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runtime and expected output #78
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Hi, the files in the output folder should probably be the temporary files (with suffix such as How many cells does the bam file contain? Sometimes it could take a long time for cellsnp-lite to genotype a big dataset, especially in mode 2a (i.e., to pileup whole chromosomes for 10x data). Could you also share your command line and the version of cellsnp-lite? Best, |
Hi, Best, |
The command line contains all the parameters you used to run cellsnp-lite, e.g.,
The 15,600 cells indicate the bam is probably a big 10x dataset. To speedup, you may
|
Ah ok, the command I used looks like this:
Yes indeed, it is a 10x dataset and I used the raw barcodes. |
For 15k cells, roughly how long did this take to run? |
hello, i ran cellsnp-lite, and it failed with"[E::idx_find_and_load] Could not retrieve index file for '/h/sunnan/VKHDATA/vkha/gex_possorted_bam.bam'", what should i do next? thank you very much! |
Hi,
I ran cellsnp-lite with one bam file. It is now already running since 3 weeks. I was wondering if this is to be expected.
Is there somewhere any information on the expected output files? There are already several files in my output folder and I am not sure if the program is actually already finished and it just appears as still running.
Best,
Anne
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