Centrifuge failed with a strange error message

[Ptero64]

Hello,

I am trying to run Centrifuge but it failed with the following error message which accumulate endlessly:

Use of uninitialized value $outputHeader in pattern match (m//) at /gpfs2/soft/2019013/Conda_env/nico/bin/centrifuge line 777.

My command is:

centrifuge \
-x /data/scratch/mpx553/Taxonomic_Assignment/Centrifuge_Base/nt \
-U $INPUTFILE1 \
--threads 4 \
--time \
--met 5 \
-S ${INPUTFILE1%.fastq}_Centrifuge_CleanedReads_classification.tsv \
--report-file ${INPUTFILE1%.fastq}_Centrifuge_CleanedReads_report.tsv \
--un ./${INPUTFILE1%.fastq}_Centrifuge_CleanedReads_unAlign.gzip 

Is someone as encounter this error before. I tried a new clean install of my centrifuge as conda environment but without success.

Thanks for the the help.

Regards

Nicolas

[Sanrrone]

Same error here, using v1.0.4 and git clone version.

[Ptero64]

Any idea what is the cause of this and how to fix it? seems related to memory maybe Error: Encountered exception: 'std::bad_alloc'

thanks

[asan-emirsaleh]

I have such error too

Warning: Could not open read file "/{PathToTheFile}/sr.forward.fastq" for reading; skipping...
Error: No input read files were valid
Use of uninitialized value $outputHeader in pattern match (m//) at /{CondaPath}/envs/centrifuge-env/bin/centrifuge line 777.

$ <slurm-{JobId}.out grep Use | wc -l 
1642235

I believe it not be the resources issue: I have allocated 240G of RAM and 84 CPU threads. The fastq file is normal, there were no problems with it in another applications. Do you have any progress with that issue?

Update: There were no problems with fastq file structure, but the path was incorrect. After the path was fixed the process started without error messages.