Kallisto output is missing abundance.h5 file (but contains tsv and run_info)

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Tanush Jagdish

Dec 21, 2020, 8:07:57 PM12/21/20
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Hi all,

I'm new to Kallisto. I used it to quantify a series of files with single end reads. ALL my output folders only have two files: abundance.tsv and run_info.json. There is no hdf5 output file (cannot find any abubdance.h5 file, which I'd need for analysis with sleuth).

One example of the script I wrote below. I just did this multiple times with different input fastq files, and the output folder each time was missing the hdf5 file.

 - kallisto quant -i transcripts.idx -o 4533_14 --single -l 300 -s 50 REL4533_14_S11_R1_001.fastq.gz

I just have two questions:
  1. Has anyone else had this problem? Am I doing something really stupid? 
  2. Could I use the tsv output files for downstream analysis with sleuth, or do I need to figure out how to get the missing h5 outputs?
Thank you so much. I'd really appreciate any help at all.


Jagdish, Tanush

Dec 21, 2020, 8:23:12 PM12/21/20
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When I run Kallisto, it displays the following warning:  Warning: kallisto was not compiled with HDF5 support so no bootstrapping
So it makes sense that .h5 files are not produced. Does anyone know how I could address this? Is it an issue with my laptop, or the version of Kallisto I installed?

Thank you again!!


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Lisa McEwen

Dec 22, 2020, 11:35:57 AM12/22/20
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Hi Tanush, 

If you build it from source, specify-DUSE_HDF5=ON when running cmake.


Modo C

Feb 3, 2021, 10:06:45 AM2/3/21
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Is it possible to convert the tsv to hdf5 after the fact?

fujun qin

Jul 8, 2022, 7:13:21 PM7/8/22
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I have same problem. How to specify -DUSE_HDF5=ON, what script or command should I use?

Thank you,

On Tuesday, December 22, 2020 at 11:35:57 AM UTC-5 lmce...@gmail.com wrote:

kalyan p

Aug 14, 2023, 6:40:26 AMAug 14
to kallisto and applications
I face the same issue could some one help 
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