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ExpressionAnalysis / STAR-SEQR

RNA Fusion Detection and Quantification
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STAR alignment not working #32

Open anoronh4 opened 1 year ago

anoronh4 commented 1 year ago

I am running STAR-SEQR from the fastqs and getting this error:

2023-01-31 22:26 - ERROR - 
EXITING because of fatal PARAMETER error: --outSAMattributes contains ch tag, which requires BAM output.
SOLUTION: re-run STAR with --outSAMtype BAM Unsorted (and/or) SortedByCoordinate option, or without ch tag in --outSAMattributes

Jan 31 22:26:06 ...... FATAL ERROR, exiting

gzip: stdout: Broken pipe

gzip: stdout: Broken pipe

2023-01-31 22:26 - ERROR - Error: STAR failed
None

My version of STAR is 2.7.9a. Seems like STAR doesn't like --outSAMattributes to contain ch when --outSAMtype None is specified (but i would think it doesn't like any outSAMattributes when not producing a bam). just wondering what's the best way to deal with this or if there's any plans to update STAR-SEQR to work with newer versions of STAR.

zgtman commented 5 months ago

Hello,

did you please solve this issue? I have the same problem (even with latest version of STAR - 2.7.11a)

2024-03-15 15:01 - ERROR - b'\nEXITING because of fatal PARAMETER error: --outSAMattributes contains ch tag, which requires BAM output.\nSOLUTION: re-run STAR with --outSAMtype BAM Unsorted (and/or) SortedByCoordinate option, or without ch tag in --outSAMattributes\n\nMar 15 15:01:07 ...... FATAL ERROR, exiting\n'
2024-03-15 15:01 - ERROR - Error: STAR failed

Best,

Paul