CITE-seq-Count run gets stuck

[Layla-R]

Hello,

I am currently attempting to run CITE-seq-Count on my data, however, it appears to get stuck and not continue at a certain point during the run. Do you have any idea what could cause this?

Additional info: I am running this using a WSL, and the tags_KH33.csv file consists of 4 tags.

CITE-seq-Count -R1 /home/layla-r/CITE-seq/KH33/KH33_S1_R1_001.fastq.gz -R2 /home/layla-r/CITE-seq/KH33/KH33_S1_R2_001.fastq.gz -t /home/layla-r/CITE-seq/KH33/tags_KH33.csv -cbf 1 -cbl 16 -umif 17 -umil 28 -cells 3745 -wl /home/layla-r/CITE-seq/KH33/barcodes.tsv -o /home/layla-r/CITE-seq/KH33/

Loading whitelist
Loading whitelist
Counting number of reads
Started mapping
Processing 47,026,147 reads
CITE-seq-Count is running with 24 cores.
Processed 1,000,000 reads in 11.72 seconds. Total reads: 1,000,000 in child 549
Processed 1,000,000 reads in 17.77 seconds. Total reads: 1,000,000 in child 550
Mapping done for process 549. Processed 1,959,422 reads
Processed 1,000,000 reads in 23.83 seconds. Total reads: 1,000,000 in child 551
Mapping done for process 550. Processed 1,959,422 reads
Processed 1,000,000 reads in 29.73 seconds. Total reads: 1,000,000 in child 552
Mapping done for process 551. Processed 1,959,422 reads
Processed 1,000,000 reads in 36.01 seconds. Total reads: 1,000,000 in child 553
Mapping done for process 552. Processed 1,959,422 reads
Processed 1,000,000 reads in 42.18 seconds. Total reads: 1,000,000 in child 554
Mapping done for process 553. Processed 1,959,422 reads
Processed 1,000,000 reads in 48.52 seconds. Total reads: 1,000,000 in child 555
Mapping done for process 554. Processed 1,959,422 reads
Processed 1,000,000 reads in 54.22 seconds. Total reads: 1,000,000 in child 556
Mapping done for process 555. Processed 1,959,422 reads
Processed 1,000,000 reads in 1.0 minute, 1.701 seconds. Total reads: 1,000,000 in child 557
Mapping done for process 556. Processed 1,959,422 reads
Processed 1,000,000 reads in 1.0 minute, 7.854 seconds. Total reads: 1,000,000 in child 558
Mapping done for process 557. Processed 1,959,422 reads
Processed 1,000,000 reads in 1.0 minute, 14.77 seconds. Total reads: 1,000,000 in child 559
Mapping done for process 558. Processed 1,959,422 reads
Processed 1,000,000 reads in 1.0 minute, 22.07 seconds. Total reads: 1,000,000 in child 560
Mapping done for process 559. Processed 1,959,422 reads
Processed 1,000,000 reads in 1.0 minute, 36.4 seconds. Total reads: 1,000,000 in child 561
Mapping done for process 560. Processed 1,959,422 reads
Processed 1,000,000 reads in 1.0 minute, 46.89 seconds. Total reads: 1,000,000 in child 562
Mapping done for process 561. Processed 1,959,422 reads
Processed 1,000,000 reads in 2.0 minutes, 2.612 seconds. Total reads: 1,000,000 in child 563
Mapping done for process 562. Processed 1,959,422 reads
Processed 1,000,000 reads in 2.0 minutes, 11.76 seconds. Total reads: 1,000,000 in child 564
Processed 1,000,000 reads in 2.0 minutes, 27.29 seconds. Total reads: 1,000,000 in child 565
Processed 1,000,000 reads in 2.0 minutes, 43.36 seconds. Total reads: 1,000,000 in child 566
Mapping done for process 565. Processed 1,959,422 reads
Mapping done for process 563. Processed 1,959,422 reads
Mapping done for process 564. Processed 1,959,422 reads
Processed 1,000,000 reads in 2.0 minutes, 56.62 seconds. Total reads: 1,000,000 in child 567
Mapping done for process 566. Processed 1,959,422 reads
Processed 1,000,000 reads in 3.0 minutes, 4.829 seconds. Total reads: 1,000,000 in child 568
Processed 1,000,000 reads in 3.0 minutes, 13.85 seconds. Total reads: 1,000,000 in child 569
Mapping done for process 567. Processed 1,959,422 reads
Mapping done for process 568. Processed 1,959,422 reads
Mapping done for process 569. Processed 1,959,422 reads
Processed 1,000,000 reads in 3.0 minutes, 32.62 seconds. Total reads: 1,000,000 in child 570
Processed 1,000,000 reads in 3.0 minutes, 54.14 seconds. Total reads: 1,000,000 in child 571
Mapping done for process 570. Processed 1,959,422 reads
Processed 1,000,000 reads in 4.0 minutes, 3.777 seconds. Total reads: 1,000,000 in child 572
Mapping done for process 571. Processed 1,959,422 reads
Mapping done for process 572. Processed 1,959,441 reads

Thanks.

[Rimanpreet1]

Hi i have same issue, did you issue resolved

[Layla-R]

@Rimanpreet1 Hi, this issue has not been resolved.

[Hoohm]

Hello @Layla-R
For how long does it get stuck?
Can you try restricting the number of threads to 8?

[Layla-R]

Hi, I would let it run for hours hoping it would continue in the background, but it wouldn't.
I won't need it anymore for a while, but I will try to limit the threads next time I do :)