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I am running masurca v3.2.3. I got an error at celera assembly step. The log report is below:
[Wed 23 May 17:16:57 BST 2018] Processing pe library reads
[Wed 23 May 17:34:23 BST 2018] Average PE r…
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Since the **abyss-pe** has been run, the first command, `ABYSS` is run and has repeatedly happend that its state has been remained on `D` state, shown in the table of `htop` command.
Is it normal…
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Running ```./canu/Linux-amd64/bin/canu -p metagenome -d /scratch/metagenome_folder genomeSize=1g -nanopore-raw metagenome_folder/metagenome.fastq```, I'm getting a Error 7 as follows:
```-- Startin…
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Hi,
I was thinking of doing an iterative scaffolding of my contig assembly using abyss, mainly because then I have more control on the usage of different libraries (and technologies) I have at hand…
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I'm wondering how robust Masurca is to restarting after getting killed during the assembly step. Basically, my cluster has a queue that is preemptable so jobs can be killed and restarted if a higher …
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Hi Team Canu,
I have a question that is related to #552. I have cosmid sequences that I am assembling but in many cases I have ~40x coverage of the same sequence. My output `asm.unasssembled.fast…
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Hi,
I am not sure exactly what error is particularly occurring. However, I am not generating unitig.fa files at the end of my ABySS run. Attached is a text file with a whole run, start to error for o…
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was running something like
vg augment vg.vg gam.gam -q 15 > augmented.vg
vg.vg had been created from a linear reference + vcfs and was chromosome chunked but put in the same id space then combined…
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Sometimes alignments are written to *.sam.gz instead of being piped to DistanceEst although *.sam.gz was not specified as an endpoint in abyss-pe.
Reads-to-unitig alignments are written to *-3.sam.gz…
kmnip updated
6 years ago
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This came up while looking at #1417. There's a link there to a fastq that contains reads of various sizes. Aligning them single-endedq takes forever with mpmap.
It looks like mpmap is on pace …