java problem with mixcr

[eprieto012]

Hi guys,

I am trying to run MIXCR but I encountered an error related to Java or a missing file. This error is being replicated on different nodes of the cluster too.

Do you have any idea how I can solve it? I have attached the script and the two outputs (.log and .err) up to the point of failure.

Any help would be much appreciated.

Thank you,
Endika

R-MIXCR_sample1.176786.err.txt
R-MIXCR_sample1.176786.log.txt
script_1.slurm.txt

[mizraelson]

HI, can you please try running the latest develop version?

[eprieto012]

I run the latest develop version, but the pipeline stops in the QC step and reports the attached errors.

R-MIXCR_sample1.179010.out.txt
R-MIXCR_sample1.179010.err.txt
script_1.slurm.txt

[mizraelson]

What command do you run?

[eprieto012]

docker run --rm
-e MI_LICENSE="E-VRKEGFHFHNBQIFCUJZOTZPNQISODMMGKRROTCOLBAOTTAOKA"
-v /mnt/petasan_immuno/raw_data/public/braun_et_al/tcrb:/raw:ro
-v /mnt/bioinfnas/immuno/eprieto/mixcr/sample1:/work
ghcr.io/milaboratory/mixcr/mixcr:4.7.0-169-develop
mixcr analyze generic-amplicon-with-umi
--species hsa
--assemble-clonotypes-by CDR3
--export-productive-clones-only
--rna
-f
--tag-pattern '^(R1:)(UMI:N{7})(R2:)'
-Massemble.consensusAssemblerParameters=null
-Massemble.cloneAssemblerParameters.addReadsCountOnClustering=true
--floating-left-alignment-boundary
--floating-right-alignment-boundary C
/raw/SRR31327102_1.fastq
/raw/SRR31327102_2.fastq
work/SRR31327102 \

[mizraelson]

The issue is because you set -Massemble.consensusAssemblerParameters=null. Can you tell more about the library structure? Why do you want to turn the consensus assembler off?

You can also add --remove-step qc and it should work.