merenlab / reads-for-assembly Goto Github PK

Is it possible to use FASTQ files as input?

Hi I searched around for a tool that could simulate reads and stumbled on this. I have some sequences generated on MiSeq or HiSeq. There are roughly 100 assembled genomes....unfortunately I don't know where the original paired-end reads are as I didn't sequence these samples. I figured I could try simulating reads but it seems your tool isn't really designed for dozens of samples or am I wrong? Thanks for creating this tool!

Hi again - I have some bacterial assemblies that were originally sequenced in another country and I am trying to use your tool. It appears all of the assemblies in my folder generate this error. I have attached an assembly for you to inspect.

ini file settings
[general]
output_sample_name = test
insert_size = 30
insert_size_std = 1
short_read_length = 250
error_rate = 0.01

Traceback (most recent call last):
  File "./gen-paired-end-reads", line 15, in <module>
    p.generate()
  File "/scicomp/groups/OID/NCHHSTP/DSTDB/LRRB/CRO_AZI_DataProcessing/reads-for-assembly-master/reads_for_assembly/generators.py", line 127, in generate
    start_pos = random.randint(0, L - (x * 2))
  File "/apps/x86_64/python/3.8.3/lib/python3.8/random.py", line 248, in randint
    return self.randrange(a, b+1)
  File "/apps/x86_64/python/3.8.3/lib/python3.8/random.py", line 226, in randrange
    raise ValueError("empty range for randrange() (%d, %d, %d)" % (istart, istop, width))
ValueError: empty range for randrange() (0, -57, -57)

395-12.zip