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Hi,
I updated the gemini as I saw in the related posts, but still getting the error as following:
Thanks for the help!
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Traceback (most recent call last):
File "/home/mn/local/share/bcbio/ana…
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I have finished the regular cancer somatic variants analysis for tumor-normal paired samples. But now I need to get CNV structural variants. Can I just input the svcaller: [lumpy, cnvkit] in the algor…
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Excluding sites in `launch_varscan` is broken. Needs to be reimplemented.
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Hi Brad,
This is probably non a major Issues but, I have noticed for pair Tumor/Normal pair some caller first place the Normal and other Place the Tumor sample in the vcf.
Freebayes, Mutect2, vardic…
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glob patterns in run-batch.py don't cover all cases (line 46 in dispatch function). Some studies seem to include two types of files for each caller. glob pattern is likely too simple, may need to re…
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Hi Brad,
My aim is to get variants called for my two bam files( I think you have heard this a lot). But I am facing the with the following error. As I check the previous entries about this error, it …
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I've been running tumor/normal paired exome cases through our bcbio pipeline and a couple weeks ago, without intentionally changing any settings, the runs went from taking 4 hours to ~37 hours! The al…
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`snpEff` gave me an error related to coordinates. Changing `LC_ALL` from `en_US.utf8` to `C` fixed this. The issue might relate to a use of GNU `sort`. Perhaps we can set `LC_ALL` to `C` for just the …
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It seems I can't run my bcbio pipeline, when I'm trying to resume a job that failed previously. It fails with the "The cluster startup timed out. This could be for a couple of reasons. ..." message. T…
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Hi Brad;
I believe I am one step away for the implementing scalpel + variants callers to the Icgc Data. I am gonna do this !! :) .On my latest run, I tried to include pindel and scalpel (on separate …