User: Tawny

gravatar for Tawny
Tawny130
Reputation:
130
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Trusted
Location:
United States
Last seen:
1 week, 1 day ago
Joined:
6 years, 10 months ago
Email:
m***********@battelle.org

Posts by Tawny

<prev • 32 results • page 1 of 4 • next >
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Answer: A: BBMap randomreads.sh exact path to ref error: Could not find or load main class
... I finally figured out the issue. I had a space before and or after the = signs in the command. When I removed all spaces around the = signs, the tool worked as expected. I did download and install the latest version today which was 38.34. Thank you to @genomax and @Pierre Lindenbaum for thei ...
written 14 days ago by Tawny130
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Comment: C: What do you consider to be raw data from Illumina sequencers? Possible legacy d
... @Gabriel R This is very helpful, I appreciate you taking the time to provide your response. ...
written 29 days ago by Tawny130
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Comment: C: What do you consider to be raw data from Illumina sequencers? Possible legacy d
... @genomax Thank you for such a detailed response. Now that you list it out, I do remember some of those programs. ...
written 29 days ago by Tawny130
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What do you consider to be raw data from Illumina sequencers? Possible legacy data.
... Today I consider the raw data to be the demultiplexed fastq files in gzip format that come off the sequencer. I believe many years ago there was a different output of data from sequencers. I have been trying to find an example of that different raw data output. Does anyone have an example of t ...
sequencing written 29 days ago by Tawny130 • updated 29 days ago by Gabriel R.2.5k
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Comment: C: BBMap randomreads.sh exact path to ref error: Could not find or load main class
... I am using version 38.32 which I downloaded and untarred today. I downloaded this from https://sourceforge.net/projects/bbmap/ . If there is a different version I should be using, please let me know where to find it. ...
written 4 weeks ago by Tawny130
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Comment: C: BBMap randomreads.sh exact path to ref error: Could not find or load main class
... I tried reducing the number of reads to 10000 and unfortunately it gave me the same error message referencing the ArrayIndexOutOfBounds Exception. ...
written 4 weeks ago by Tawny130
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Comment: C: BBMap randomreads.sh exact path to ref error: Could not find or load main class
... N1a1.fastq is much smaller. It is a human mitochondrial genome so ~16.5K base pairs long. ...
written 4 weeks ago by Tawny130
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Comment: C: BBMap randomreads.sh exact path to ref error: Could not find or load main class
... I tried your change and still get this error: [cmp07 bbmap]$ ./randomreads.sh -Xmx10g ref = /home/mina/reference-genomes/N1a1.fasta out= /home/mina/reference-genomes/N1a1-synth.fastq length = 171 reads = 1258301 overwrite = f seed = -1 snprate = 0.001 maxq = 40 midq = 30 minq = 10 java ...
written 4 weeks ago by Tawny130
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Comment: C: BBMap randomreads.sh exact path to ref error: Could not find or load main class
... java -version openjdk version "1.8.0_191" OpenJDK Runtime Environment (build 1.8.0_191-b12) OpenJDK 64-Bit Server VM (build 25.191-b12, mixed mode) ...
written 4 weeks ago by Tawny130
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Comment: C: BBMap randomreads.sh exact path to ref error: Could not find or load main class
... Very good point genomax. I realized I wasn't running the latest version. I downloaded version 38.32 and untarred/zipped the file. Now when running `randomreads.sh` I get a different error: [cmp07 bbmap]$ ./randomreads.sh ref = /home/mina/reference-genomes/N1a1.fasta out=/home/mina/reference- ...
written 4 weeks ago by Tawny130

Latest awards to Tawny

Scholar 14 days ago, created an answer that has been accepted. For A: BBMap randomreads.sh exact path to ref error: Could not find or load main class
Popular Question 29 days ago, created a question with more than 1,000 views. For How can I retrieve the Protein 'name' using my BLAST tab delimited results?
Epic Question 7 months ago, created a question with more than 10,000 views. For What Is The Refseq Id For Illumina Phix Control?
Popular Question 21 months ago, created a question with more than 1,000 views. For Is There Any File That Links The Enzyme Comission Number To Gi Numbers?
Good Question 2.6 years ago, asked a question that was upvoted at least 5 times. For What Is The Refseq Id For Illumina Phix Control?
Great Question 3.3 years ago, created a question with more than 5,000 views. For What Is The Refseq Id For Illumina Phix Control?
Popular Question 3.3 years ago, created a question with more than 1,000 views. For What Is The Refseq Id For Illumina Phix Control?
Appreciated 4.5 years ago, created a post with more than 5 votes. For What Is The Refseq Id For Illumina Phix Control?
Student 4.5 years ago, asked a question with at least 3 up-votes. For What Is The Refseq Id For Illumina Phix Control?
Popular Question 6.5 years ago, created a question with more than 1,000 views. For What Is The Refseq Id For Illumina Phix Control?
Popular Question 6.5 years ago, created a question with more than 1,000 views. For What Is The Refseq Id For Illumina Phix Control?

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