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I wanted to test nonpareil with the new gzip functionality, however I'm encountering a variety of errors.
When using the bioconda recipe (which is the same as the previous, just with the new code and a zlib dependency), I get the following error on all files I test
$ nonpareil -s ERX5474932_ERR5766176_1.fastq.gz -T kmer -f fastq -b output
Nonpareil v3.5.1
[ 0.0] The file ERX5474932_ERR5766176_1.fastq.gz.enve-tmp.158173 was created
[ 0.0] reading ERX5474932_ERR5766176_1.fastq.gz.enve-tmp.158173
[ 0.0] Picking 10000 random sequences
[ 0.0] Started counting
Fatal error:
The file provided does not have the proper fastq format
[ 0.0] Fatal error: The file provided does not have the proper fastq format
So I went to try the compiled version you included on the release here on GitHub,
The two test files I tried this on I've placed on dropbox here, which are valid FASTQ files as I use them for a vairety of pipelines I use.
Note that in all cases empty tmp files are generated, e.g. with:
e.g. for the three most recent (Failed) tests:
-rw-rw-r-- 1 james james 0 Jun 24 10:12 ERX5474932_ERR5766176_1.fastq.gz.enve-tmp.160124
-rw-rw-r-- 1 james james 0 Jun 24 10:16 ERX5474932_ERR5766176_1.fastq.gz.enve-tmp.161707
-rw-rw-r-- 1 james james 0 Jun 24 10:17 ERX5474932_ERR5766176_1.fastq.gz.enve-tmp.162390
The text was updated successfully, but these errors were encountered:
jfy133
changed the title
Error: "The file provided does not have the proper fastq format" when supplying gzipped files
Error: "The file provided does not have the proper fastq format" or hanging when supplying gzipped files
Jun 24, 2024
Thank you for all the testing @jfy133 , and hopefully this is the last of the faulty releases. Apologies for that. Please feel free to reopen if the new version doesn't work for you (I'll be creating a release very soon).
That appears to work better now :D noted someething else (will make a separate issue), but it appears to run without erroring now. I'll look into updating bioconda
I wanted to test nonpareil with the new gzip functionality, however I'm encountering a variety of errors.
When using the bioconda recipe (which is the same as the previous, just with the new code and a zlib dependency), I get the following error on all files I test
So I went to try the compiled version you included on the release here on GitHub,
and while it works if I uncompress the file (uncompressd to 'test.fastq')
$ ./nonpareil-3.5.1-Linux_x86_64 -s test.fastq -T kmer -f fastq -b output Nonpareil v3.5.1 [ 0.0] reading test.fastq [ 0.0] Picking 10000 random sequences [ 0.0] Started counting [ 0.1] Read file with 632060 sequences [ 0.1] Average read length is 151.000000bp [ 0.1] Worker 0 @start_samples. [ 0.1] Sub-sampling library [ 0.2] Worker 0 @start_checkings. [ 0.2] Evaluating consistency [ 0.2] Everything seems correct [ 0.2] Worker 0 @exit.
It just hangs forever. on the following...
The two test files I tried this on I've placed on dropbox here, which are valid FASTQ files as I use them for a vairety of pipelines I use.
Note that in all cases empty
tmp
files are generated, e.g. with:e.g. for the three most recent (Failed) tests:
The text was updated successfully, but these errors were encountered: