GMcloser Activity
Closing the gaps in scaffolds with preassembled contigs
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Activity for GMcloser
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Jonathon Baker posted a comment on ticket #2
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...
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Shunichi Kosugi posted a comment on ticket #4
Thank 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.
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Alicia Clum created ticket #4
replacing nucmer
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Alex created ticket #3
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GMcloser released /GMcloser-1.6.2.tar.gz
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Zachary Stewart posted a comment on ticket #2
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.
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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...
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GMcloser argument errors
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Andrey Yurchenko posted a comment on ticket #1
The same problem for me bowtie2-2.2.9/bowtie2-align-s: unrecognized option '--auto'
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Sven Klages created ticket #1
bowtie2: unrecognized option '--auto'
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