Error : mixcr line 215: 20652 Killed $java -Dmi.license.file="$dir/mi.license" -D${app}.path="$dir" -D${app}.command=${app} "${javaArgs[@]}" -jar "$jar" "${appArgs[@]}"

[liu9756]

Hi! I use mixcr analyze 10x-sc-xcr-vdj command to process my files, however, in refineTagsAndSort section, I am informed that /users/PAS2177/liu9756/mixcr/mixcr: line 215: 20652 Killed $java -Dmi.license.file="$dir/mi.license" -D${app}.path="$dir" -D${app}.command=${app} "${javaArgs[@]}" -jar "$jar" "${appArgs[@]}"

The following is the command output:

` Average R1 nucleotides trimmed right: 8.506156640558773E-6 Tag parsing report: Execution time: 0ns Total reads: 205850900 Matched reads: 205850900 (100%) Projection +R1 +R2: 205850900 (100%) For variant 0: For projection +R1 +R2: CELL:Left position: 0 UMI:Left position: 16 CELL:Right position: 16 UMI:Right position: 26 R2:Left position: 0 Variants: 0 Cost: 0 CELL length: 16 UMI length: 10 R2 length: 101

mixcr refineTagsAndSort <<<<<<<<<<<<<<<<< Running: mixcr refineTagsAndSort --report results_10x.refine.report.txt --json-report results_10x.refine.report.json results_10x.vdjca results_10x.refined.vdjca Correction will be applied to the following tags: CELL, UMI Sorting will be applied to the following tags: CELL, UMI The following whitelist will be used for CELL: WhitelistFromAddress(address=builtin:737K-august-2016) Initialization: progress unknown Initialization: 0.9% Initialization: 11% ETA: 00:03:24 Initialization: 21.5% ETA: 00:10:16 Initialization: 22.6% ETA: 03:37:25 Initialization: 25.2% ETA: 01:35:36 Initialization: 27.4% ETA: 01:18:30 Initialization: 28.8% ETA: 01:56:00 /users/PAS2177/liu9756/mixcr/mixcr: line 215: 20652 Killed $java -Dmi.license.file="$dir/mi.license" -D${app}.path="$dir" -D${app}.command=${app} "${javaArgs[@]}" -jar "$jar" "${appArgs[@]}" [liu9756@owens-login04 NEW_BCR_S7]$ `

[mizraelson]

How much memory did you use? It seems like the process was killed due to the lack of RAM.

[liu9756]

100G

[liu9756]

I will try 200G

[mizraelson]

Sometimes for a very large datasets 100G might not be enough. Let's see if 200G will do.

[mizraelson]

Did it work?

[mizraelson]

I am gonna close it for now. Feel free to reopen.