vpc-ccg/haslr

Failing while checking minia

Oieswarya opened this issue · 0 comments

Hello I have installed haslr and my bin includes all the 6 files:

bin/fastutils
bin/haslr_assemble
bin/haslr.py
bin/minia
bin/minimap2
bin/minia_nooverlap

I tried with the example command:

python haslr.py -t 8 -o /haslr/ecoli -g 4.6m -l /haslr/ecoli_filtered.fastq.gz -x pacbio -s /haslr/ecoli_miseq.1.fastq.gz /haslr/ecoli_miseq.2.fastq.gz`

And I am getting this error:

checking /haslr/bin/haslr_assemble: ok
checking /haslr/bin/minia_nooverlap: ok
checking /haslr/bin/fastutils: ok
checking /haslr/bin/minia: failed

I know it is because it is failing to locate minia but it's installed. After make I got this (Just adding the minia part):

Saving to: "minia-v3.2.1-bin-Linux.tar.gz"

100%[=============================================================================================================>] 6,978,468 39.3M/s in 0.2s

2021-02-20 19:33:54 (39.3 MB/s) - "minia-v3.2.1-bin-Linux.tar.gz" saved [6978468/6978468]

minia-v3.2.1-bin-Linux/LICENSE
minia-v3.2.1-bin-Linux/lib/
minia-v3.2.1-bin-Linux/lib/libhdf5.settings
minia-v3.2.1-bin-Linux/bin/
minia-v3.2.1-bin-Linux/bin/gatb-h5dump
minia-v3.2.1-bin-Linux/bin/minia
minia-v3.2.1-bin-Linux/test/
minia-v3.2.1-bin-Linux/test/genome10K.fasta
minia-v3.2.1-bin-Linux/test/10k_test.sh
minia-v3.2.1-bin-Linux/test/bubble.solution.fa
minia-v3.2.1-bin-Linux/test/1seq_90bp.reads.fq
minia-v3.2.1-bin-Linux/test/buchnera_test.sh
minia-v3.2.1-bin-Linux/test/buchnera.fasta
minia-v3.2.1-bin-Linux/test/ERR039477.md5
minia-v3.2.1-bin-Linux/test/1seq_90bp_circ.fa
minia-v3.2.1-bin-Linux/test/compare_fasta.py
minia-v3.2.1-bin-Linux/test/1seq.fa
minia-v3.2.1-bin-Linux/test/ERR039477.md5-gcc47
minia-v3.2.1-bin-Linux/test/bubble.fa
minia-v3.2.1-bin-Linux/test/X.solution.fa
minia-v3.2.1-bin-Linux/test/1seq_90bp.fa
minia-v3.2.1-bin-Linux/test/README
minia-v3.2.1-bin-Linux/test/tip.fa
minia-v3.2.1-bin-Linux/test/1seq_90bp_simulate_reads.sh
minia-v3.2.1-bin-Linux/test/ec.solution.fa
minia-v3.2.1-bin-Linux/test/X.fa
minia-v3.2.1-bin-Linux/test/high_abundance.fa
minia-v3.2.1-bin-Linux/test/ec.fa
minia-v3.2.1-bin-Linux/test/read50x_ref10K_e001.fa
minia-v3.2.1-bin-Linux/test/simple_test.sh
minia-v3.2.1-bin-Linux/test/buchnera_simulate_reads.sh
minia-v3.2.1-bin-Linux/test/test_ERR039477.sh
minia-v3.2.1-bin-Linux/test/tip.solution.fa
minia-v3.2.1-bin-Linux/README.md

May I know where I am going wrong?