Hello, I am running the chipseq pipeline, and my command

nextflow run nf-core/chipseq --input /home/ludzkia/miniconda3/envs/ChIPseq/UtyChIPseqAugust/nfcore/samplesheet.csv --fasta /hpc/home/ludzkia/Genome_files/GRCm39.primary_assembly.genome_copy.fa.gz --gtf /hpc/home/ludzkia/Genome_files/GENCODE_comprehensiveGeneAnnotation_M35_CHR.gtf --save_reference --blacklist /hpc/home/ludzkia/Genome_files/mm9-blacklist.bed.gz --three_prime_clip_r1 1 --three_prime_clip_r2 1 --trim_nextseq 20 --save_trimmed --narrow_peak --macs_fdr 0.05 --macs_gsize 2654621783 --min_reps_consensus 2 --save_macs_pileup --skip_diff_analysis --outdir /home/ludzkia/miniconda3/envs/ChIPseq/UtyChIPseqAugust/nfcore -profile cedars -r 2.0.0

threw the error: fromIndex = -1 or in the log: ERROR nextflow.extension.OperatorImpl - @unknown java.lang.IndexOutOfBoundsException: fromIndex = -1 I am using the workflow profile cedars I am using Nextflow version 24.04.4, build 5917 (01-08-2024 07:05 UTC)

// nextflow.config
process.clusterOptions = '-S /bin/bash'
env {
  TMPDIR="/scratch/ludzkia/"
}

I can see that the pipeline failed somewhere during alignment filtering, because there are no files in bwa/library. There are files in bwa/mergedLibrary for 2 of my 4 samples, and none of them have the final filename pattern .mLb.clN.* (though two of four samples in bwa/mergedLibrary/samtools_stats have this name pattern). I couldn't find anything when I googled this error! Can anyone advise what might be happening? Thanks!

Hi, might be that your samples name are not correctly formatted take a look to this thread 👉🏻 https://nfcore.slack.com/archives/CFP55NZ5G/p1702477213906759 We are about to release and this will be fixed as we won’t remain anymore in encoding information in the sample names but the user would need to provide it explicitly in the samplesheet

Thanks, Jose!! Will investigate - I promise I searched the error here in slack and this didn't come up! Fingers crossed...

No worries, slack is not the best place to find out previous conversations 😓 🤞🏻