Process LoadPlatform (Load sequencing platform output) terminated with an error exit status (123)

[tanayb001]

Hi @FedericaBrando
I had an insstalled version of Intogen but due to new update some paths have been changed.

I tried the test run after adding new paths in intogen.nf and I am getting this error:

(intogenbuild) lab4iitk@serverlab4:/media/lab4iitk/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e2/Toolkit/intogen-plus$ NXF_VER=22.10.8 nextflow run intogen.nf -resume -profile local --input /media/lab4iitk/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e2/Toolkit/intogen-plus/test/pipeline/input/cbioportal_prad_broad/output.tsv --output /media/lab4iitk/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e2/Toolkit/intogen-plus/output --datasets /media/lab4iitk/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e2/Toolkit/intogen-plus/datasets --containers /media/lab4iitk/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e2/Toolkit/intogen-plus/build/containers --annotations /media/lab4iitk/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e2/Toolkit/intogen-plus/test/pipeline/input/cbioportal_prad_broad/metadata.yaml
N E X T F L O W  ~  version 22.10.8
Launching `intogen.nf` [angry_montalcini] DSL1 - revision: 2352904c63
executor >  local (3)
[e7/ded6ec] process > ParseInput (Parse input output.tsv)            [100%] 1 of 1, cached: 1 ✔
[a2/8c0308] process > LoadCancer (Load cancer type output)           [  0%] 0 of 1
[40/8c93cd] process > LoadPlatform (Load sequencing platform output) [  0%] 0 of 1
[26/f9b12c] process > LoadGenome (Load reference genome output)      [  0%] 0 of 1
[-        ] process > ProcessVariants                                -
[-        ] process > FormatSignature                                -
[-        ] process > ComputeProfile                                 -
[-        ] process > FormatFML                                      -
[-        ] process > OncodriveFML                                   -
[-        ] process > FormatCLUSTL                                   -
[-        ] process > OncodriveCLUSTL                                -
[-        ] process > FormatDNDSCV                                   -
[-        ] process > dNdScv                                         -
[-        ] process > FormatVEP                                      -
[-        ] process > VEP                                            -
[-        ] process > ProcessVEPoutput                               -
[-        ] process > FilterNonSynonymous                            -
[-        ] process > FormatSMRegions                                -
[-        ] process > SMRegions                                      -
[-        ] process > FormatCBaSE                                    -
[-        ] process > CBaSE                                          -
executor >  local (3)
[e7/ded6ec] process > ParseInput (Parse input output.tsv)            [100%] 1 of 1, cached: 1 ✔
[a2/8c0308] process > LoadCancer (Load cancer type output)           [100%] 1 of 1, failed: 1 ✘
[40/8c93cd] process > LoadPlatform (Load sequencing platform output) [100%] 1 of 1, failed: 1 ✘
[26/f9b12c] process > LoadGenome (Load reference genome output)      [100%] 1 of 1, failed: 1 ✘
[-        ] process > ProcessVariants                                -
[-        ] process > FormatSignature                                -
[-        ] process > ComputeProfile                                 -
[-        ] process > FormatFML                                      -
[-        ] process > OncodriveFML                                   -
[-        ] process > FormatCLUSTL                                   -
[-        ] process > OncodriveCLUSTL                                -
[-        ] process > FormatDNDSCV                                   -
[-        ] process > dNdScv                                         -
[-        ] process > FormatVEP                                      -
[-        ] process > VEP                                            -
[-        ] process > ProcessVEPoutput                               -
[-        ] process > FilterNonSynonymous                            -
[-        ] process > FormatSMRegions                                -
[-        ] process > SMRegions                                      -
[-        ] process > FormatCBaSE                                    -
[-        ] process > CBaSE                                          -
[-        ] process > FormatMutPanning                               -
[-        ] process > MutPanning                                     -
[-        ] process > FormatHotMAPS                                  -
[-        ] process > HotMAPS                                        -
[-        ] process > Combination                                    -
[-        ] process > FormatdeconstructSigs                          -
[-        ] process > deconstructSigs                                -
[-        ] process > CohortCounts                                   -
[-        ] process > CohortSummary                                  -
[-        ] process > MutationsSummary                               -
[-        ] process > DriverDiscovery                                -
[-        ] process > DriverSummary                                  -
[-        ] process > ParseProfile                                   -
[-        ] process > DriverSaturation                               -
[-        ] process > FilterMNVS                                     -
WARN: There's no process matching config selector: Signature
Error executing process > 'LoadPlatform (Load sequencing platform output)'

Caused by:
  Process `LoadPlatform (Load sequencing platform output)` terminated with an error exit status (123)

Command executed:

  get_field.sh output.parsed.tsv.gz PLATFORM

Command exit status:
  123

Command output:
  (empty)

Command error:
  printf: missing operand
  Try 'printf --help' for more information.

Work dir:
  /media/lab4iitk/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e2/Toolkit/intogen-plus/work/40/8c93cdd5893588d0de17d3221f53c5

Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line

See the make datasets command:

(intogenbuild) lab4iitk@serverlab4:/media/lab4iitk/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e2/Toolkit/intogen-plus/build$ make datasets 
datasets/dndscv.mk:5: warning: overriding recipe for target '../datasets/dndscv'
datasets/dndscv (copy).mk:5: warning: ignoring old recipe for target '../datasets/dndscv'
datasets/dndscv.mk:11: warning: overriding recipe for target '../datasets/dndscv/RefCDS.rda'
datasets/dndscv (copy).mk:11: warning: ignoring old recipe for target '../datasets/dndscv/RefCDS.rda'
datasets/signature.mk:4: warning: overriding recipe for target '../datasets/signature'
datasets/signature (copy).mk:4: warning: ignoring old recipe for target '../datasets/signature'
datasets/signature.mk:10: warning: overriding recipe for target '../datasets/signature/cds.counts.gz'
datasets/signature (copy).mk:10: warning: ignoring old recipe for target '../datasets/signature/cds.counts.gz'
datasets/signature.mk:19: warning: overriding recipe for target '../datasets/signature/wg.counts.gz'
datasets/signature (copy).mk:19: warning: ignoring old recipe for target '../datasets/signature/wg.counts.gz'
datasets/vep/vep.mk:6: warning: overriding recipe for target '../datasets/vep'
datasets/vep/vep (copy).mk:6: warning: ignoring old recipe for target '../datasets/vep'
datasets/vep/vep.mk:12: warning: overriding recipe for target '../datasets/vep/.vep111_cache'
datasets/vep/vep (copy).mk:12: warning: ignoring old recipe for target '../datasets/vep/.vep111_cache'
datasets/vep/vep.mk:20: warning: overriding recipe for target '../datasets/vep/vep.tsv.gz'
datasets/vep/vep (copy).mk:20: warning: ignoring old recipe for target '../datasets/vep/vep.tsv.gz'
datasets/vep/vep.mk:25: warning: overriding recipe for target '../datasets/vep/vep.tsv.gz.tbi'
datasets/vep/vep (copy).mk:25: warning: ignoring old recipe for target '../datasets/vep/vep.tsv.gz.tbi'
Downloading bgdata datasets
bgdata get datasets/genomereference/hg19
2026-07-01 20:05:29 bgdata.manager INFO -- Tag "master" for "datasets/genomereference/hg19" resolved as 20190201
2026-07-01 20:05:29 bgdata INFO -- Dataset downloaded
../datasets/bgdata/datasets/genomereference/hg19-20190201
bgdata get datasets/genomereference/hg38
2026-07-01 20:05:30 bgdata.manager INFO -- Tag "master" for "datasets/genomereference/hg38" resolved as 20161209
2026-07-01 20:05:30 bgdata INFO -- Dataset downloaded
../datasets/bgdata/datasets/genomereference/hg38-20161209
bgdata get intogen/coverage/hg19
2026-07-01 20:05:31 bgdata.manager INFO -- Tag "master" for "intogen/coverage/hg19" resolved as 20191209
2026-07-01 20:05:31 bgdata INFO -- Dataset downloaded
../datasets/bgdata/intogen/coverage/hg19-20191209/hg19_100bp.coverage.regions.gz
bgdata get intogen/coverage/hg38
2026-07-01 20:05:31 bgdata.manager INFO -- Tag "master" for "intogen/coverage/hg38" resolved as 20191209
2026-07-01 20:05:31 bgdata INFO -- Dataset downloaded
../datasets/bgdata/intogen/coverage/hg38-20191209/hg38_100bp.coverage.regions.gz
bgdata get intogen/dndscv/pan
2026-07-01 20:05:32 bgdata.manager INFO -- Tag "master" for "intogen/dndscv/pan" resolved as 20200818
2026-07-01 20:05:32 bgdata INFO -- Dataset downloaded
../datasets/bgdata/intogen/dndscv/pan-20200818/PCATLAS_WXS_PAN.out.gz
Creating phylop datasets
datasets/boostdm/hg38.download.sh ../datasets/boostdm
+ DEST=../datasets/boostdm
+ path_output=../datasets/boostdm/hg38.phyloP100way.bw
+ rsync -avz --progress rsync://hgdownload.cse.ucsc.edu/goldenPath/hg38/phyloP100way/hg38.phyloP100way.bw ../datasets/boostdm/hg38.phyloP100way.bw
receiving incremental file list

sent 24 bytes  received 67 bytes  16.55 bytes/sec
total size is 9,870,053,206  speedup is 108,462,123.14

And the make is showing this:

(intogenbuild) lab4iitk@serverlab4:/media/lab4iitk/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e2/Toolkit/intogen-plus/build$ make
datasets/dndscv.mk:5: warning: overriding recipe for target '../datasets/dndscv'
datasets/dndscv (copy).mk:5: warning: ignoring old recipe for target '../datasets/dndscv'
datasets/dndscv.mk:11: warning: overriding recipe for target '../datasets/dndscv/RefCDS.rda'
datasets/dndscv (copy).mk:11: warning: ignoring old recipe for target '../datasets/dndscv/RefCDS.rda'
datasets/signature.mk:4: warning: overriding recipe for target '../datasets/signature'
datasets/signature (copy).mk:4: warning: ignoring old recipe for target '../datasets/signature'
datasets/signature.mk:10: warning: overriding recipe for target '../datasets/signature/cds.counts.gz'
datasets/signature (copy).mk:10: warning: ignoring old recipe for target '../datasets/signature/cds.counts.gz'
datasets/signature.mk:19: warning: overriding recipe for target '../datasets/signature/wg.counts.gz'
datasets/signature (copy).mk:19: warning: ignoring old recipe for target '../datasets/signature/wg.counts.gz'
datasets/vep/vep.mk:6: warning: overriding recipe for target '../datasets/vep'
datasets/vep/vep (copy).mk:6: warning: ignoring old recipe for target '../datasets/vep'
datasets/vep/vep.mk:12: warning: overriding recipe for target '../datasets/vep/.vep111_cache'
datasets/vep/vep (copy).mk:12: warning: ignoring old recipe for target '../datasets/vep/.vep111_cache'
datasets/vep/vep.mk:20: warning: overriding recipe for target '../datasets/vep/vep.tsv.gz'
datasets/vep/vep (copy).mk:20: warning: ignoring old recipe for target '../datasets/vep/vep.tsv.gz'
datasets/vep/vep.mk:25: warning: overriding recipe for target '../datasets/vep/vep.tsv.gz.tbi'
datasets/vep/vep (copy).mk:25: warning: ignoring old recipe for target '../datasets/vep/vep.tsv.gz.tbi'
Building combination container
containers/build.sh containers/combination ../containers/intogen-combination.simg
ERROR  : Failed to create mount namespace: mount namespace requires privileges, check Singularity installation
make: *** [containers/combination/combination.mk:15: ../containers/intogen-combination.simg] Error 1

Please let me know how to use correctly without re-building everything from the scratch.

Regards,
Tanay

[FedericaBrando]

Hi @tanayb001 !

When you refer to new update are you referring to an intogen update or on your side?

In your make log you have:

Building combination container
containers/build.sh containers/combination ../containers/intogen-combination.simg
ERROR  : Failed to create mount namespace: mount namespace requires privileges, check Singularity installation
make: *** [containers/combination/combination.mk:15: ../containers/intogen-combination.simg] Error 1

Here it is telling you that you don't have priviledge to build a container. Are you on your local laptop or on the HPC? What OS are you running singularity on?

[tanayb001]

Hi @FedericaBrando
I'm on an Ubuntu local server. Regarding update, I'm referring to my OS update.
Let me know what to do.

Regards,
Tanay

[tanayb001]

Hi @FedericaBrando
Can you please help. I need to run Intogen again and its really urgent.

Thank you.

Regards,
Tanay