filterCRs IndexError:list index out of range

[bio-xtt]

Hello! When I run the software according to the following code, there is an index error. How can I solve this problem? Here's my code:

step1:build index

scTE_build -g panTro6

step2: filter bam

samtools view possorted_genome_bam.bam -h | awk '/^@/ || /CB:/' | samtools view -h -b > possorted_genome_bam_CB.bam samtools view possorted_genome_bam.bam -h | awk '/^@/ || /UB:/' | samtools view -h -b > possorted_genome_bam_UB.bam

step3: TE count

scTE -i /work/xtt/data_input/fastq_out/Pan_troglodytes_C1_out/outs/possorted_genome_bam_UB.bam \ -o Pan_troglodytes_C1 \ -x /work/xtt/biosoft/scTE_ref/panTro6.exclusive.idx \ --hdf5 True -CB CB -UMI UB -p 40 echo "Pan_troglodytes_C1 done!"

The possorted_genome_bam_UB.bam file format is as follows:

The error message is as follows:

[jphe]

For step2, scTE requires the reads has both CB and UB tags.

How dose the Pan_troglodytes_C1_scTEtmp/o1 and Pan_troglodytes_C1_scTEtmp/o2 folder looks like, seems the format of *count.gz file under the Pan_troglodytes_C1_scTEtmp/o2 are incorrect.

[bio-xtt]

Hello, I used the above command to perform UB,CB filtering on bam, so my bam file should contain these two tags, o1,o2 directory structure is as follows:

[jphe]

What's the *count.gz file looks like?

[bio-xtt]

Hello, my count.gz and bed.gz formats are as follows:

[jphe]

I can't see any problem. Could you try using a different file? Maybe this error is specific to this file. Can you run scTE succssufully for the test.bam file under the scTE folder?

[bio-xtt]

I have a total of four samples, then all of them were quantified using cellranger atac, scTE for TE count, the other three were normal, only this sample data showed the following error

[jphe]

Yes, there are some hidden problems with this input file, I'm also not aware of what issues there might be