Bekah W
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Activity overview
Latest activity by Bekah W-
Bekah W commented,
Yes this runs now! Apologies again entirely my fault!
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Bekah W commented,
Oh yes sorry ... I ran an older script version I had tested previously, the modified version has .0 added! I'll see if this one works with the file! Sorry again!
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Bekah W commented,
Ah okay thank you! That makes sense I will see what happens. It ran okay with the second option so i continued with that. However I am now having issues with the filtering variants! I passed the ou...
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Bekah W commented,
I tried this and it gave the same output even with a smaller number of input files. I've contacted my IT support to see if it is something integral. thank you for your quick response.I also tried r...
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Bekah W commented,
I tried this yesterday but got a java heap error now and no out put at all Using GATK jar /opt/gridware/depots/54e7fb3c/el7/pkg/apps/gatk/4.2.2.0/noarch/gatk-4.2.2.0/gatk-package-4.2.2.0-local.jarR...
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Bekah W commented,
Out temp directory created has: Directory: NC_027300.1$1$159038749 which contains : __0172b34e-004a-4f6e-8a11-62c90f8df98e140159776184064_1638273785929 and genomicsdb_meta_dir directoriesas well as...
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Bekah W commented,
Is this te stacktrace? Paths edited for confidentialityUsing GATK jar /opt/gridware/depots/54e7fb3c/el7/pkg/apps/gatk/4.2.2.0/noarch/gatk-4.2.2.0/gatk-package-4.2.2.0-local.jarRunning:java -Dsamjdk...
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Bekah W commented,
Command is in the original post?What do you mean by more info about the output? and what is the stacktrace?
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Bekah W commented,
I reuploaded the files and it ran to completion using just --intervals NC_027300.1 as a test with three files but the output gives nothing under the headers in the resulting file#CHROM POS ID REF A...
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Bekah W commented,
I tried using the NC that is the name of the chr but it gave the same error - was just simpler to write Chr in the post as an example SN:NC_027300.1