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Atal Saha

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Recent activity by Atal Saha Sort by recent activity Recent activity Votes
  • Thanks again, David. Re-calling started.   cheers Atal

  • Thanks very much, David.   I did manage to produce all my vcf files. Seemed using 20-30 gb memory was a good solution. However, I accidentally did not include -ERC GVCF option while running haploty...

  • Hi David, Thanks very much for your reply on this. Running Spark version was much faster, but I am worried about warning about this version (as it says that we should not use spark if we care about...

  • Hi Wondessen Ayalew, Did you get any support on this? I am having the same problem - it took a week to finish generating g.vcf for 1 sample. The command I used: /gpfs/gpfs0/software/rhel7/eucleia/g...

  • Thanks again, Louis! Answer to your questions: 1. it was silent exit with no clear error 2. Its monkfish data, whole genomes 3. inputs sorted by coordinates I have just given it up with Spark, as i...

  • Hi Louis, Thanks for your reply on this. The problem was initially solved by increasing Xmx20g to Xmx160g. However, my files are around 20GB each (and 60files in total) and so taking forever to fin...