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NCI-RBL / iCLIP

RNA Biology Pipeline to Characterize protein-RNA Interactions
https://rbl-nci.github.io/iCLIP/
MIT License
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seedPerwindowNmax bug in STAR #116

Closed slsevilla closed 2 years ago

slsevilla commented 2 years ago

Getting the following error with align

BUG: iA>=P.seedPerWindowNmax in stitchPieces, exiting

Command used: 

STAR --runMode alignReads --genomeDir /data/CCBR_Pipeliner/iCLIP/index/active/2022_0505/mm10/index --sjdbGTFfile /data/CCBR_Pipeliner/iCLIP/index/active/2022_0505/mm10/ref/gencode.vM23.annotation.gtf --readFilesCommand zcat --readFilesIn /data/RBL_NCI/Wolin/mESC_clip_4_v2.0/01_preprocess/01_fastq/Ro1hrCyt_Clip.fastq.gz --outFileNamePrefix /lscratch/41436806/Ro1hrCyt_Clip_ --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --alignEndsType Local --alignIntronMax 50000 --alignSJDBoverhangMin 3 --alignSJoverhangMin 5 --alignTranscriptsPerReadNmax=10000 --alignWindowsPerReadNmax=10000 --outFilterMatchNmin 15 --outFilterMatchNminOverLread 0.9 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --outFilterMultimapNmax 10000 --outFilterMultimapScoreRange 0 --outFilterScoreMin 0 --outFilterType Normal --outSAMattributes All --outSAMunmapped None --outSJfilterCountTotalMin 3 1 1 1 --outSJfilterOverhangMin 30 12 12 12 --outSJfilterReads All --seedMultimapNmax=10000 --seedNoneLociPerWindow=20 --seedPerReadNmax=10000 --seedPerWindowNmax=10000 --sjdbScore 2 --winAnchorMultimapNmax=10000

file location: /data/RBL_NCI/Wolin/mESC_clip_4_v2.0/log/20220609_1150/05_star.41436806.sp=Ro1hrCyt_Clip.err

slsevilla commented 2 years ago

Issue has been brought up in STAR: https://github.com/alexdobin/STAR/issues/1583

slsevilla commented 2 years ago

Currently the seedPerWindowNmax is set to 10000. After researching this error, this is likely too high a value. Going to attempt to lower the window and see if this clears the issue.

Setting seedPerWindowNmax to 5000 in project: /data/RBL_NCI/Wolin/mESC_clip_4_v2.0

NOTE: two samples completed with the original max value of 10,000. If new value works, will need to re-run these samples

slsevilla commented 2 years ago

Decreasing seedPerWindowNMax to 5000 did not fix the error for all samples. Two additional samples did complete alignment.

Error still appears:

BUG: iA>=P.seedPerWindowNmax in stitchPieces, exiting
Jun 16 16:45:28 ...... FATAL ERROR, exiting

Sample Summary

ACTION: To attempt to complete alignment, the parameter will be decreased to 1000 in the remaining samples

slsevilla commented 2 years ago

Decreasing seedPerWindowNMax to 1000 did not fix the error for any samples.

Error still appears:

BUG: iA>=P.seedPerWindowNmax in stitchPieces, exiting
Jun 17 10:10:29 ...... FATAL ERROR, exiting

ACTION: To attempt to complete alignment, the parameter will be decreased to the default (50) in the remaining samples.

slsevilla commented 2 years ago

Decreasing seedPerWindowNMax to default (50) did not fix the error for any samples.

ACTION: To attempt to complete alignment, the parameter will be decreased to 10 in the remaining samples.

slsevilla commented 2 years ago

Error was resolved in two samples:

Samples finished with 10000

Samples finished with 5000

Samples finished with 10 Ro7hr_Clip Ro1hr_Clip

Samples still failing Ro1hrNuc_Clip Ro1hrCyt_Clip Ro7hrNuc_Clip Ro7hrCyt_Clip

ACTION: To attempt to complete alignment, the parameter will be decreased to 5 in the remaining samples.

Setting seedPerWindowNmax to 5 in project: /data/RBL_NCI/Wolin/mESC_clip_4_v2.0

slsevilla commented 2 years ago

resolved by decreasing the anchor while also decreasing the seed, keeping it above the minimum default value of 50

completed with commit d485f583aff422e4434de1edd57ba7ee37bee0fa & commit 360a77285b186b7a48a778afe36b509629dabfc9