Comments (2)
I only get a tmp folder when I run it, these are the files in the folder:
64-mers-c509A3interleaved.fastq.gz format_fastq_runid_05ac3df88eb24bde9b71a59e49db5685b8ba44b8_0.fastq quorum_corrected.log
64-mers-c509A3interleaved.fastq.gz.pgsa long_quorum_corrected.fa quorum_corrected_mer_database.jf
Alignments mers.db.kmc_pre RC_long_quorum_corrected.fa
all_long_quorum_corrected.fa mers.db.kmc_suf sortxhe8qS
dumped_64-mers-c509A3interleaved.fastq.gz quorum_corrected.fa tmp_c509A3interleaved.fastq.gz_on_fastq_runid_05ac3df88eb24bde9b71a59e49db5685b8ba44b8_0.fastq
from hg-color.
Hi,
First of all, sorry for the (very) long delay.
You should, indeed, get a proper output file, located outside of the temp. dir.
However, I can see that this folder contains .fastq.gz files.
What types of files did you provide as an input to HG-CoLoR? Please note that it only supports .fastq format for the short reads, and .fasta format for the long reads.
If you provided a .fastq.gz file as an input, for long reads or for short reads, this might very well be the cause of your issue.
I should be able to answer quicker now (done writing my thesis and taking a break), so don't hesitate to contact me again if you have any further question.
Best,
Pierre
from hg-color.
Related Issues (17)
- Error messages HOT 12
- Serious safety problem, --tmpdir parameter is deleted with no checking HOT 2
- Fail due to erroneous string in alignment file? HOT 1
- avoid reverse complement files HOT 1
- blasr doesn't use multiple threads? HOT 1
- Error HOT 1
- Disk quota exceeded when there is enough space on disk HOT 6
- optimal short read data HOT 2
- runtime estimation HOT 3
- Error HOT 2
- Error (core dumped) HOT 4
- Error While Running QuorUM HOT 5
- compile error: fatal error: test/testdata.h: No such file or directory HOT 1
- tmp files deleted before job is finished HOT 2
- Running time? HOT 4
- Run fails and only prints 'Correcting the short reads' HOT 2
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from hg-color.