Hello!
I've been encountering a problem on my macbook working with fasterq-dump (3.2.1), where I receive "error code 3" when producing fastq files in certain directories. This appears to be associated with unicode emojis I have in my folder names, but I can't resolve exactly why this is happening.
Here is how I can produce the error
First, i'm prefetching the data, this never causes an error.
nate@MyMac:~/🔬Research/🚸Colleagues$ prefetch SRR350925
2025-10-22T13:57:33 prefetch.3.2.1: 1) Resolving 'SRR350925'...
2025-10-22T13:57:35 prefetch.3.2.1: Current preference is set to retrieve SRA Lite files with simplified base quality scores
2025-10-22T13:57:36 prefetch.3.2.1: 1) Downloading 'SRR350925.sralite'...
2025-10-22T13:57:36 prefetch.3.2.1: SRA Lite file is being retrieved
2025-10-22T13:57:36 prefetch.3.2.1: Downloading via HTTPS...
2025-10-22T13:59:05 prefetch.3.2.1: HTTPS download succeed
2025-10-22T13:59:06 prefetch.3.2.1: 'SRR350925.sralite' is valid: 254889781 bytes were streamed from 254889310
2025-10-22T13:59:06 prefetch.3.2.1: 1) 'SRR350925.sralite' was downloaded successfully
However, I get an error which seems to be associated with writing the data to my directory:
nate@MyMac:~/🔬Research/🚸Colleagues$ fasterq-dump SRR350925
spots read : 4,990,511
reads read : 9,981,022
=============================================================
An error occurred during processing.
A report was generated into the file '/Users/jax/ncbi_error_report.txt'.
If the problem persists, you may consider sending the file
to 'sra-tools@ncbi.nlm.nih.gov' for assistance.
=============================================================
fasterq-dump quit with error code 3
Subsequent fasterq-dump runs give errors in an unpredictable manner, seemingly dependent on my directory name, following the same workflow with prefetch.
nate@MyMac:~/Desktop/🔬Research/🚸Another_dir$ fasterq-dump SRR350925 # returns error 3
nate@MyMac:~/Desktop/🔬Research/🚸B$ fasterq-dump SRR350925 # returns error 3
nate@MyMac:~/Desktop/🔬Research$ fasterq-dump SRR350925 # works!
nate@MyMac:~/Desktop/🚸B$ fasterq-dump SRR350925 # works!
nate@MyMac:~/Desktop/🔬Research/areallylongnamethatislikelytorunoverthebuffer$ fasterq-dump SRR350925 # works!
nate@MyMac:~/Desktop/🔬Research/🔬different$ fasterq-dump SRR350925 # returns error 3
It appears that this is associated with having more than one unicode 6.0 characters in the path.
Has anyone seen this before?
Hello!
I've been encountering a problem on my macbook working with fasterq-dump (3.2.1), where I receive "error code 3" when producing fastq files in certain directories. This appears to be associated with unicode emojis I have in my folder names, but I can't resolve exactly why this is happening.
Here is how I can produce the error
First, i'm prefetching the data, this never causes an error.
However, I get an error which seems to be associated with writing the data to my directory:
Subsequent fasterq-dump runs give errors in an unpredictable manner, seemingly dependent on my directory name, following the same workflow with prefetch.
It appears that this is associated with having more than one unicode 6.0 characters in the path.
Has anyone seen this before?