Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Sample data not working #5

Open
chklopp opened this issue Dec 14, 2020 · 0 comments
Open

Sample data not working #5

chklopp opened this issue Dec 14, 2020 · 0 comments

Comments

@chklopp
Copy link

chklopp commented Dec 14, 2020

When I try to run the single end sample data I get an empty assembly file.

python src/FabFos.py -m tests/test_data/test_SE_miffed.csv -b tests/test_data/trim_sequences.fasta -r tests/test_data/ -p se -t F -a megahit --force -f ./tmpFabFos version 1.9
Software versions used:
blastn 2.2.31+
bwa 0.7.12-r1039
makeblastdb 2.2.31+
megahit v1.2.9
samtools 1.11
trimmomatic.jar 0.39
Creating a new FabFos directory in './tmp'Processing 'test_SE_FosmidPool'. Outputs will written to ./tmp/TEST/test_SE_FosmidPool/
Finding number of reads in fastq files... done.
Number of raw reads = 100000
Filtering off-target reads... done.
Converting BAM file to FastQ format... done.
Finding number of reads in fastq files... done.
21637 reads removed by filtering background (21.637%).
Trimming reads... done.
Finding number of reads in fastq files... done.
Preparing quality FASTQ files for assembly... done.
Approximate fosmid coverage = 14.25991875
Assembling sequences using megahit
Parameters:
--k-min = 71 --k-max = 147 --k-step = 8 --min-count = 10
Cleaning up assembly outputs... done.
N50 = 0
Longest contig = 0bp

Is there a problem with the megahit parameter used?

Tony-xy-Liu added a commit that referenced this issue Jun 21, 2024
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant