empty files

[isadeghi87]

Hi,
I'm running redeemV on 10x scRNA/ATAC from human but I get this error and files are empty.
what could be the issue?

rror in read.table(RawGenotypesFile) : no lines available in input Execution halted Traceback (most recent call last): File "/home/i439h/projects/heroes-aya-pools/AG_Thongjuea/Software/bulkWGS/Sadeghi/redeemV/REDEEM-V/mitoConsensus//RemoveStrandBias.py", line 16, in <module> with open(StrandBiaseBlackList_file) as f: FileNotFoundError: [Errno 2] No such file or directory: '/home/i439h/projects/heroes-aya-pools/AG_Thongjuea/Result/bulkWGS/mitochondria/redeem/pool3/final/StrandBiaseBlackList'

Best
Iman

[isadeghi87]

@chenweng1991 any idea?

[dstyaaaaaa]

Hi, I ran the test data and got the same problem and I wonder why. I ran the test code in get started following a consistent process and got the following results. However due to device limitations I only used 12 threads and was unable to use bsub， but I think this may have had no effect on the results.
Here are my results.

And here are log files below:
Tutorial_MT-QCplot is consistent of the manuscript

Parse barcode has no contents in log file.
variant prepare

variant calling

concat

@chenweng1991 your comment will be very helpful to us. Thanks!

[dstyaaaaaa]

But there is another issue to note, I don't get an error reported when I run redeemV, but the BlackList I get is indeed empty and the bias plot is different. The current data is able to be read into redeemR, but it has 0 variants after filtering using default parameters.
Fig like these:


Hoping you can help me to solve the problem. Very Thanks!
Shitong

[chenweng1991]

Hi @dstyaaaaaa:

Thanks for your comments! What you showed is expected. The test data is very small (a tiny chunk from real data so that it is fast enough for trouble shooting) and therefore the results itself is expected to be almost empty. But as long as it can general all files as you showed, it is good. The purpose of this test is to examine if the pipeline can run through. Based on what you showed, it is all set and you can use the same code to run a real data(eg, actual dataset can be downloaded from here GSE219015)

Hope this answer helps.

Hi @isadeghi87: Hope the above comments and discussions are also helpful for your previous question. Sorry for the delayed response. Please let me know if you have any remaining questions.

Best regards
Chen

[dstyaaaaaa]

Oh, so it is! Very thanks for your reply!

[isadeghi87]

@chenweng1991 I ran it on read data and I continue to get that errror. Also, the output files are as following which are empty:

[isadeghi87]

here is my preprocess code

`module load python/3.10.1

redeem=/home/i439h/projects/heroes-aya-pools/AG_Thongjuea/Software/bulkWGS/Sadeghi/redeemV/REDEEM-V
MyMultiome=$redeem/MyMultiome/
mitoConsensus=$redeem/mitoConsensus/

fasta="/home/i439h/projects/heroes-aya-pools/AG_Thongjuea/Code/10x_multiomics/Sadeghi/Demultiplexing/references/hg38/genome.fa"
bam=/home/i439h/projects/heroes-aya-pools/AG_Thongjuea/Result/10x_multiomics/CellRanger_ARC/1016715_pool3_hg38/outs/atac_possorted_bam.bam
WD=/home/i439h/projects/heroes-aya-pools/AG_Thongjuea/Result/bulkWGS/mitochondria/redeem/pool3
#barcode=/home/i439h/projects/heroes-aya-pools/AG_Thongjuea/Result/10x_multiomics/CellRanger_ARC/1016715_pool3_hg38/outs/filtered_feature_bc_matrix/barcodes.tsv.gz
barcode=/home/i439h/projects/heroes-aya-pools/AG_Thongjuea/Code/bulkWGS/Sadeghi/mgatk/barcodes.tsv
mkdir -p $WD

Threads=24

python3.10 $mitoConsensus/Preprocess.py -i $bam
-c $Threads
-b $barcode
-o $WD
-bt BC
-sd $mitoConsensus`

[chenweng1991]

Hi @isadeghi87: Have you tried running through the pipeline using example files?
Seems like you are trying to start with Cell ranger output bam files? If that's the case you may want to check the barcode string in your bam file, I believe -bt should be CB with Cellranger. Let me know if this helps

Chen