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Sample data not working #5
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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?
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