User: junsionglow

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junsionglow20
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2 hours ago
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1 week, 6 days ago
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j**********@gmail.com

Posts by junsionglow

<prev • 16 results • page 1 of 2 • next >
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Comment: C: Very low unique mapped reads - STAR alignment
... yeah, they do belong to the right GRCh38 assembly... i'm puzzled! ...
written 2 hours ago by junsionglow20
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Comment: C: Very low unique mapped reads - STAR alignment
... Thanks guys, these fastq files are from published GEO SRA https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM3109339 and I obtained the Fastq via fastq-dump. They used GENCODE GRCh38 v26 gene annotation, while I used these to make the index, GCF_000001405.26_GRCh38_genomic.fna GCF_00 ...
written 16 hours ago by junsionglow20
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Very low unique mapped reads - STAR alignment
... Hi all, while looking at my `log.final.out` file, it dawned on me that my uniquely mapped reads is really low. See below: Mapping speed, Million of reads per hour | 113.33 Number of input reads | 11050047 Average i ...
rna-seq written 20 hours ago by junsionglow20 • updated 2 hours ago by h.mon18k
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Comment: C: STAR alignment killed
... Dear Marks and Genomax, Finally gotten it to work. There was 2 part problem, one was my indexing, the other was memory (I believe). So when I submitted a Slurm job requesting for memory, that worked! Thanks guys! ...
written 2 days ago by junsionglow20
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Comment: C: STAR alignment killed
... Thanks genomax and Marks. I will see what work around and get back to you guys. ...
written 4 days ago by junsionglow20
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Comment: C: STAR alignment killed
... ah, this is it. Tasks: 699 total, 1 running, 696 sleeping, 2 stopped, 0 zombie %Cpu(s): 0.0 us, 0.4 sy, 0.3 ni, 99.2 id, 0.0 wa, 0.0 hi, 0.0 si, 0.0 st KiB Mem : 13131726+total, 352784 free, 6140812 used, 12482367+buff/cache KiB Swap: 16777212 total, 16484712 free, ...
written 8 days ago by junsionglow20
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Comment: C: STAR alignment killed
... Thanks Marks. there isnt a `log.progress.out` or `log.final.out` associated with that run. But i did try the `genomeChrBinNbits` and the run was aborted with the follow: Aug 10 07:16:06 ..... started STAR run Aug 10 07:16:06 ... starting to generate Genome files terminate called after t ...
written 8 days ago by junsionglow20
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Comment: C: STAR alignment killed
... Hi Marks, I've uploaded the `log.out` file onto pastebin like your suggested https://pastebin.com/WUhxYpix ...
written 8 days ago by junsionglow20
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Comment: C: STAR alignment killed
... I cant copy it, so here's an image of the top 4-5lines at the `top` of the window! https://s22.postimg.cc/mxqg8764x/top.png ...
written 8 days ago by junsionglow20
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Comment: C: STAR alignment killed
... I'm running on a cluster on interactive bash... how can i determine the memory? i ran /usr/bin/time in front of the STAR command. 11.76user 4.19system 0:16.34elapsed 97%CPU (0avgtext+0avgdata 5243688maxresident) does this help? ...
written 8 days ago by junsionglow20

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