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minoda-lab / universc

UniverSC: a flexible cross-platform single-cell data processing pipeline
https://genomec.gsc.riken.jp/gerg/UniverSC/UniverSC_app_release/
GNU General Public License v3.0
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BD-rhapsody data analysis #19

Closed g0656116 closed 9 months ago

g0656116 commented 11 months ago

I would like to analyze single cell RNASeq data obtained from BD using your Universc. The contents below describe the process from the installation of universc to the current running status.

universc installation

root@Song:/home/song# git clone https://github.com/minoda-lab/universc.git

Cloning into 'universc'... remote: Enumerating objects: 5307, done. remote: Counting objects: 100% (504/504), done. remote: Compressing objects: 100% (199/199), done. remote: Total 5307 (delta 318), reused 481 (delta 295), pack-reused 4803 Receiving objects: 100% (5307/5307), 299.91 MiB | 3.34 MiB/s, done. Resolving deltas: 100% (3400/3400), done. Updating files: 100% (215/215), done. Filtering content: 100% (44/44), 249.31 MiB | 3.13 MiB/s, done. Encountered 1 file that should have been a pointer, but wasn't: test/shared/cellranger-tiny-fastq/1.2.0/read-RA_si-TTTCATGA_lane-008-chunk-001.fastq.gz

BD-rhasody setup

song@Song:~/다운로드/universc$ bash launch_universc.sh -t "bd-rhapsody" --setup

cript running in /home/song/다운로드/universc/launch_universc.sh... ... script called from /home/song/다운로드/universc '.' resolves to '/home/song/다운로드/universc' Running launchuniversc.sh in '/home/song/다운로드/universc' UniverSC Copyright (C) 2019 Tom Kelly; Kai Battenberg This program comes with ABSOLUTELY NO WARRANTY; for details type 'cat LICENSE'. This is free software, and you are welcome to redistribute it under certain conditions; type 'cat LICENSE' for details. Cell Ranger is called as third-party dependency and is not maintained by this project. Please ensure you comply with the End User License Agreement for all software installed where applicable; for details type 'cat README.md'. Using 10x version 2 chemistry to support UMIs ***WARNING: conversion was turned on because directory input4cellranger was not found*** checking if UniverSC is running already creating .lock file

Input information

SETUP and exit: true WARNING: launch_universc.sh will exit once whitelist is converted FORMAT: bd-rhapsody BARCODES: /home/song/다운로드/universc/whitelists/bd_rhapsody_barcode.txt WARNING: no FASTQ files were selected, launch_universc.sh will exit after setting up the whitelist SAMPLE: LANE: ID: DESCRIPTION: WARNING: no description given, setting to ID value REFERENCE: NCELLS: (no cell number given) CHEMISTRY: SC3Pv2 JOBMODE: local WARNING: --jobmode "sge" is recommended if running script with qsub CONVERSION: true ##########

whitelist setup begin updating barcodes in /home/song/Cell_Ranger/cellranger-7.2.0/lib/python/cellranger/barcodes for Cell Ranger version cellranger-7.2.0 installed in /home/song/Cell_Ranger/cellranger-7.2.0/cellranger ... restoring Cell Ranger cp: cannot stat '/home/song/Cell_Ranger/cellranger-7.2.0/cellranger-cs/cellranger-7.2.0/lib/python/cellranger/webshim/template/navbar.html': No such file or directory cp: cannot stat '/home/song/Cell_Ranger/cellranger-7.2.0/cellranger-cs/cellranger-7.2.0/lib/python/cellranger/webshim/template/navbar.html': No such file or directory sed: can't read /home/song/Cell_Ranger/cellranger-7.2.0/cellranger-cs/cellranger-7.2.0/lib/python/cellranger/check.py: No such file or directory /home/song/Cell_Ranger/cellranger-7.2.0/cellranger set for bd-rhapsody converting whitelist barcode adjust: 0 whitelist converted verbose setup complete running in local mode (no cluster configuration needed) setup complete. exiting launch_universc.sh

analyze BD-rhasody(*.fastq)

song@Song:~/다운로드/universc$ bash launch_universc.sh --id "MJ" --technology "bd-rhapsody" --reference "test/cellranger_reference/cellranger-tiny-ref/3.0.0" --read1 "/home/song/Raw_data/NGS230926_S1_L001_R1_001" --read2 "/home/song/Raw_data/NGS230926_S1_L001_R2_001" --localcores 16 --localmem 64 script running in /home/song/다운로드/universc/launch_universc.sh... ... script called from /home/song/다운로드/universc '.' resolves to '/home/song/다운로드/universc' Running launch_universc.sh in '/home/song/다운로드/universc' UniverSC Copyright (C) 2019 Tom Kelly; Kai Battenberg This program comes with ABSOLUTELY NO WARRANTY; for details type 'cat LICENSE'. This is free software, and you are welcome to redistribute it under certain conditions; type 'cat LICENSE' for details. Cell Ranger is called as third-party dependency and is not maintained by this project. Please ensure you comply with the End User License Agreement for all software installed where applicable; for details type 'cat README.md'. /home/song/Raw_data/NGS230926_S1_L001_R1_001.fastq file found /home/song/Raw_data/NGS230926_S1_L001_R2_001.fastq file found Using 10x version 2 chemistry to support UMIs WARNING: conversion was turned on because directory input4cellranger_MJ was not found checking if UniverSC is running already creating .lock file

Input information

SETUP and exit: false FORMAT: bd-rhapsody BARCODES: /home/song/다운로드/universc/whitelists/bd_rhapsody_barcode.txt INPUT(R1): /home/song/Raw_data/NGS230926_S1_L001_R1_001.fastq INPUT(R2): /home/song/Raw_data/NGS230926_S1_L001_R2_001.fastq SAMPLE: NGS230926 LANE: 1 ID: MJ DESCRIPTION: MJ WARNING: no description given, setting to ID value REFERENCE: test/cellranger_reference/cellranger-tiny-ref/3.0.0 NCELLS: (no cell number given) CHEMISTRY: SC3Pv2 JOBMODE: local WARNING: --jobmode "sge" is recommended if running script with qsub CONVERSION: true ##########

whitelist setup begin updating barcodes in /home/song/Cell_Ranger/cellranger-7.2.0/lib/python/cellranger/barcodes for Cell Ranger version cellranger-7.2.0 installed in /home/song/Cell_Ranger/cellranger-7.2.0/cellranger ... restoring Cell Ranger cp: cannot stat '/home/song/Cell_Ranger/cellranger-7.2.0/cellranger-cs/cellranger-7.2.0/lib/python/cellranger/webshim/template/navbar.html': No such file or directory cp: cannot stat '/home/song/Cell_Ranger/cellranger-7.2.0/cellranger-cs/cellranger-7.2.0/lib/python/cellranger/webshim/template/navbar.html': No such file or directory sed: can't read /home/song/Cell_Ranger/cellranger-7.2.0/cellranger-cs/cellranger-7.2.0/lib/python/cellranger/check.py: No such file or directory /home/song/Cell_Ranger/cellranger-7.2.0/cellranger set for bd-rhapsody converting whitelist barcode adjust: 0 whitelist converted verbose setup complete running in local mode (no cluster configuration needed) creating a folder for all Cell Ranger input files ... directory input4cellranger_MJ created for converted files moving file to new location handling /home/song/Raw_data/NGS230926_S1_L001_R1_001.fastq ... handling /home/song/Raw_data/NGS230926_S1_L001_R2_001.fastq ... converting input files to confer cellranger format ... adjustment parameters: barcodes: 0 bp at its head UMIs: -2 bp at its tail making technology-specific modifications ... ... remove adapter and phase blocks for bd-rhapsody ... remove adapter and phase blocks for bd-rhapsody

Screenshot from 2023-12-25 16-45-06

If you look at the screenshot, it looks like something is going on. I'm not sure if this has stopped or is ongoing. Did something go wrong during the process? Please tell me what I should fix

kbattenb commented 11 months ago

Hi,

Due to IP issues, we cannot help you if cellranger-7.2.0 is used with UniverSC. Please try using the open access version of cellranger 3.0.2 instead. If you still run into problems, we can help you again.

Kai Battenberg