Hi everyone! My name is Taimor I am a bioinformatics RA at BCH. I am trying to run Nextflow chipseq pipeline for some of the researchers in my lab and am encountering some issuses. Currently the error i’m getting is related to the sample sheet i don’t understand how to make it. I’m currently using,

(env_nf) **\[**\~/Nextflow**\]**

taimor**@**RDT01154 $ cat chengxin_samplesheet.csv
sample,fastq_1,fastq_2,replicate,antibody,control,control_replicate
WT_BCATENIN_IP,/storage2/researchers/chengxian/ChIP_seq/AltN468/trimmed_fastq/CXL1239_R1.trimmed.fastq.gz,,1,BCATENIN,WT_INPUT,1
WT_BCATENIN_IP,/storage2/researchers/chengxian/ChIP_seq/AltN468/trimmed_fastq/CXL1239_R2.trimmed.fastq.gz,,2,BCATENIN,WT_INPUT,2

and the error i get is,

Command output:

  ERROR: Please check samplesheet -> Control identifier and replicate has to match a provided sample identifier and replicate!

  Control: 'WT_INPUT_REP1'

Command error:

  WARNING: Skipping mount /usr/local/var/singularity/mnt/session/etc/resolv.conf \[files\]: /etc/resolv.conf doesn't exist in container

  ERROR: Please check samplesheet -> Control identifier and replicate has to match a provided sample identifier and replicate!

  Control: 'WT_INPUT_REP1'

The exact command i run is,

nextflow run nf-core/chipseq \\
    -profile singularity \\
    --input chengxin_samplesheet.csv \\
    --outdir chengxin_out \\
    --fasta /storage/genomes/mm9_AJ851868ins/mm9_AJ851868ins.fa \\
    --gtf /storage/genomes/mm9_AJ851868ins/annotation/genes.mm9_AJ851868ins.gtf \\
    --read_length 100 \\
    --save_reference

I am new to this as this is my 1st time any help would be appreciated! I understand the problem is my sample sheet but I don't understand how to make a correct 1. both the fastq are WT. The 1st is read 1 the 2nd is read 2 best, Taimor

Hi Taimor, It looks like a simple fix. The sample names indicate that the files are of the same sample, and they are just paired reads. So, the contents of the samplesheet should be as follows:

sample,fastq_1,fastq_2,replicate,antibody,control,control_replicate
WT_BCATENIN_IP,/storage2/researchers/chengxian/ChIP_seq/AltN468/trimmed_fastq/CXL1239_R1.trimmed.fastq.gz,/storage2/researchers/chengxian/ChIP_seq/AltN468/trimmed_fastq/CXL1239_R2.trimmed.fastq.gz,1,BCATENIN,WT_INPUT,1

Thanks for the help! I tried the new sheet and am getting, """ Command output: ERROR: Please check samplesheet -> Control identifier and replicate has to match a provided sample identifier and replicate! Control: 'WT_INPUT_REP1' ERROR: Please check samplesheet -> Control identifier and replicate has to match a provided sample identifier and replicate! Control: 'WT_INPUT_REP1' """ Is there like and office hour or someting i can join to talk with someone? Or if anyone is available to zoom I'd be very grateful.

Seems to me as you don't specify the control in the sample sheet, if you just copied muralis suggestion. Could you share your new manifest?

yes you're totally right, I got it tow ork by doing this, sample,fastq_1,fastq_2,replicate,antibody,control,control_replicate WT_CTCF_IP,CXL1240_R1.trimmed.fastq.gz,CXL1240_R2.trimmed.fastq.gz,1,CTCF,WT_INPUT,1 WT_INPUT,CXL1239_R1.trimmed.fastq.gz,CXL1239_R2.trimmed.fastq.gz,1,,, TY for help!!!!

Nice! Then happy peak calling