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linnarsson-lab / loompy

Python implementation of the Loom file format - http://loompy.org
BSD 2-Clause "Simplified" License
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Got error when running tutorial #172

Closed FionaMoon closed 1 year ago

FionaMoon commented 2 years ago

Hi, I'm learning how to use loompy. I download dataset from tutorial and run the following code. I got error but don't know why. 

loompy fromfq 1kPBMC.loom 1kPBMC \
    /LY_software/loompy_hg/human_GRCh38_gencode.v31.600 ../metadata.tab \
    pbmc_1k_v3_S1_L001_R1_001.fastq.gz pbmc_1k_v3_S1_L001_R2_001.fastq.gz \
    pbmc_1k_v3_S1_L002_R1_001.fastq.gz pbmc_1k_v3_S1_L002_R2_001.fastq.gz

Loompy v3.0.6 by Linnarsson Lab 🌸 (http://linnarssonlab.org & http://loompy.org)

2022-06-06 15:54:00,223 - INFO - Using 12 threads.
2022-06-06 15:54:00,270 - INFO - kallisto bus -i /xtdisk/fangxd_group/liangyue/LY_software/loompy_hg/human_GRCh38_gencode.v31.600/gencode.v31.fragments.idx -o /tmp/tmpg_61kzko -x 10xv3 -t 12 pbmc_1k_v3_S1_L001_R1_001.fastq.gz pbmc_1k_v3_S1_L001_R2_001.fastq.gz pbmc_1k_v3_S1_L002_R1_001.fastq.gz pbmc_1k_v3_S1_L002_R2_001.fastq.gz
2022-06-06 15:54:00,297 - INFO - Error: invalid command bus
2022-06-06 15:54:00,297 - INFO - kallisto 0.44.0
2022-06-06 15:54:00,297 - INFO - Usage: kallisto <CMD> [arguments] ..
2022-06-06 15:54:00,298 - INFO - Where <CMD> can be one of:
2022-06-06 15:54:00,298 - INFO -     index         Builds a kallisto index 
2022-06-06 15:54:00,298 - INFO -     quant         Runs the quantification algorithm 
2022-06-06 15:54:00,298 - INFO -     pseudo        Runs the pseudoalignment step 
2022-06-06 15:54:00,298 - INFO -     h5dump        Converts HDF5-formatted results to plaintext
2022-06-06 15:54:00,298 - INFO -     inspect       Inspects and gives information about an index
2022-06-06 15:54:00,298 - INFO -     version       Prints version information
2022-06-06 15:54:00,298 - INFO -     cite          Prints citation information
2022-06-06 15:54:00,298 - INFO - Running kallisto <CMD> without arguments prints usage information for <CMD>

I would be appreciate if anyone can help!

jsokol94 commented 1 year ago

I am encountering the same issue

jsokol94 commented 1 year ago

I suspect that this issue may be because we are using a too new version of kallisto? I am using kallisto version 0.44.0.

jsokol94 commented 1 year ago

I have an update: this error resulted from running a too old version of kallisto. Once I updated kallisto to a newer version, I was able to run it. The older version of kallisto didn't accept my sequencing technology, which led to that error message that you posted @FionaMoon .

pl-ki commented 1 year ago

Version >= 0.46.0 of kallisto is required. This will now be updated in the github doc. Thanks for pointing this out.