Warning message Query V350183366L1C005R01400986149/1 is marked as paired, but its mate does not occur next to it in your BAM file. Skipping.

[yc508]

Hi, I got the following a lot of the following warning message. How should I fix it?

*****WARNING: Query V350183366L1C005R01400986149/1 is marked as paired, but its mate does not occur next to it in your BAM file. Skipping.

This is the code I used

scTEATAC -i day1.bam \ -x mm39.te.atac.idx \ --hdf5 True \ -o day1_atac_scte \ -UMI True -CB True

[yc508]

And I recieved this message at the end. INFO : Calculating expression... 2024-02-19 13:33:48 INFO : Detect 0 cells expressed at least 0 genes, results output to day1_atac_scte.csv INFO : Finished calculating expression 2024-02-19 13:33:48 INFO : Done with 0d 0h 50m 16s

A view of my bam file is as following. Thank you! V350183366L3C006R00700609834/1 99 chr1 3050058 60 50M = 3050082 74 GAATAGAAATAGATCTATCAGAGATATTGTCAGGACCCGAAAGAAATGAA IFFAIIGII:I*I<9IIICGII2D6I=EIIIIIIIBI>I2IIGDIIIAIE NM:i:1 MD:Z:11C38 CB:Z:CCGAGGTTGGAATTCTAATT V350183366L4C004R06501327210/2 163 chr1 3050060 60 50M = 3050131 121 ATAGAAATATATCTATCAGAGATATTGTCAGGACCCGAAAGAAATGAAAC IIIIGIIEIIIIIIIIIIIIIIHIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 MD:Z:9C40 CB:Z:GGAGTACGTATTCTCCAGCG V350183366L4C005R02800325551/2 163 chr1 3050074 60 50M = 3050087 63 ATCAGAGATATTGTCAGGACCCGAAAGAAATGAAACCCAAAGTGGAGGTC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 MD:Z:50 CB:Z:TACGAAGTGCCAGGAACGAG V350183366L3C006R00700609834/2 147 chr1 3050082 60 50M = 3050058 -74 TATTGTCAGGACCCGAAAGAAATGAAACCCAAAGTGGAGGACCACTAGTG IIIIIEIIII9FI@I?IAIEGA=IIBA?BIIIEI1IIFIIIIII NM:i:1 MD:Z:40T9 CB:Z:CCGAGGTTGGAATTCTAATT V350183366L4C005R02800325551/1 83 chr1 3050087 60 50M = 3050074 -63 TCAGGACCCGAAAGAAATGAAACCCAAAGTGGAGGTCCACTAGTGAGTAT IIIIIIIIIIIIIIHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 MD:Z:50 CB:Z:TACGAAGTGCCAGGAACGAG

[jphe]

You need to sort the bam file by name to get paired reads next to each other before run scTEATAC