#2 GMcloser argument errors

[Zachary Stewart]

Hi,

I am unable to get GMcloser 1.6 to accept arguments and begin the program, and various arguments specified in the usage list fail to work. For example, if I run the command specified in the user manual for long reads with my own value inputs, i.e.,

$GMCDIR/gmcloser -t $GENOMEDIR/$GENOMENAME -q $CORRREADS -lr -it 3 -mq 2 -p gmclose_hgap -l 100 -i 500 -d 50 -c -n 12

I receive the following errors:

Value "r" invalid for option l (number expected)
Value "t" invalid for option i (number expected)
Value "r" invalid for option l (number expected)
Value "t" invalid for option i (number expected)

From this I assume that the -lr and -it arguments are broken. I switch these out to their unabbreviated counterparts, i.e.,

$GMCDIR/gmcloser -t $GENOMEDIR/$GENOMENAME -q $CORRREADS --long_read --iterate 3 -mq 2 -p gmclose_hgap -l 100 -i 500 -d 50 -c -n 12

And now I receive the following error:

Unknown option: mq
--prefix_out option is not specied:

Which tells me that the -mq argument is broken. I switch it out...

$GMCDIR/gmcloser -t $GENOMEDIR/$GENOMENAME -q $CORRREADS --long_read --iterate 3 --min_qalign 2 -p gmclose_hgap -l 100 -i 500 -d 50 -c -n 12

And I receive this:

Alignments with query long reads was performed with BLAST
Value "n" invalid for option i (number expected)

I don't see how the -i argument should be relevant when using long reads, so I remove the argument and the same error occurs. If I use the unabbreviated counterpart of the -i argument (--insert), I again receive the same error.

Is there something I'm missing? My perl version is 5.22 and the other prerequisites are appropriately updated and referenced in my PATH. I'd like to give GMcloser a try with my assembly, but can't see where I'm going wrong. Hopefully you still check these tickets!

Thanks,
Zac.

[Shunichi Kosugi]

GMcloser uses Getopt::Long module in perl. Your perl environment seems
not to use the module properly. If possible, try to install another
version of perl and use it.

Shunichi

----- Original Message -----

---

** [tickets:#2] GMcloser argument errors**

Status: open
Milestone: 1.0
Labels: Error
Created: Fri Oct 13, 2017 10:30 PM UTC by Zachary Stewart
Last Updated: Fri Oct 13, 2017 10:30 PM UTC
Owner: Shunichi Kosugi

Hi,

I am unable to get GMcloser 1.6 to accept arguments and begin the
program, and various arguments specified in the usage list fail to work.
For example, if I run the command specified in the user manual for long
reads with my own value inputs, i.e.,
$GMCDIR/gmcloser -t $GENOMEDIR/$GENOMENAME -q $CORRREADS -lr -it 3 -mq 2 -p gmclose_hgap -l 100 -i 500 -d 50 -c -n 12
I receive the following errors:
Value "r" invalid for option l (number expected) Value "t" invalid for option i (number expected) Value "r" invalid for option l (number expected) Value "t" invalid for option i (number expected)

From this I assume that the -lr and -it arguments are broken. I
switch these out to their unabbreviated counterparts, i.e.,
$GMCDIR/gmcloser -t $GENOMEDIR/$GENOMENAME -q $CORRREADS --long_read - -iterate 3 -mq 2 -p gmclose_hgap -l 100 -i 500 -d 50 -c -n 12
And now I receive the following error:
Unknown option: mq --prefix_out option is not specied:
Which tells me that the -mq argument is broken. I switch it out...
$GMCDIR/gmcloser -t $GENOMEDIR/$GENOMENAME -q $CORRREADS --long_read - -iterate 3 --min_qalign 2 -p gmclose_hgap -l 100 -i 500 -d 50 -c -n 12
And I receive this:
Alignments with query long reads was performed with BLAST Value "n" invalid for option i (number expected)
I don't see how the -i argument should be relevant when using long
reads, so I remove the argument and the same error occurs. If I use the
unabbreviated counterpart of the -i argument (--insert), I again receive
the same error.

Is there something I'm missing? My perl version is 5.22 and the other
prerequisites are appropriately updated and referenced in my PATH. I'd
like to give GMcloser a try with my assembly, but can't see where I'm
going wrong. Hopefully you still check these tickets!

Thanks,
Zac.

---

Sent from sourceforge.net because you indicated interest in <
https://sourceforge.net/p/gmcloser/tickets/2/>

To unsubscribe from further messages, please visit <
https://sourceforge.net/auth/subscriptions/>

[Zachary Stewart]

Thanks for the quick response. I tried reinstalling Getopt::Long in the environment I was using but it didn't seem to make a difference (SUSE). I was able to run the program using emulated Ubuntu however, so I'm not entirely certain where the problem lies. Regardless, since the program runs reasonably quickly, using an emulated OS isn't a problem to me.

Zac.

[Jonathon Baker]

Has anybody solved this issue? I am having the same problem. I have tried installing GMcloser and the dependencies using the Bioconda recipe: https://bioconda.github.io/recipes/gmcloser/README.html
(both locally on my laptop and on a Linux server), and I get the same error:

$ gmcloser \
>     --target_scaf flye_pilon7_fixstart.fasta \
>     --query_seq corrected_nanopore.fastq \
>     --long_read \
>     --read_file final_pure_reads_1.fastq final_pure_reads_2.fastq \
>     --read_len 151 \
>     --insert 411 \
>     --sd_insert 125 \
>     --read_format fastq \
>     -n 16 \
>     --prefix_out sample
--prefix_out option is not specied: