This is a test version of Biostars. For the public version, visit https://www.biostars.org.
STARsolo issue

Hello,

I'm performing STARsolo on fastq files and I'm using the reference genome from 10X genomics but I have this issu that I can't understand (the reference genome is indexed)

STAR version: 2.7.10b   compiled: 2022-11-01T09:53:26-04:00 :/home/dobin/data/STAR/STARcode/STAR.master/source
Mar 13 14:42:48 ..... started STAR run
Mar 13 14:42:48 ..... loading genome
EXITING because of FATAL ERROR: Genome version: 20201 is INCOMPATIBLE with running STAR version: 2.7.10b
SOLUTION: please re-generate genome from scratch with running version of STAR, or with version: 2.7.4a
Mar 13 14:42:48 ...... FATAL ERROR, exiting

this is the command line that I'm using:

/opt/conda/envs/scRNA/bin/STAR \
  --genomeDir /lab/user/bricks/reference/refdata-gex-GRCh38-2020-A/star \
  --readFilesIn R2.fastq.gz R1.fast.gz
  --soloType CB_UMI_Simple \
  --soloCBwhitelist /cellranger-7.1.0/lib/python/cellranger/barcodes/737K-arc-v1.txt \
  --soloUMIlen 12 \
  --soloCBlen 16 \
  --soloUMIstart 17 \
  --soloFeatures GeneFull
starsolo scrnaseq
• 2,786 views • link
written by friguiahlem8 • friguiahlem8

1 answer

Learning to read error messages is critical. Please read it, it even tells you the solution. It says SOLUTION: ....

• 0 views • link
written by ATpoint ATpoint

thank for your answer but it was wird for me that he asks to do the indexation. Anyway I performed the indexation process but now I have this type of error

Mar 13 16:05:42 ..... started STAR run
Mar 13 16:05:43 ..... loading genome
Mar 13 16:05:53 ..... started mapping
ReadAlignChunk_processChunks.cpp:204:processChunks EXITING because of FATAL ERROR in input reads: wrong read ID line format: the read ID lines should start with @ or > 
Offending line for read # 1
�BC�9��˒�:�d��+�l�] 
                    �zkղ����J6���%�s�"�u
�~w�vm�/<_���p�ޟ�ǯ�?��W;�_��    o/̏����'�>�z}��_,�s׶��ݮ���r���������_�����������z�����n�?���w���z<����?���z<�ϯ���������<�__��됚G�x���'xͫ�.���������������QM����s
                                                    ���k�ߚ
SOLUTION: verify and correct the input read files**

Mar 13 16:05:54 ...... FATAL ERROR, exiting

NB: my fastq files starts with "@" :/

• 0 views • link
updated by Ram Ram • written by friguiahlem8 • friguiahlem8

Your files are gzipped.

You need to add --readFilesCommand zcat

• 0 views • link
written by dsull dsull

Log in to answer this question.

More posts like this