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shubhamchandak94 / Spring

FASTQ compression
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Running into an issue #5

Closed sagnikbanerjee15 closed 6 years ago

sagnikbanerjee15 commented 6 years ago

Hello,

I am running the following command and I am running into the following problem.

spring -c -1 A1_ATCACG_L001_R1_001.fastq -p -t 10 -i -o A1_ATCACG_L001_R1_001.fastq.spring.compressed

The error I am getting is:

Preprocessing Max Read length: 100 Total number of reads: 31599231 Total number of reads without N: 31415745 Preprocessing Done!

real 0m41.783s user 0m13.218s sys 0m24.238s Reading file: ./tmp.tf8zs715T7/input_clean.dna Constructing dictionaries Reordering reads Reordering done, 1985451 were unmatched Writing to file Done!

real 1m38.688s user 12m28.488s sys 0m47.109s Maximum Read length: 100 Number of non-singleton reads: 30165601 Number of singleton reads: 1250144 Number of reads with N: 183486 Encoding reads Encoding done: 655929 singleton reads were aligned 128993 reads with N were aligned

real 0m25.394s user 2m21.037s sys 0m8.393s This is bsc, Block Sorting Compressor. Version 3.1.0. 8 July 2012. Copyright (c) 2009-2012 Ilya Grebnov Ilya.Grebnov@gmail.com.

./tmp.tf8zs715T7/read_pos.tar compressed 30965760 into 6323226 in 2.938 seconds. This is bsc, Block Sorting Compressor. Version 3.1.0. 8 July 2012. Copyright (c) 2009-2012 Ilya Grebnov Ilya.Grebnov@gmail.com.

./tmp.tf8zs715T7/read_noise.tar compressed 45281280 into 7072242 in 4.488 seconds.

7-Zip [64] 16.02 : Copyright (c) 1999-2016 Igor Pavlov : 2016-05-21 p7zip Version 16.02 (locale=en_US.UTF-8,Utf16=on,HugeFiles=on,64 bits,32 CPUs x64)

Can't load './7z.dll' (./7z.so: cannot open shared object file: No such file or directory)

ERROR: 7-Zip cannot find the code that works with archives.

Please help with this.

Thank you.

shubhamchandak94 commented 6 years ago

Hi Sagnik, Please update to the latest version. 7-zip is no longer used in SPRING, so you shouldn't be facing this issue. Regards, Shubham

sagnikbanerjee15 commented 6 years ago

Thank you Shubham Sagnik Banerjee Graduate Research Assistant Bioinformatics and Computational Biology Department of Plant Pathology and Microbiology Dr. Roger Wise's Lab Iowa State University

*"The moment I have realized God sitting in the temple of every human body, the moment I stand in reverence before every human being and see God in him

ᐧ

On Tue, Oct 2, 2018 at 9:24 PM Shubham Chandak notifications@github.com wrote:

Hi Sagnik, Please update to the latest version. 7-zip is no longer used in SPRING, so you shouldn't be facing this issue. Regards, Shubham

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