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I found it hard to make a standalone application using Python. Can you pleqse suggest me a easy zay out?

I run MIRA on my dataset and got the following error. I have /tmp directory mounted on non-NFS protocol. I wanted to use it for temporary location. How to do that? Sorry, M new to MIRA.

WARNING WARNING WARNING!

It looks like the directory MIRA uses for temporary files
/home/user/MIRA/mira_4.0.2_linux-gnu_x86_64_static//Test_Asbly_d_tmp_MJYclL
is on a NFS (Network File System) mount. This will slow down MIRA *considerably*
... by about a factor of 10!

If you don't want that, you have three possibilities:

1) RECOMMENDED! Use -DI:trt to redirect the tmp directory somewhere else on a
local disk or even SSD.
2) ALSO POSSIBLE: put the whole project somewhere else on your file system.
3) ABSOLUTELY NOT RECOMMENDED AT ALL: use "-NW:cnfs=warn" to tell MIRA not
to stop when it finds the tmp directory on NFS.

If you do not know what NFS is and which directory to use in "-DI:trt", ask
your local system administrator to guide you.

I wanted to remove the duplicates from fastq file. I planned to use fastuniq but it does not have good tutorial. Can you please tell me how to use it?

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0052249

Looking for files named in data ...Pushing back filename: "clean_a2017.R1.fq"
Could not determine filetype from data 'clean_Avaga2017.R1.fq' ("clean_a2017.R1.fq")
Pushing back filename: "clean_a2017.R2.fq"
Could not determine filetype from data 'clean_a2017.R2.fq' ("clean_a2017.R2.fq")

Fatal error (may be due to problems of the input data or parameters):

********************************************************************************
* Some 'data' entries named in the manifest file could not be verified, see *
* the log above. *
* Maybe some files are missing, not readable or there is a typo in the *
* manifest file? *
********************************************************************************

I usually report and estimate the genome size by looking into file size of the contigs. Is this right way? 

In school the teachers refer to both terms as one, but according to what I have read they are not the same and don't use the same methologies so I am a bit confused.

I used the following command to print the blast hit.

[Terminal] blastn -query aaa.fa -db blastdb/nt -evalue 10e-5 -num_threads 4 -max_target_seqs 1 -outfmt '6 qseqid staxid qstart qend sallseqi sstart send evalue length frames qcovs' -out testBlastSee

But the outfile print many hits, I only want the top one.

[Terminal] more testBlastSee                                                                                                                  []
Lactococcus_lactis    1    63350    1    63350    0.0    63350    1/1    100
Lactococcus_lactis    52453    55105    138601    141250    0.0    2654    1/1    100
Lactococcus_lactis    52393    53898    629230    627727    0.0    1508    1/1    100
Lactococcus_lactis    52411    53898    2217595    2216111    0.0    1489    1/1    100
Lactococcus_lactis    52413    53898    2157259    2155777    0.0    1487    1/1    100
Lactococcus_lactis    52452    53898    838503    837059    0.0    1449    1/1    100
Lactococcus_lactis    52453    53860    374322    375726    0.0    1409    1/1    100
Lactococcus_lactis    53859    55105    2154570    2155816    0.0    1247    1/1    100
Lactococcus_lactis    53860    55105    626521    627766    0.0    1246    1/1    100
Lactococcus_lactis    53858    55105    835851    837098    0.0    1248    1/1    100
Lactococcus_lactis    53860    55105    2214905    2216150    0.0    1246    1/1    100
Lactococcus_lactis    53860    55104    374321    373077    0.0    1245    1/1    100
Lactococcus_lactis    53860    55104    138600    137356    0.0    1245    1/1    100
Lactococcus_lactis    53860    55104    839748    838504    0.0    1245    1/1    100
Lactococcus_lactis    40213    41128    508317    507400    0.0    922    1/1    100
Lactococcus_lactis    28448    28695    543445    543703    9e-96    260    1/1    100
Lactococcus_lactis    42193    42376    506963    506780    4e-64    184    1/1    100
Lactococcus_lactis    61964    62163    61646    61845    6e-53    200    1/1    100
Lactococcus_lactis    61646    61845    61964    62163    6e-53    200    1/1    100
Lactococcus_lactis    37541    37672    512963    512832    3e-50    132    1/1    100
Lactococcus_lactis    28816    28933    2360018    2359903    7e-32    118    1/1    100
Lactococcus_lactis    35284    35410    1439702    1439828    1e-30    129    1/1    100
Lactococcus_lactis    28272    28363    1412439    1412348    1e-29    92    1/1    100
Lactococcus_lactis    28193    28270    2360127    2360050    2e-28    78    1/1    100
Lactococcus_lactis    28695    28813    542396    542514    6e-23    122    1/1    100
Lactococcus_lactis    28695    28813    1981268    1981150    6e-23    122    1/1    100
Lactococcus_lactis    28695    28813    2341071    2340953    6e-23    122    1/1    100
Lactococcus_lactis    28695    28812    2360250    2360133    2e-22    121    1/1    100
Lactococcus_lactis    28695    28796    2218330    2218229    8e-22    103    1/1    100
Lactococcus_lactis    28695    28796    2260841    2260740    8e-22    103    1/1    100
Lactococcus_lactis    55066    55147    2154609    2154528    2e-17    82    1/1    100
Lactococcus_lactis    55066    55148    626559    626478    5e-14    83    1/1    100
Lactococcus_lactis    52392    52456    373013    373076    2e-12    65    1/1    100
Lactococcus_lactis    55105    55148    375723    375766    1e-09    44    1/1    100
Lactococcus_lactis    52393    52457    839809    839745    1e-09    66    1/1    100

When I tried Perl on my cluster/server it gives following error !! How to resolve it?

$ perl
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
LANGUAGE = (unset),
LC_ALL = (unset),
LC_PAPER = "de_BE.UTF-8",
LC_ADDRESS = "de_BE.UTF-8",
LC_MONETARY = "de_BE.UTF-8",
LC_NUMERIC = "de_BE.UTF-8",
LC_TELEPHONE = "de_BE.UTF-8",
LC_IDENTIFICATION = "de_BE.UTF-8",
LC_MEASUREMENT = "de_BE.UTF-8",
LC_TIME = "de_BE.UTF-8",
LC_NAME = "de_BE.UTF-8",
LANG = "en_US.UTF-8"
are supported and installed on your system.
perl: warning: Falling back to a fallback locale ("en_US.UTF-8").