User: Poetic_Premium6

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Posts by Poetic_Premium6

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Comment: C: Bowtie2: Error: No input read files were valid
... Did you make sure that you've given that directory permissions to write to the files in that directory? You should also simplify your directories, because that could be a headache to deal with :) ...
written 9 months ago by Poetic_Premium60
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SortMeRNA 'buildtrie' command
... Hi guys, I am having some trouble getting the `buildtrie` executable to work for SortMeRNA v2.1 which is used in the SAMSA2 pipeline. I installed the package via sourcecode from Github, used the nano editor to add the line ` export SORTMERNADIR="/path/to/sortmerna-vx"` to the file, and even created ...
metatranscriptomics software error rna-seq written 9 months ago by Poetic_Premium60 • updated 9 months ago by Biostar ♦♦ 20
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Comment: C: STAR-RNA Segmentation Fault
... Thanks Bastien, I assumed that too and re-did QC to check. I'll post if anything comes up. Best wishes! ...
written 20 months ago by Poetic_Premium60
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Comment: C: STAR-RNA Segmentation Fault
... Hey Jeffin, I just tried this without any success in fixing the segmentation fault. But surely, you are correct...this would be great to keep in my code :P Best, ~Jonathan J.S ...
written 20 months ago by Poetic_Premium60
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Comment: C: STAR-RNA Segmentation Fault
... Bastien, I tried this change too without any luck. I think that I will have to reach out to the software developer, Alex for help. Thank again for all of your help and time, it was greatly appreciated!!! ...
written 20 months ago by Poetic_Premium60
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Comment: C: STAR-RNA Segmentation Fault
... Haha sorry for the tilt, as I mentioned in the header... I am a **noob** :P . Besides, I kept both files w/ & w/o gzip in the directory just to try to see if it would result in a memory difference and must have confused them in the original post but..... I tried both options from your new com ...
written 20 months ago by Poetic_Premium60
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Comment: C: STAR-RNA Segmentation Fault
... Oh lovely, it is just a fatal input error now based on a read input rather than a "Segmentation Fault". Anyway, the log.out file exceeds the character limitation, which specific portions are necessary for diagnostics? ...
written 20 months ago by Poetic_Premium60
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Comment: C: STAR-RNA Segmentation Fault
... Good point, as it is redundant! Sure, here are the results: -rw-rw-rw- 1 jonathan7 jonathan7 19483 Jun 4 09:53 Log.out -rw-rw-rw- 1 jonathan7 jonathan7 236 Jun 4 09:53 Log.progress.out drwxrwxrwx 10 jonathan7 jonathan7 4096 Jun 4 09:53 . -rw-rw-rw- 1 jonathan7 jonathan7 ...
written 20 months ago by Poetic_Premium60
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Comment: C: STAR-RNA Segmentation Fault
... Hey Bastien, thank you for your clarification in splitting the commands. This is way is cleaner for sure! While the genome generation has not been a problem, I am still receiving the "segmentation fault" error the alignment portion. Additionally, I think that the `--readFilesCommand zcat` must foll ...
written 20 months ago by Poetic_Premium60
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STAR-RNA Segmentation Fault
... Hey all, I've been stalking this website for a few months for help (with success), and now I've run into my first problem that I can't solve :O . I am a wet-biologist by training so I'm still a noob at bioinformatics! I am using STAR for E. coli reads and lately I have been receiving "segmentation ...
debian segmentation error star rna-seq mapping written 20 months ago by Poetic_Premium60 • updated 20 months ago by Jeffin Rockey1.1k

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Popular Question 10 months ago, created a question with more than 1,000 views. For STAR-RNA Segmentation Fault
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