hi again,
my first trial was a success but for the...
# chipseqm
MervevK
05/28/2024, 5:57 PMhi again,
my first trial was a success but for the real run i an having problems. there was this specific sample: 3k27ac_ms_b_ENCSR364OIK.
At first it was giving error, so i redownloaded everything. all my 153 samples were uploaded and aligned but this time it gives a trimming problem. this is the error:
trimming : ERROR ~ Error executing process > 'NFCORE_CHIPSEQCHIPSEQFASTQC_TRIMGALORE:TRIMGALORE (h3k27ac_ms_b_ENCSR364OIK_T1)' Caused by: Process
NFCORE_CHIPSEQ:CHIPSEQ:FASTQC_TRIMGALORE:TRIMGALORE (h3k27ac_ms_b_ENCSR364OIK_T1)bash .command.runNFCORE_CHIPSEQ:CHIPSEQ:FASTQC_TRIMGALORE:TRIMGALORE (h3k27ac_ms_b_ENCSR364OIK_T1)bash .command.runMervevK
05/30/2024, 10:07 AMI excluded the sample which created the problem, but now, another one appeared. i re-downloaded and checked these samples. what could be wrong, do you have any suggestions please?
a
Ashley Dederich
05/30/2024, 6:33 PMWhat is your filename that you are inputting? ;Looks like you are not gzipping your input files per this error message:
Copy code
line 825, in run raise e gzip.BadGzipFile: Not a gzipped file (b'Fi') Cutadapt terminated with exit signal: '256'. Copy code
gzip filename.fam
MervevK
05/30/2024, 6:40 PMThank you so much for returning.
The file name h3k27ac_ms_b_ENCSR364OIK. The original files i downloaded were all gunzipped. All i did was concatanate to make them one file. Once i encountered this problem, i redownloaded them, and concatanated these new files from the beginning. So i am suspecting of some corruption of the files or there is a problem during upload of the inputs.
a
Ashley Dederich
05/30/2024, 6:41 PMIf they were all g-unzipped, then it sounds like you need to gzip the file (concatenated or not)
m
MervevK
05/30/2024, 6:43 PMI concatanated as they are gunzipped and all of them are. Interestingly only some of these files are giving problem. So far 60 of them gone without trouble
MervevK
05/30/2024, 6:49 PMwhen i re-gunzip this is the error: gzip: h3k27ac_ms_b_ENCSR364OIK.fastq.gz already has .gz suffix -- unchanged
a
Ashley Dederich
05/30/2024, 7:05 PMI think you are meaning to say gzipped? So your files end in .fastq.gz?
Ashley Dederich
05/30/2024, 7:08 PMCan you tell me exactly what input you are uploading and how you exactly prepared that input? Starting from your download command.
m
MervevK
05/30/2024, 7:17 PMthey are gzipped all the time, from download to uploading to input. they had never been ungunzipped. i downloaded, i concatenated, and i uploaded. that's all
a
Ashley Dederich
05/30/2024, 7:23 PMI guess I don't fully understand what you are doing - can you please provide your nextflow run nf-core/chipseq command that you are using?
m
MervevK
05/30/2024, 8:06 PMthe text which is attached is for the run. it worked perfectly for the 2 samples i tried.
if i need to explain what i had done so far:
i got the sequence such as this: wget https://www.encodeproject.org/files/ENCFF594QFH/@@download/ENCFF594QFH.fastq.gz
but every sample has 30-40 fastq.gz files, so i needed to concatenated them. i did concatenated each of them with cat command, then i put them under a folder.
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