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mrvollger / SDA

Segmental Duplication Assembler (SDA).
MIT License
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How to run SDAtest? #6

Closed YuntaoTan closed 5 years ago

YuntaoTan commented 5 years ago

Hi, SDA developer, I am intrest in SDA, I am trying to run it. But failed. I need for your help. I run SDAtest like this:

cd /export/personal/tanyt/software/SDA/
/export/personal/tanyt/software/SDA/SDA /export/personal/tanyt/software/SDA/TestCases/SDAtest/ref.fasta /export/personal/tanyt/software/SDA/TestCases/SDAtest/reads.orig.bam

my sda.config.json is this in /export/personal/tanyt/software/SDA/:

{
    "MINCOV":27,
    "MAXCOV":54,
    "MINTOTAL":83,
    "project":"CHM1_V4",
}

But got following error:

/export/personal/tanyt/software/SDA
/export/personal/tanyt/software/SDA/
MINCOV:27
MAXCOV:54
MINTOTAL:83
NO INPUT READS!!!
SystemExit in line 143 of /export/personal/tanyt/software/SDA/SDA.1.snakemake.py:
None
  File "/export/personal/tanyt/software/SDA/SDA.1.snakemake.py", line 143, in <module>
  File "/export/personal/tanyt/software/miniconda3/envs/sda-python-3/lib/python3.6/_sitebuiltins.py", line 26, in __call__

NO INPUT READS!!! yes, I observed. but there is no example reads, I know your sda.config.json is like this,

{
        "MINCOV" : 27,
        "MAXCOV" : 54,
        "MINTOTAL" : 83,

        "asm" : "/net/eichler/vol2/home/mvollger/assemblies/Mitchell_CHM1_V3/internalassmbly/CHM1.fasta",
        "reads" : "/net/eichler/vol2/home/mvollger/assemblies/CHM1/reads.2017.fofn",
        "reference": "~mvollger/assemblies/hg38/ucsc.hg38.no_alts.fasta",
        "project": "CHM1_V4",
    "genes": "/net/eichler/vol2/home/mvollger/assemblies/hg38/hg38.gene.locations.bed",
        "bax_per_job" : 15
}

But in test data there is no such files.

mrvollger commented 5 years ago

Ref.fasta and reads.orig.bam are not positional arguments. You must be in the directory with those files in order to run SDA.