https://sourceforge.net/p/gmcloser/activity/Recent activity for GMcloserenThu, 26 Mar 2020 03:31:19 -0000https://sourceforge.net/p/gmcloser/tickets/2/?limit=25#e1e6Has 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...Jonathon BakerThu, 26 Mar 2020 03:31:19 -0000https://sourceforge.net/p/gmcloser/tickets/2/?limit=25#e1e6https://sourceforge.net/p/gmcloser/tickets/4/?limit=25#a9f9Thank you for providing the useful comment. I would consider to use E-MEM as a replacement of MUMMER/Nucmer in the future. Currently GMcloser can use blastn in place of Nucmer by using the option -b.Shunichi KosugiSat, 29 Sep 2018 01:32:58 -0000https://sourceforge.net/p/gmcloser/tickets/4/?limit=25#a9f9https://sourceforge.net/p/gmcloser/tickets/4/replacing nucmerAlicia ClumFri, 28 Sep 2018 19:11:59 -0000https://sourceforge.net/p/gmcloser/tickets/4/https://sourceforge.net/p/gmcloser/tickets/3/, AlexWed, 02 May 2018 13:24:00 -0000https://sourceforge.net/p/gmcloser/tickets/3/https://sourceforge.nethttps%3A//sourceforge.net/projects/gmcloser/files/GMcloser-1.6.2.tar.gz/downloadGMcloserThu, 01 Mar 2018 00:51:04 -0000https://sourceforge.net/projects/gmcloser/files/GMcloser-1.6.2.tar.gz/downloadhttps://sourceforge.nethttps%3A//sourceforge.net/projects/gmcloser/files/GMcloser-1.6.1.tar.gz/downloadGMcloserSat, 06 Jan 2018 02:48:02 -0000https://sourceforge.net/projects/gmcloser/files/GMcloser-1.6.1.tar.gz/downloadhttps://sourceforge.nethttps%3A//sourceforge.net/projects/gmcloser/files/GMcloser-1.6.1.tar.gz/downloadGMcloserThu, 04 Jan 2018 06:46:02 -0000https://sourceforge.net/projects/gmcloser/files/GMcloser-1.6.1.tar.gz/downloadhttps://sourceforge.net/p/gmcloser/tickets/2/?limit=25#993a/ffdaThanks 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.Zachary StewartSat, 14 Oct 2017 02:25:43 -0000https://sourceforge.net/p/gmcloser/tickets/2/?limit=25#993a/ffdahttps://sourceforge.net/p/gmcloser/tickets/2/?limit=25#993aGMcloser 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...Shunichi KosugiSat, 14 Oct 2017 01:51:59 -0000https://sourceforge.net/p/gmcloser/tickets/2/?limit=25#993ahttps://sourceforge.net/p/gmcloser/tickets/2/GMcloser argument errorsZachary StewartFri, 13 Oct 2017 22:30:36 -0000https://sourceforge.net/p/gmcloser/tickets/2/https://sourceforge.net/p/gmcloser/tickets/1/?limit=25#71f6The same problem for me bowtie2-2.2.9/bowtie2-align-s: unrecognized option '--auto'Andrey YurchenkoWed, 14 Jun 2017 15:38:41 -0000https://sourceforge.net/p/gmcloser/tickets/1/?limit=25#71f6https://sourceforge.nethttps%3A//sourceforge.net/projects/gmcloser/files/GMcloser-1.6.tar.gz/downloadGMcloserTue, 01 Nov 2016 03:26:01 -0000https://sourceforge.net/projects/gmcloser/files/GMcloser-1.6.tar.gz/downloadhttps://sourceforge.net/p/gmcloser/tickets/1/bowtie2: unrecognized option '--auto'Sven KlagesFri, 18 Dec 2015 10:27:14 -0000https://sourceforge.net/p/gmcloser/tickets/1/https://sourceforge.nethttp%3A//sourceforge.net/projects/gmcloser/files/GMvalue-1.3.tar.gz/downloadGMcloserThu, 12 Mar 2015 11:56:02 -0000http://sourceforge.net/projects/gmcloser/files/GMvalue-1.3.tar.gz/downloadhttps://sourceforge.nethttp%3A//sourceforge.net/projects/gmcloser/files/GMcloser-1.5.1.tar.gz/downloadGMcloserTue, 06 Jan 2015 12:07:02 -0000http://sourceforge.net/projects/gmcloser/files/GMcloser-1.5.1.tar.gz/downloadhttps://sourceforge.nethttp%3A//sourceforge.net/projects/gmcloser/files/GMcloser-1.5.tar.gz/downloadGMcloserThu, 13 Nov 2014 01:45:04 -0000http://sourceforge.net/projects/gmcloser/files/GMcloser-1.5.tar.gz/downloadhttps://sourceforge.nethttp%3A//sourceforge.net/projects/gmcloser/files/GMcloser-1.5.tar.gz/downloadGMcloserWed, 12 Nov 2014 09:57:03 -0000http://sourceforge.net/projects/gmcloser/files/GMcloser-1.5.tar.gz/downloadhttps://sourceforge.nethttp%3A//sourceforge.net/projects/gmcloser/files/GMvalue-1.2.tar.gz/downloadGMcloserWed, 12 Nov 2014 09:56:02 -0000http://sourceforge.net/projects/gmcloser/files/GMvalue-1.2.tar.gz/downloadhttps://sourceforge.nethttp%3A//sourceforge.net/projects/gmcloser/files/GMvalue-1.1.tar.gz/downloadGMcloserThu, 30 Oct 2014 02:28:05 -0000http://sourceforge.net/projects/gmcloser/files/GMvalue-1.1.tar.gz/downloadhttps://sourceforge.nethttp%3A//sourceforge.net/projects/gmcloser/files/GMvalue-1.1.tar.gz/downloadGMcloserMon, 27 Oct 2014 06:12:03 -0000http://sourceforge.net/projects/gmcloser/files/GMvalue-1.1.tar.gz/downloadhttps://sourceforge.nethttp%3A//sourceforge.net/projects/gmcloser/files/GMvalue-1.5.tar.gz/downloadGMcloserMon, 27 Oct 2014 06:03:04 -0000http://sourceforge.net/projects/gmcloser/files/GMvalue-1.5.tar.gz/downloadhttps://sourceforge.nethttp%3A//sourceforge.net/projects/gmcloser/files/GMcloser-1.4.tar.gz/downloadGMcloserMon, 18 Aug 2014 01:51:03 -0000http://sourceforge.net/projects/gmcloser/files/GMcloser-1.4.tar.gz/downloadhttps://sourceforge.nethttp%3A//sourceforge.net/projects/gmcloser/files/GMcloser-1.3.tar.gz/downloadGMcloserThu, 10 Apr 2014 10:42:04 -0000http://sourceforge.net/projects/gmcloser/files/GMcloser-1.3.tar.gz/downloadhttps://sourceforge.nethttp%3A//sourceforge.net/projects/gmcloser/files/GMcloser-1.2.tar.gz/downloadGMcloserMon, 10 Feb 2014 10:22:05 -0000http://sourceforge.net/projects/gmcloser/files/GMcloser-1.2.tar.gz/downloadhttps://sourceforge.nethttp%3A//sourceforge.net/projects/gmcloser/files/Sample_data.tar.gz/downloadGMcloserMon, 10 Feb 2014 10:18:08 -0000http://sourceforge.net/projects/gmcloser/files/Sample_data.tar.gz/download