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CummeRbund shows 95% NAs for gene lists bjackson Bioinformatics 1 05-12-2015 09:09 AM

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Old 06-08-2015, 04:23 AM   #1
mido1951
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Unhappy NaS (Nanopore Synthetic-long) help

I compiled NaS but the return message in linux.
Code:
root@midox-VGN-NS11S-S:/home/midox/Bureau/NaS-master# $(pwd)/NaS_v2/NaS --fq1 NaS_example_acineto/AWK_DOSF_1_1_A5KR6.IND3_clean.10prc.fastq --fq2 NaS_example_acineto/AWK_DOSF_1_2_A5KR6.IND3_clean.10prc.fastq --nano NaS_example_acineto/MinION_reads_Acinetobacter_baylyi.fa --out NaS_example --nb_proc 5
Number of parallel task : 5
[lundi 8 juin 2015, 14:14:24 (UTC+0200)] Create output directory : NaS_example
[lundi 8 juin 2015, 14:14:24 (UTC+0200)] Create fasta file from fastq...
/home/midox/Bureau/NaS-master/NaS_v2/FastaToTbl: 60: /home/midox/Bureau/NaS-master/NaS_v2/FastaToTbl: gawk: not found
/home/midox/Bureau/NaS-master/NaS_v2/TblToFasta: 60: /home/midox/Bureau/NaS-master/NaS_v2/TblToFasta: gawk: not found
paste: NaS_example_acineto/AWK_DOSF_1_2_A5KR6.IND3_clean.10prc.fastq: No such file or directory
[lundi 8 juin 2015, 14:14:24 (UTC+0200)] Alignement step in fast mode...
[lundi 8 juin 2015, 14:14:24 (UTC+0200)] Select reads...
[lundi 8 juin 2015, 14:14:24 (UTC+0200)] Retrieve similar reads...
[lundi 8 juin 2015, 14:14:25 (UTC+0200)] Generate NaS reads...
cat: NaS_example/assemblies/*/NaS_hqctg_reads_final.fa: No such file or directory
/home/midox/Bureau/NaS-master/NaS_v2/TblToFasta: 60: /home/midox/Bureau/NaS-master/NaS_v2/TblToFasta: gawk: not found
/home/midox/Bureau/NaS-master/NaS_v2/FastaToTbl: 60: /home/midox/Bureau/NaS-master/NaS_v2/FastaToTbl: gawk: not found
[lundi 8 juin 2015, 14:14:25 (UTC+0200)] Generate statistics...
fastalength: error while loading shared libraries: libglib-1.2.so.0: cannot open shared object file: No such file or directory
fastacomposition: error while loading shared libraries: libglib-1.2.so.0: cannot open shared object file: No such file or directory
/home/midox/Bureau/NaS-master/NaS_v2/assemblyMetrics: 108: /home/midox/Bureau/NaS-master/NaS_v2/assemblyMetrics: gawk: not found
fastalength: error while loading shared libraries: libglib-1.2.so.0: cannot open shared object file: No such file or directory
fastacomposition: error while loading shared libraries: libglib-1.2.so.0: cannot open shared object file: No such file or directory
/home/midox/Bureau/NaS-master/NaS_v2/assemblyMetrics: 108: /home/midox/Bureau/NaS-master/NaS_v2/assemblyMetrics: gawk: not found
NbReads=  -1  CumulativeSize=  number=  N50size=    minSize=  -1  maxSize=  -nan  avgSize=    =>  NaS_example/NANO_reads.stats
NbReads=  -1  CumulativeSize=  number=  N50size=    minSize=  -1  maxSize=  -nan  avgSize=    =>  NaS_example/NaS_hqctg_reads.stats
do you have an idea on what kind of errors?
thankyou
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Old 06-08-2015, 04:28 AM   #2
GenoMax
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If you look through the error messages you generally get a hint of what is missing/in error. In this case looks like you need the gawk package.

Code:
$ sudo apt-get install gawk
You also may need to install glib.
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Old 06-08-2015, 05:05 AM   #3
mido1951
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Default new PROBLEMS NaS

i installed gawd and I recompiled
there a new problems.

Code:
root@midox-VGN-NS11S-S:/home/midox/Bureau/NaS-master# $(pwd)/NaS_v2/NaS --fq1 /home/midox/Bureau/NaS_example_acineto/AWK_DOSF_1_1_A5KR6.IND3_clean.10prc.fastq --fq2 /home/midox/Bureau/NaS_example_acineto/AWK_DOSF_1_2_A5KR6.IND3_clean.10prc.fastq --nano /home/midox/Bureau/NaS_example_acineto/MinION_reads_Acinetobacter_baylyi.fa --out NaS_example --nb_proc 5
Number of parallel task : 5
[lundi 8 juin 2015, 14:56:09 (UTC+0200)] Create output directory : NaS_example
[lundi 8 juin 2015, 14:56:09 (UTC+0200)] Create fasta file from fastq...
[lundi 8 juin 2015, 14:58:16 (UTC+0200)] Alignement step in fast mode...
[lundi 8 juin 2015, 14:58:23 (UTC+0200)] Select reads...
[lundi 8 juin 2015, 14:58:23 (UTC+0200)] Retrieve similar reads...
[lundi 8 juin 2015, 14:58:24 (UTC+0200)] Generate NaS reads...
cat: NaS_example/assemblies/*/NaS_hqctg_reads_final.fa: No such file or directory
[lundi 8 juin 2015, 14:58:25 (UTC+0200)] Generate statistics...
fastalength: error while loading shared libraries: libglib-1.2.so.0: cannot open shared object file: No such file or directory
fastacomposition: error while loading shared libraries: libglib-1.2.so.0: cannot open shared object file: No such file or directory
awk: cmd. line:1: fatal: division by zero attempted
awk: cmd. line:1: fatal: division by zero attempted
gawk: cmd. line:1: fatal: division by zero attempted
fastalength: error while loading shared libraries: libglib-1.2.so.0: cannot open shared object file: No such file or directory
fastacomposition: error while loading shared libraries: libglib-1.2.so.0: cannot open shared object file: No such file or directory
awk: cmd. line:1: fatal: division by zero attempted
awk: cmd. line:1: fatal: division by zero attempted
gawk: cmd. line:1: fatal: division by zero attempted
NbReads=    CumulativeSize=    N50size=    minSize=    maxSize=    avgSize=    =>  NaS_example/NANO_reads.stats
NbReads=    CumulativeSize=    N50size=    minSize=    maxSize=    avgSize=    =>  NaS_example/NaS_hqctg_reads.stats
have any ideasa about this errors?
Thankyou
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Old 06-08-2015, 05:11 AM   #4
A.N.Other
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Please only post your issues in SeqAnswers OR BioStars - it's a waste of people's time to respond to things that have already been answered elsewhere.

I was about to reply in BioStars, but I see GenoMax has already said it - you need to install glib.
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Old 06-08-2015, 05:17 AM   #5
GenoMax
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In addition there are other problems. It appears that this directory/file is not there.

NaS_example/assemblies/*/NaS_hqctg_reads_final.fa
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Old 06-08-2015, 07:22 AM   #6
pmiguel
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Quote:
Originally Posted by A.N.Other View Post
Please only post your issues in SeqAnswers OR BioStars - it's a waste of people's time to respond to things that have already been answered elsewhere.
That's your opinion, A.N.

I say post to as many sites as you like. If more than one person answers a question in 2 different forums--well that gives the answer additional weight, doesn't it?

--
Phillip
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