CIBERSORTxFractions ERROR: Could not read /src/outdir//temp.Fractions.simfracs.tsv

Question

[markddesimone]

Hello, can anyone offer any insight into the following problem? I am trying to run the following CIBERSORTx function locally:

docker run \
-v /media/mark/seagate2/data/CIBERSORTx_GC:/src/data \
-v /media/mark/seagate2/data/CIBERSORTx_GC:/src/outdir \
cibersortx/fractions \
--username <my_user_name> \
--token <my_token> \
--single_cell TRUE \
--refsample reference.txt \
--mixture rsem_mixture_TPM.tsv \
--fraction 0 \
--rmbatchSmode TRUE

I get the following output to the terminal:

>Running CIBERSORTxFractions...
>[Options] username: <my_user_name>
>[Options] token: <my_token>
>[Options] single_cell: TRUE
>[Options] refsample: reference.txt
>[Options] mixture: rsem_mixture_TPM.tsv
>[Options] fraction: 0
>[Options] rmbatchSmode: TRUE
Killed
ERROR: Could not read /src/outdir//temp.Fractions.simfracs.tsv
ERROR: Could not read /src/outdir//temp.Fractions.adj_save.tsv

I did not kill it, it terminated with this error. The files:

temp.Fractions.simfracs.tsv
temp.Fractions.adj_save.tsv

are indeed are not in the outdir. It was however able to write the following files to the outdir:

CIBERSORTx_cell_type_sourceGEP.txt
CIBERSORTx_reference_inferred_phenoclasses.CIBERSORTx_reference_inferred_refsample.bm.K999.pdf
CIBERSORTx_reference_inferred_phenoclasses.CIBERSORTx_reference_inferred_refsample.bm.K999.txt
CIBERSORTx_reference_inferred_phenoclasses.txt
CIBERSORTx_reference_inferred_refsample.txt

But based on a sample run I performed using Fig2ab-NSCLC_PBMCs (from the downloaded examples which ran normally), failure was before the following files were to be written:

CIBERSORTx_Adjusted.txt
CIBERSORTx_Mixtures_Adjusted.txt
CIBERSORTx_sigmatrix_Adjusted.txt

My reference file and mixture file have the same layout as the examples.

I have over 1tb free space on the drive /media/mark/seagate2.

Thank you

Answer 1

[markddesimone]

Update...running the bash command dmesg indicates that the docker container ran out of memory and was killed and then CIBERSORTx terminated with a segfault. I will look into how to increase memory for the docker container.