over the correction phase as suggested in the FAQs on the read-the-docs.
I am on the second iteration -- i.e. the first time using the previous set of corrected reads.
…
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Hi,
I am at this stage of canu where it is building the ovlStore. Some of the jobs exited with the following error:
`Removing incomplete bucket
...ovlStore.BUILDING/create0455
Max processes per use…
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Hi,
we are trying to assemble a 800M genome (70x coverage, pacbio reads) on a SLURM grid engine. Unfortunately step 10 crashed with the following error message:
`-- 3516 overlap store sorter jobs f…
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I have been using **CANU** v1.2 on my Torque/PBS system with no issues, however it seems that the latest version v1.3 has some problems. When I run **CANU** on my latest dataset, it fails almost immed…
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Hello,
When I start to run canu (v1.3), it said the running is done, no error report, but the output data with only
5 files (canu-logs canu-scripts correction correction.html correction.html.fi…
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Hi,
I recently began running a lot of Canu jobs again. In case it is of interest, I am sharing here parts of the pipeline that are being killed due to exceeding memory. Recall, I'm on SLURM (if that …