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Hi, just tried running the loompy from fastq using the tutorial files. Everything ran fine up to the last step. I tried uninstalling and reinstalling h5py per suggestions from similar errors on stack …
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Hi, when I run "slurm.scripts" on a grid as follows:
```
#!/bin/bash
#SBATCH -N1
#SBATCH --qos=debug
#SBATCH --job-name=assemble
#SBATCH --array=10-20
chrom='chr'$SLURM_ARRAY_TASK_ID
…
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Hi,
These are our first experiments with Nanopore sequencing and we are just practicing with different types of samples from our department.
I tried to assemble a PCR-generated 8 kb fragment (prepa…
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Hello,
I am using Canu 1.8 on PacBio data with 110 coverage with the following settings:
```
canu \
-p Oasisia -d /data/scratch/btx604/Oasisia/canu_V8 \
-pacbio-raw /data/SBCS-MartinDuranLab/…
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Issue 1: When I use an even number k with --no_rc, I get more kmer counts than I expect. For example, using a 145bp sequence with k=4, I expect 142 counts. But different 145bp sequences get different …
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Hi,
I ran the canu pipeline, using the following script.
```
#!/bin/bash
module load canu/1.8
canu -p dix_pb -d tgel \
genomeSize=3.0g \
correctedErrorRate=0.105 \
gridOptions…
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This is not an issue but just a question: what would be the optimal settings for __fast__ generation of unitigs? I expect running on a SSD or even better a ram drive should help. What about any of the…
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Hi, pseudoalignments are an interesting application for metagenomics. However I failed to build a database based on the current bacterial NCBI refseq database. Here is the output:
```
time kallisto …
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I have tried to index a large metagenomic reference set using the binary distribution kallisto_linux-v0.42.5 on a machine with CentOs 7.1.1503. The process did not go past the "counting k-mers" step.
…
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Hi,
I have just started to assemble bacterial strains from my first MinION run. In the polishing step I get the error OSError: [Errno 26] Text file busy: '/media/sf_BioLinux-vymena_dat/Run1_part_da…