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I want to re-run oncoanalyser but use the existing...
# oncoanalyser
c
I want to re-run oncoanalyser but use the existing reference. I have already ran 
--mode prepare_reference
. I need to point to the index file (
bwamem2_index = "/path/to/bwa-mem2_index/"
) in the config but I do not see it in the folder 
/reference_data/2.3.0
The reference folder only contains as below. Is the bwamem index elsewhere?
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GRCh38_masked_exclusions_alts_hlas.fasta
GRCh38_masked_exclusions_alts_hlas.fasta.dict
GRCh38_masked_exclusions_alts_hlas.fasta.fai
GRCh38_masked_exclusions_alts_hlas.fasta.img
gridss_index-2.13.2
hmf_pipeline_resources.38_v2.3.0--2
j
@Stephen Watts or @Rayan HassaĂŻne ?
🙏 1
s
Hi @Cathal, when provisioning the reference data with the 
--mode prepare_reference
approach, the specific files retrieved depends on the values provided to the 
--ref_data_types
argument
🙌 1
More information on this approach and values accepted by 
--ref_data_types
can be found here
And if you’re wanting a simple solution, you can also manually download + decompress the bwamem2 index then set the appropriate parameters in your Nextflow configuration oncoanalyser 2.3.0 reference data links • Listing of all reference URLs [link] • Direct GRCh38 bwamem2 index URL [link]
c
Hi @Stephen Watts My data is WGS dna samples. Does that mean I need 
bwamem2_index or dna_alignment
? When I first ran 
prepare_reference
I just supplied 
--ref_data_types wgs
And not sure if its related to the reference @Stephen Watts But I got an error when running a recent batch:
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nextflow.processor.TaskRun - Unable to dump error of process 'NFCORE_ONCOANALYSER:WGTS:READ_ALIGNMENT_DNA:BWAMEM2_ALIGN (BT153-5C_BT153-5C-MED_0001)' -- Cause: java.nio.file.NoSuchFileException: /hpc/vnx_homes//work/bb/d2d64d8c920cefb03c064e473d2c32/.command.err
May-04 07:17:43.095 [main] DEBUG nextflow.processor.TaskRun - Unable to dump output of process 'NFCORE_ONCOANALYSER:WGTS:READ_ALIGNMENT_DNA:BWAMEM2_ALIGN (MED_0001)' -- Cause: java.nio.file.NoSuchFileException:
s
Yes that’s right, 
--ref_data_types wgs,bwamem2_index
will retrieve files needed for analysis of WGS data plus those needed for alignment
On the error, have you previously been able to run other samples with your setup / configuration? Would you be able to send over the .nextflow.log file or similar?
Thanks for DM’ing the log, I noticed this error message:
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Caused by:
  Process `NFCORE_ONCOANALYSER:WGTS:READ_ALIGNMENT_DNA:BWAMEM2_ALIGN (<removed>)` terminated for an unknown reason -- Likely it has been terminated by the external system
Can you take a look at the SLURM logging information for the corresponding job? That will hopefully point you to the cause
And if you haven’t already it’s worth relaunching your analysis with 
-resume
as these errors that are non-specific / have an apparent external cause are often sporadic and often self-resolve
c
Thanks. Where can I find the SLURM log? There seems to be logs for each process, as well as the 
.nextflow.log
file
I can try to re-run with 
-resume
s
There should be some information in the work directory of your analysis for that specific job:
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/path/to/execution-dir/work/bb/d2d64d8c920cefb03c064e473d2c32
On most SLURM-based systems you can also review information through 
sacct
or 
scontrol
, e.g.:
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scontrol show job <your-job-id>
In the case of the process I pointed to above, the SLURM jobid looks to be 844366 but I would carefully check this before making any conclusions from the information associated with it
c
In that dir there is
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.
..
.command.run
.command.sh
s
That matches with the subsequent error messages in your logs; Nextflow was for some reason unable to write any additional files to that directory:
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May-04 00:08:06.808 [TaskFinalizer-7] DEBUG nextflow.processor.TaskRun - Unable to dump output of process 'NFCORE_ONCOANALYSER:WGTS:READ_ALIGNMENT_DNA:BWAMEM2_ALIGN (<removed>)' -- Cause: java.nio.file.NoSuchFileException: /path/to/execution-dir/work/bb/d2d64d8c920cefb03c064e473d2c32/.command.out
May-04 00:08:06.811 [TaskFinalizer-7] DEBUG nextflow.processor.TaskRun - Unable to dump error of process 'NFCORE_ONCOANALYSER:WGTS:READ_ALIGNMENT_DNA:BWAMEM2_ALIGN (<removed>)' -- Cause: java.nio.file.NoSuchFileException: /path/to/execution-dir/work/bb/d2d64d8c920cefb03c064e473d2c32/.command.err
May-04 00:08:06.813 [TaskFinalizer-7] DEBUG nextflow.processor.TaskRun - Unable to dump error of process 'NFCORE_ONCOANALYSER:WGTS:READ_ALIGNMENT_DNA:BWAMEM2_ALIGN (<removed>)' -- Cause: java.nio.file.NoSuchFileException: /path/to/execution-dir/work/bb/d2d64d8c920cefb03c064e473d2c32/.command.log
So I suspect the issue lies with the HPC in either SLURM job management or the filesystem, small chance there is some error occurring in Nextflow but that is less likely imo
c
Ok, Il investigate if its a HPC issue and also try to 
-resume
the run Thanks @Stephen Watts
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