CELLRANGER VDJ PIPELINE ERROR: cannot find the fastq files at the location, check if the lanes are properly named, the location is correctly mentioned

Question

[Kimaya]

Hello,i sequenced two samples with 10x genomics and I have got the fastq files.

I got the following from the person who did mkfastq analysis:

1_RED_S1_L001_I1_001.fastq
1_RED_S1_L001_I1_001.fastq.gz
1_RED_S1_L001_R1_001.fastq.gz
1_RED_S1_L001_R2_001.fastq.gz
2_GREEN_S2_L001_I2_001.fastq.gz
2_GREEN_S2_L001_R2_001.fastq.gz

Now, I aim to further run cellranger vdj on these fastq files to get the output files to analyze the clonotypes. I already ran cellranger vdj for one set of sample (1_RED) using university cluster but for the other set '2_GREEN' i am getting error of 'fastq not found', or 'check if the file is correctly named' etc.

I cant think of any reason for this as the files are correctly named, i am giving the correct path and there are no other files in the folder containing these files. The only reason i can think about is that the 2_GREEN sample does not have the R1 file. which is strange. Is it because of that? Since it is a paired end analysis, i would expect R1 file for GREEN sample as well. I am new to this whole analysis, any help to solve the error would be appreciated

[GenoMax]

Is it because of that?

Yes. If that is the entire list of files you seem to be missing files and potentially have incorrect names.

For 2_GREEN e.g. 2_GREEN_S2_L001_R1_001.fastq.gz is missing. Also you seem to have 2_GREEN_S2_L001_I2_001.fastq.gz. Should that file be called I1, if 1_RED sample worked with files you have?

[Kimaya]

Thanks a lot for your reply! I will contact the concerned person to enquire about the missing mkfastq output. I am not sure about if the Green file should be I1 instead of I2 for it to work.