What is the proper output file

[drs357]

Which output file should be used for subsequent sequencing? The program only gave me output files in the temporary directory.

[drs357]

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

[morispi]

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