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vpc-ccg / haslr

A fast tool for hybrid genome assembly of long and short reads
GNU General Public License v3.0
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assembling long reads using HASLR... failed #16

Open HanKMU opened 4 years ago

HanKMU commented 4 years ago

Hi, I'm trying to assemble 10x chromium data with nanopore data.

$ /home/std/hyli/haslr/bin/haslr.py -t 4 -g 1g -l /home/std/hyli/nanopore/reEEG357mix.fastq.gz /home/std/hyli/nanopore/reEEG376mix.fastq.gz /home/std/hyli/nanopore/EEG388_100fmol_KAPA60_mix.fastq.gz /home/std/hyli/nanopore/reEEG388_100fmol_ONT30mix.fastq.gz /home/std/hyli/nanopore/EEG389_100fmol_LNB15_mix.fastq.gz /home/std/hyli/nanopore/EEG389_100fmol_LNB60_mix.fastq.gz /home/std/hyli/nanopore/EEG389_200fmol_LNB30_mix.fastq.gz /home/std/hyli/nanopore/EEG850_EB_15min_mix.fastq.gz /home/std/hyli/nanopore/EEG850_H2O_15min_mix.fastq.gz /home/std/hyli/nanopore/EEG851_EB_30min_mix.fastq.gz /home/std/hyli/nanopore/EEG851_H2O_30min_mix.fastq.gz -x nanopore -s /home/std/hyli/WGS10X/EEG50_51/raw_data/EEG-50-51_S1_L005_R1_001.fastq.gz /home/std/hyli/WGS10X/EEG50_51/raw_data/EEG-50-51_S1_L005_R2_001.fastq.gz

Here is the error information,

[18-Jun-2020 16:40:17] subsampling 25x long reads to /home/std/hyli/hybrid_assembly/miniaceus/HASLR/miniaceus/lr25x.fasta... done [18-Jun-2020 16:57:53] assembling short reads using Minia... done [18-Jun-2020 22:48:58] removing overlaps in short read assembly... done [18-Jun-2020 22:50:29] removing short sequences in short read assembly... done [18-Jun-2020 22:50:40] aligning long reads to short read assembly using minimap2... done [19-Jun-2020 01:57:58] assembling long reads using HASLR... failed ERROR: "haslr_assemble" returned non-zero exit status

Any suggestion for fixing this problem? Thank you in advance for your time!

ehrenbentz commented 3 years ago

I get the exact same error. Any progress on figuring this out? Thanks!

comery commented 3 years ago

I am trying to assembly pre-assembled contigs generated by short reads with Pacbio reads using the command:

my-path/haslr.py -c scafSeq.fill.FG.gz  -l pacbio_reads/B18-05-2020-2.fasta.gz -g 200m -x pacbio -o output -t 4 --aln-sim 0.9 --cov-lr 50

I also got the same error information:

[25-Feb-2021 21:09:11] removing overlaps in short read assembly... done [25-Feb-2021 21:09:16] removing short sequences in short read assembly... done [25-Feb-2021 21:09:17] aligning long reads to short read assembly using minimap2... done [25-Feb-2021 22:16:01] assembling long reads using HASLR... failed ERROR: "haslr_assemble" returned non-zero exit status