User: c.e.chong

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c.e.chong10
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Posts by c.e.chong

<prev • 20 results • page 1 of 2 • next >
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Comment: C: Java error message when using BBDuk
... That worked! Such a simple fix!! Thank you very much! ...
written 1 day ago by c.e.chong10
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Comment: C: Java error message when using BBDuk
... That worked! Such a simple fix!! Thank you very much! ...
written 1 day ago by c.e.chong10
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Comment: C: Java error message when using BBDuk
... Yes, my files are already trimmed for adapters I am now doing a quality trim. I tried with the lower number of RAM and threads and got this error: Exception in thread "main" java.lang.NullPointerException at shared.Parser.parseTrim(Parser.java:333) at jgi.BBDuk.(BBDuk.java:176) ...
written 1 day ago by c.e.chong10 • updated 1 day ago by genomax64k
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Comment: C: Java error message when using BBDuk
... I run validateFiles on my fastq files and the output was "Error count 0" ...
written 1 day ago by c.e.chong10
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Java error message when using BBDuk
... Hi all, I am trying to run BBDuk to quality trim and filter my illumina whole genome sequences. I have used this program before and haven't had any problems. However when I run the command: bbduk.sh -Xmx80g in1=17198wC1_Sample_3_1_trimmed.fastq in2=17198wC1_Sample_3_2_trimmed.fastq out1=~/c ...
genome java bbduk qc bbtools written 1 day ago by c.e.chong10 • updated 1 day ago by genomax64k
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Roary MSG: Got a sequence without letters. Could not guess alphabet
... Hi, I am trying to run Roary on a set of skin isolate sequences to create a pan genome to use in further comparative analyses. I have QC'd, assembled (Unicycler) and annotated (Prokka) my sequences which are all *Staphylococcus capitis*. To confirm this I pulled out the 16S rRNA, rpoB and gap ge ...
genome assembly pangenome software error written 25 days ago by c.e.chong10
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Comment: C: Using VelvetOptimiser.pl within a forloop
... Thank you all for your help I have resolved the issue now, using extra '. '-shortPaired -fastq '$i' '${i%%_1_trimmed_prinseq.fastq}_2_trimmed_prinseq.fastq'' ...
written 8 weeks ago by c.e.chong10
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Comment: C: Using VelvetOptimiser.pl within a forloop
... When I replace the ' with " I get this error Number of CPUs available: 64 Current free RAM: 496.545GB Velvet OMP compiler setting: 1 Unknown option: shortpaired bb_17198wa9_sample_65_1_trimmed_prinseq.fastq bb_17198wa9_sample_65_2_*.fastq Usage: /pub38/cchong/miniconda2/envs/vel ...
written 8 weeks ago by c.e.chong10 • updated 8 weeks ago by jrj.healey11k
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Comment: C: Using VelvetOptimiser.pl within a forloop
... VelvetOptimiser.pl -t 12 -s 19 -v --d ~/comp_genomics/velvet_optimiser_jo/bb_17198wB1_Sample_2_assembly -f '-shortPaired -fastq bb_17198wB1_Sample_2_1_trimmed_prinseq.fastq bb_17198wB1_Sample_2_2_trimmed_prinseq.fastq' is not the output of for i in *_1_*.fastq; do echo '-fastq -shortPaire ...
written 8 weeks ago by c.e.chong10
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Comment: C: Using VelvetOptimiser.pl within a forloop
... Thanks for getting back to me! I tried using " but this didn't work either. The input read files have to be within a ' to call Velveth. I understand that Velvet is old news now, I was just trying to carry out some comparison assemblies as my group used to use velvet. ...
written 9 weeks ago by c.e.chong10

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