CRITICAL ERROR: Unable to remove spaces from identifiers in input file

Hello !
i hope you are all well in these difficult times of the covid pandemic. Be well and take care

I wanted to post about this humann error i received. “CRITICAL ERROR: Unable to remove spaces from identifiers in input file”
the fastq files are used as the input. actually 2 paired end fastq files concatenated.


thanks in advance

Can you post a few reads from your input file? Or at least their headers? HUMAnN tries to remove spaces from these headers since downstream mappers often truncate query names at he first space, which can lead to (e.g.) paired reads becoming indistinguishable. It looks like there is an error happening in that process.

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i have to add that during the procedure a 133 gigabyte file was produced as a temporary file. For sure my quota was exceeded during the run. Is it possible that this correlates to that error?

@SRR5754715.1 1/1
@SRR5754715.2 2/1
@SRR5754715.3 3/1

thanks for the fast reply i appreciate it
also i wanted to ask, i was having little trouble to see if i could use the bowtie file that i got from metaphlan 3.0 of an analysis as an input to humann 3.0

how does someone actually use a bowtie output file as an input to humann 3.0

Those reads look OK. They do have spaces, and that’s what HUMAnN is trying to fix when it throws the error. Other possibilities here are that you’re running out of storage space when trying to write the temp file (OR) you’re trying to write to a location where you don’t have write permission.

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Indeed space was the problem. Thank you again