a strange gzip error

[Hoon Kim]

Hello,

I didn't have this error during my test run, but this time, I have a strange error related to 'gzip' when I tried to run 'Known miRNA' analysis. I wonder if you know what could be wrong with my system or fastq files.

#########################################################################
#   miARma, miRNA and RNASeq Multiprocess Analysis                      #
#                miARma v 1.5 (Apr-2016)                                #
#                                                                       #
#   Created at Computational Biology and Bioinformatics Group (CbBio)   #
#   Institute of Biomedicine of Seville. IBIS (Spain)                   #
#   Copyright (c) 2016 IBIS. All rights reserved.                       #
#   mail : [e-mail]                                        #
#########################################################################

[Sun Aug 14 23:29:47 2016] Starting a miARma analysis for miRNA
[Sun Aug 14 23:29:47 2016] Checking provided parameters for: Quality,Aligner,ReadCount.
[Sun Aug 14 23:29:47 2016] Checking General-output_dir parameter ... Exists!
[Sun Aug 14 23:29:47 2016] The folder specified in (output_dir=/scratch/bcb/hkim6/SH-mouse-miRNA/work/merged-fastq/miARmaSeq/Known_miRNAs/results_mmu.gff3/miRNA_primary_transcript/strand=no/) alrea                                        dy exists.
[Sun Aug 14 23:29:47 2016] Wait 5 seconds to overwrite the folder. Cancel otherwise:   0
[Sun Aug 14 23:29:53 2016] Continue.
[Sun Aug 14 23:29:53 2016] All parameters are correct.
[Sun Aug 14 23:29:53 2016] Starting Quality Analysis.
[Sun Aug 14 23:39:06 2016] Quality Analysis finished.
[Sun Aug 14 23:39:06 2016] No processed files are found [neither cutadapt, nor reaper nor adaptrimming folders], assuming /scratch/bcb/hkim6/SH-mouse-miRNA/work/merged-fastq/reads/ don't need to be                                         proccessed
[Sun Aug 14 23:39:06 2016] Starting a "Bowtie1" Alignment Analysis
gzip: invalid option -- 'k'
Try `gzip --help' for more information.
gzip: invalid option -- 'k'
Try `gzip --help' for more information.
gzip: invalid option -- 'k'
Try `gzip --help' for more information.
gzip: invalid option -- 'k'
Try `gzip --help' for more information.
gzip: invalid option -- 'k'
Try `gzip --help' for more information.
gzip: invalid option -- 'k'
Try `gzip --help' for more information.
gzip: invalid option -- 'k'
Try `gzip --help' for more information.
gzip: invalid option -- 'k'
Try `gzip --help' for more information.
gzip: invalid option -- 'k'
Try `gzip --help' for more information.
gzip: invalid option -- 'k'
Try `gzip --help' for more information.
gzip: invalid option -- 'k'
Try `gzip --help' for more information.
gzip: invalid option -- 'k'
Try `gzip --help' for more information.
[Sun Aug 14 23:39:29 2016] "Bowtie1" Alignment Analysis finished
[Sun Aug 14 23:39:29 2016] Starting a Readcount Analysis
[Sun Aug 14 23:39:31 2016] Readcount Analysis finished.

My fastq files have been compressed as:

[hkim6@cnode205 strand=no]$ ls /scratch/bcb/hkim6/SH-mouse-miRNA/work/merged-fastq/reads/
S177_ATCGTT.fastq.gz  S180_GTTCTT.fastq.gz  S85_AGCTTT.fastq.gz  S90_GGTGTT.fastq.gz
S178_GACGTT.fastq.gz  S83_ATGTTT.fastq.gz   S86_GTATTT.fastq.gz  S91_AATGTT.fastq.gz
S179_AGAGTT.fastq.gz  S84_GAGTTT.fastq.gz   S89_ACATTT.fastq.gz  S92_GCGGTT.fastq.gz

Thank you in advance,

Hoon

[Eduardo Andres Leon]

Yes, It's really strange .... -k is an option from gzip to keep input files during uncompressing. For us it's important not to touch input files:

It's included in linux

gzip -help
Usage: gzip [OPTION]... [FILE]...
Compress or uncompress FILEs (by default, compress FILES in-place).

Mandatory arguments to long options are mandatory for short options too.

  -c, --stdout      write on standard output, keep original files unchanged
  -d, --decompress  decompress
  -f, --force       force overwrite of output file and compress links
  -h, --help        give this help
  -k, --keep        keep (don't delete) input files
  -l, --list        list compressed file contents
  -L, --license     display software license
  -n, --no-name     do not save or restore the original name and time stamp
  -N, --name        save or restore the original name and time stamp
  -q, --quiet       suppress all warnings
  -r, --recursive   operate recursively on directories
  -S, --suffix=SUF  use suffix SUF on compressed files
  -t, --test        test compressed file integrity
  -v, --verbose     verbose mode
  -V, --version     display version number
  -1, --fast        compress faster
  -9, --best        compress better
  --rsyncable       Make rsync-friendly archive

With no FILE, or when FILE is -, read standard input.

Report bugs to <[e-mail]>.

$>gzip -V   
gzip 1.6
Copyright (C) 2007, 2010, 2011 Free Software Foundation, Inc.
Copyright (C) 1993 Jean-loup Gailly.
This is free software.  You may redistribute copies of it under the terms of
the GNU General Public License <http://www.gnu.org/licenses/gpl.html>.
There is NO WARRANTY, to the extent permitted by law.

Written by Jean-loup Gailly.

and in Mac:

gzip -help
Apple gzip 251
usage: gzip [-123456789acdfhklLNnqrtVv] [-S .suffix] [<file> [<file> ...]]
 -1 --fast            fastest (worst) compression
 -2 .. -8             set compression level
 -9 --best            best (slowest) compression
 -c --stdout          write to stdout, keep original files
    --to-stdout
 -d --decompress      uncompress files
    --uncompress
 -f --force           force overwriting & compress links
 -h --help            display this help
 -k --keep            don't delete input files during operation
 -l --list            list compressed file contents
 -N --name            save or restore original file name and time stamp
 -n --no-name         don't save original file name or time stamp
 -q --quiet           output no warnings
 -r --recursive       recursively compress files in directories
 -S .suf              use suffix .suf instead of .gz
    --suffix .suf
 -t --test            test compressed file
 -V --version         display program version
 -v --verbose         print extra statistics

$> gzip -V
Apple gzip 251

Which gzip and Os are you using ?

[Hoon Kim]

Thank you for your quick response. It is really related to my linux. my gzip is very old. I am sorry for having asked this awkward question. I will close this ticket.

[hkim6@cnode205 strand=no]$ gzip -help
Usage: gzip [OPTION]... [FILE]...
Compress or uncompress FILEs (by default, compress FILES in-place).

Mandatory arguments to long options are mandatory for short options too.

  -c, --stdout      write on standard output, keep original files unchanged
  -d, --decompress  decompress
  -f, --force       force overwrite of output file and compress links
  -h, --help        give this help
  -l, --list        list compressed file contents
  -L, --license     display software license
  -n, --no-name     do not save or restore the original name and time stamp
  -N, --name        save or restore the original name and time stamp
  -q, --quiet       suppress all warnings
  -r, --recursive   operate recursively on directories
  -S, --suffix=SUF  use suffix SUF on compressed files
  -t, --test        test compressed file integrity
  -v, --verbose     verbose mode
  -V, --version     display version number
  -1, --fast        compress faster
  -9, --best        compress better
    --rsyncable   Make rsync-friendly archive

With no FILE, or when FILE is -, read standard input.

Report bugs to <[e-mail]>.
[hkim6@cnode205 strand=no]$ gzip -V
gzip 1.3.12
Copyright (C) 2007 Free Software Foundation, Inc.
Copyright (C) 1993 Jean-loup Gailly.
This is free software.  You may redistribute copies of it under the terms of
the GNU General Public License <http://www.gnu.org/licenses/gpl.html>.
There is NO WARRANTY, to the extent permitted by law.

Written by Jean-loup Gailly.