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Old 06-08-2015, 04:23 AM   #1
mido1951
Senior Member
 
Location: Tunisia

Join Date: May 2014
Posts: 123
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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