Comments (7)
It says it has trouble parsing the command line. Could you please post your command line here?
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Hi @stschiff , here it goes:
./msmc -o testmsmc_chr1 chr1.msmc.input
Since this is my first trial, I did a single input (one chromosome), and didn't specify any other options apart from the output, as stated in the guide for more simple runs.
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I cannot reproduce this. I copied your content from your input file above into a file and then simply ran the command line you gave here. It started normally (didn't check whether it finishes, though). But definitely no command line error.
Your error doesn't quite fit the command line. It complains that it can't parse a "g" where it expects a number. But you haven't given any option and nothing with a letter g
. Can you check again that the error above occurs with exactly the command line you've posted here? Doesn't seem right.
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Note that I anyway recommend MSMC2 (https://github.com/stschiff/msmc2)
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@stschiff Thanks for the patience in trying to troubleshoot this. I've made a screenshot showing the error appearing, both when running MSMC and MSMC2 (precompiled binaries, I also recompiled MSMC from source):
https://drive.google.com/file/d/1HqglSG3xWWhz6Va_3RJ8COmv89E71Nsr/view?usp=sharing
I've checked my installation of GSL and it appears fine, it is installed in /usr/local/lib do you think this could be a issue?
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Hmm... bizarre. Perhaps this is due to a change in the standard library of D. I will have to recompile and check on our linux cluster, perhaps I can reproduce it there.
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Still can't reproduce this with v1.1.1. I'm gonna have to close this.
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Related Issues (20)
- AssertError bootstrap HOT 2
- another Segmentation Fault HOT 1
- error running msmc HOT 2
- running msmc without final result HOT 1
- install error HOT 1
- MSMC running with the divergent individuals HOT 1
- MSMC error HOT 12
- decode time units HOT 3
- Effect of introgression and selfing for estimation of population split HOT 1
- Abnormal results of MSMC, and need help ~ HOT 2
- trying to replicate Fig2 of Schiffels & Durbin (2014) HOT 6
- How to install MSMC HOT 1
- powell exceeding maximum iterations HOT 6
- precompiled binaries not working on macOS Catalina HOT 1
- "The sequence "chr1" was not found" HOT 1
- MSMC2- install error HOT 2
- Error in installing software
- AssertionError while using generate_multihetsep.py HOT 1
- using the phased-vcf files as input for MSMC2 HOT 1
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