User: Merope

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Merope0
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Posts by Merope

<prev • 7 results • page 1 of 1 • next >
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Comment: C: JBrowse tool crashes on VCF files w/ "No such file or directory" -> dependency i
... I haven't tried copying but looking back on it what I did made little sense in the first place. I may still try it later though. Thanks for the suggestion. As for the region, it should not matter, as an empty region should not look like a neverending series of red error panels. Here is what it look ...
written 16 days ago by Merope0
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Comment: C: JBrowse tool crashes on VCF files w/ "No such file or directory" -> dependency i
... Ok you're confirming that I had no idea what I was doing :'D Thanks for the info! But then would you agree that getting an error because x.vcf and x.vcf.tbi are missing doesn't make sense? ...
written 19 days ago by Merope0
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Comment: C: General question regarding tool dependency
... Hello, I'm having the same issue, 18 months later. Admin tool deps page says conda installed samtools for bowtie2 but it's still not found at runtime and my jobs crash miserably. Have you had any updates on the issue since then? Have you found any solution to this? Or are you still scratching your ...
written 7 weeks ago by Merope0
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Comment: C: JBrowse tool crashes on VCF files w/ "No such file or directory" -> dependency i
... Ok, no. I definitely don't get it. Why is it looking for non bgzip'ed files? How does a .vcf.tbi file make sense? ...
written 3 months ago by Merope0
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Comment: C: JBrowse tool crashes on VCF files w/ "No such file or directory" -> dependency i
... Update: still doesn't work. VCF tracks display 404 errors, because the following files are missing int he results: - 1670cbf6e5390abdaeb29b71ad82f70b_0.vcf.tbi - 1670cbf6e5390abdaeb29b71ad82f70b_0.vcf Manually did the following as a desperate shot in the dark: ln -s 1670cbf6e5390abdaeb29b7 ...
written 3 months ago by Merope0
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Answer: A: JBrowse tool crashes on VCF files w/ "No such file or directory" -> dependency i
... Ok, a keener eye than mine managed to spot something in the strace output: [...] execve("/galaxy-central/database/dependencies/_conda/envs/mulled-v1-4f60687598c40f0675c7de956d89c6ebcb6abb8d1faef576907dbea7330e0778/bin/bgzip", ["bgzip", "data/raw/1670cbf6e5390abdaeb29b7"...], [/* 108 var ...
written 3 months ago by Merope0
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JBrowse tool crashes on VCF files w/ "No such file or directory" -> dependency issue?
... Hello, I'm using the JBrowse tool maintained by iuc, but trying to visualize VCF files makes it crash. It looks a lot like a missing dependency (much like [here][1], [here][2], [here][3] and [here][4]), but they're all satisfied. Also, it mentions freebayes which is not in the dependency list. Coul ...
vcf jbrowse software error written 3 months ago by Merope0 • updated 16 days ago by Jennifer Hillman Jackson23k

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Scholar 3 months ago, created an answer that has been accepted. For A: JBrowse tool crashes on VCF files w/ "No such file or directory" -> dependency i

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