How to fix MemoryError (f" bam file #{k} could not be sorted by cells. \n\ in run10x and run?

Hi there,

I encountered issue with “Out of memory” when I run10x in velocyto. Looking at the .err file returned from the server cluster, i had issues shown below.

MemoryError (f" bam file #{k} could not be sorted by cells. \n\ in run10x

It further says the error is probably related to an old version of samtools, please install samtools >= 1.6 but I checked and samtools version 1.10 was used.

It says to set the --samtools_memory option to a value compatible with my system. Otherwise sort mannually by samtools

sort -l [compression] -m [mb_to_use]M -t [tagname] -O BAM -@ [threads_to_use] -o cellsorted_[bamfile] [bamfile]

Anyone has any suggestion how to fix this error?

Thank you so much!

Commands I had in my sh script to run on our server cluster:

[AAA-3]

I can’t help with the GTF file - I don’T even know how you managed to edit it 😮

[denvercal1234GitHub]

Thank you all.

I finally got it to generate loom file. I think there were two main issues with the run10x:

• For my cluster which might be different for your cluster, do not create virtual environment. Just use the packages installed by the server administrators
• Ensure you have the directory of the count output as directiory that contains the outs folder.
• Ensure you have barcodes file as zip version and not unzipped!
• Ensure you have the right gtf (it should be one located in /genes/genes.gtf) and masked files downloaded correctly (do md5 checksum if needed).
• Ensure you do the manual sorting first of your bam file and that the cellsorted_possorted bam and the original bam.bai files are in the same directory

I wish everyone the best of luck! I managed to get it to generate a loom file, but when I examined the error log, it said “Could not retrieve index file for the cellsorted_possorted_genome_bam.bam.” – See issue #321

Any thoughts @cdiaz45 @AAA-3?