Valerie Crolley
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Activity overview
Latest activity by Valerie Crolley-
Valerie Crolley commented,
Hi, Sorry it's been so long, but my local HPC has been down for some time. For future reference, I managed to solve the issue - turns out that I had to manually set --tmp-dir as part of SplitNCigar...
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Valerie Crolley commented,
Hi, Thank you for your help. I've tried running SplitNCigarReads with GATK 4.4.0.0 but I'm still having issues. I get the error: htsjdk.samtools.util.RuntimeIOException: Problem writing temporary...
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Valerie Crolley commented,
Hi, Apologies for the late reply, I've just come back from an overseas conference and it turns out that the replies from the RC Support at my institution were going missing before I could receive ...
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Valerie Crolley commented,
Hi, Sorry for the late reply, I was on call this weekend. I am trying your new commands, and I will let you know if they fix the issue. I'll need to ask to find the answers about the HPC, but I kn...
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Valerie Crolley commented,
Hi Gökalp Çelik, I've uploaded the script, output file and one of the BAMs to the FTP server. Apologies, I couldn't get the snippet to work properly, so I've uploaded the whole BAM. The file is GAT...
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Valerie Crolley commented,
I just checked, and it's not stopping at the exact same place: Third run (same parameters as second run: 18:59:35.971 INFO ProgressMeter - chr7:72982428 97.4 2560280...
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Valerie Crolley commented,
Hi Gökalp Çelik, Thank you for your continued help with this. I'm still waiting to see if I can get access to a newer version of GATK, but in the meantime: 1. I'm using nfcore rnaseq version 3.12.0...
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Valerie Crolley commented,
Hi Gökalp Çelik I'm still waiting to hear about the installation of GATK 4.4.4.0, but I've tried adding your command. It still isn't working, but I get a different error message: 19:14:21.776 INFO ...
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Valerie Crolley commented,
Hi Gökalp Çelik, Thank you for getting back to me. I agree; I don't think the input files are the issue. I've tried running a single file with a specified large --tmp-dir but I'm having the same is...
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Valerie Crolley commented,
Hi Gökalp Çelik, Thank you for getting back to me. This happens with all of my samples (I have 128 in total). It happens at a different point on each sample, and all of them when running simultane...